Merge remote-tracking branch 'origin/staging' into feat/workspace-metadata-versioning-patch

# Conflicts:
#	src/agent/heartbeat.rs
#	src/db/libsql_migrations.rs

.env.example

@@ -191,10 +191,9 @@ HEARTBEAT_NOTIFY_CHANNEL=cli
 HEARTBEAT_NOTIFY_USER=default
 
 # Memory hygiene settings (automatic cleanup of stale workspace documents)
-# Runs on each heartbeat tick; identity files (IDENTITY.md, SOUL.md) are never deleted
+# Runs on each heartbeat tick; discovers cleanup targets from .config metadata
 # MEMORY_HYGIENE_ENABLED=true
-# MEMORY_HYGIENE_DAILY_RETENTION_DAYS=30         # delete daily/ docs older than this many days
-# MEMORY_HYGIENE_CONVERSATION_RETENTION_DAYS=7   # delete conversations/ docs older than this many days
+# MEMORY_HYGIENE_VERSION_KEEP_COUNT=50           # max versions to keep per document
 # MEMORY_HYGIENE_CADENCE_HOURS=12                # minimum hours between cleanup passes
 
 # Docker Sandbox

Cargo.lock

@@ -3150,7 +3150,7 @@ dependencies = [
  "libc",
  "percent-encoding",
  "pin-project-lite",
- "socket2 0.5.10",
+ "socket2 0.6.3",
  "system-configuration",
  "tokio",
  "tower-service",
@@ -3439,6 +3439,7 @@ dependencies = [
  "pgvector",
  "postgres-types",
  "pretty_assertions",
+ "pty-process",
  "rand 0.8.5",
  "readabilityrs",
  "refinery",
@@ -3524,7 +3525,7 @@ checksum = "3640c1c38b8e4e43584d8df18be5fc6b0aa314ce6ebf51b53313d4306cca8e46"
 dependencies = [
  "hermit-abi",
  "libc",
- "windows-sys 0.59.0",
+ "windows-sys 0.61.2",
 ]
 
 [[package]]
@@ -4906,6 +4907,16 @@ dependencies = [
  "syn 1.0.109",
 ]
 
+[[package]]
+name = "pty-process"
+version = "0.5.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "71cec9e2670207c5ebb9e477763c74436af3b9091dd550b9fb3c1bec7f3ea266"
+dependencies = [
+ "rustix 1.1.4",
+ "tokio",
+]
+
 [[package]]
 name = "pulley-interpreter"
 version = "28.0.1"
@@ -4930,7 +4941,7 @@ dependencies = [
  "quinn-udp",
  "rustc-hash 2.1.1",
  "rustls 0.23.37",
- "socket2 0.5.10",
+ "socket2 0.6.3",
  "thiserror 2.0.18",
  "tokio",
  "tracing",
@@ -4967,9 +4978,9 @@ dependencies = [
  "cfg_aliases",
  "libc",
  "once_cell",
- "socket2 0.5.10",
+ "socket2 0.6.3",
  "tracing",
- "windows-sys 0.59.0",
+ "windows-sys 0.60.2",
 ]
 
 [[package]]

Cargo.toml

@@ -189,6 +189,10 @@ json5 = { version = "0.4", optional = true }
 [target.'cfg(target_os = "macos")'.dependencies]
 security-framework = "3"
 
+# PTY allocation for Claude CLI stdout buffering fix (Unix only)
+[target.'cfg(unix)'.dependencies]
+pty-process = { version = "0.5", features = ["async"] }
+
 # Linux secret-service (GNOME Keyring, KWallet)
 [target.'cfg(target_os = "linux")'.dependencies]
 secret-service = { version = "4", features = ["rt-tokio-crypto-rust"] }

channels-src/discord/src/lib.rs

@@ -28,6 +28,9 @@ use std::{cmp::Ordering, collections::HashMap};
 use ed25519_dalek::{Signature, Verifier, VerifyingKey};
 use serde::{Deserialize, Serialize};
 
+/// Discord REST API v10 base URL.
+const DISCORD_API_BASE: &str = "https://discord.com/api/v10";
+
 use exports::near::agent::channel::{
     AgentResponse, ChannelConfig, Guest, HttpEndpointConfig, IncomingHttpRequest,
     OutgoingHttpResponse, PollConfig, StatusUpdate,
@@ -427,7 +430,7 @@ impl Guest for DiscordChannel {
             (
                 "PATCH",
                 format!(
-                    "https://discord.com/api/v10/webhooks/{}/{}/messages/@original",
+                    "{DISCORD_API_BASE}/webhooks/{}/{}/messages/@original",
                     application_id, token
                 ),
             )
@@ -438,20 +441,7 @@ impl Guest for DiscordChannel {
             payload["allowed_mentions"] = serde_json::json!({
                 "replied_user": true
             });
-            let mention_payload = serde_json::to_vec(&payload)
-                .map_err(|e| format!("Failed to serialize mention payload: {}", e))?;
-            let mention_url = format!(
-                "https://discord.com/api/v10/channels/{}/messages",
-                metadata.channel_id
-            );
-            let result = channel_host::http_request(
-                "POST",
-                &mention_url,
-                &discord_auth_headers_json(true),
-                Some(&mention_payload),
-                None,
-            );
-            return map_discord_response(result);
+            return send_channel_message(&metadata.channel_id, payload);
         } else {
             return Err("Unsupported Discord response metadata".to_string());
         };
@@ -469,8 +459,8 @@ impl Guest for DiscordChannel {
 
     fn on_status(_update: StatusUpdate) {}
 
-    fn on_broadcast(_user_id: String, _response: AgentResponse) -> Result<(), String> {
-        Err("broadcast not yet implemented for Discord channel".to_string())
+    fn on_broadcast(user_id: String, response: AgentResponse) -> Result<(), String> {
+        broadcast_dm(&user_id, &response.content)
     }
 
     fn on_shutdown() {
@@ -501,6 +491,21 @@ fn map_discord_response(
     }
 }
 
+/// Post a JSON payload to a Discord channel as a new message.
+fn send_channel_message(channel_id: &str, payload: serde_json::Value) -> Result<(), String> {
+    let payload_bytes = serde_json::to_vec(&payload)
+        .map_err(|e| format!("Failed to serialize message: {}", e))?;
+    let url = format!("{DISCORD_API_BASE}/channels/{}/messages", channel_id);
+    let result = channel_host::http_request(
+        "POST",
+        &url,
+        &discord_auth_headers_json(true),
+        Some(&payload_bytes),
+        None,
+    );
+    map_discord_response(result)
+}
+
 fn load_runtime_config() -> DiscordRuntimeConfig {
     channel_host::workspace_read("config.json")
         .and_then(|raw| serde_json::from_str::<DiscordRuntimeConfig>(&raw).ok())
@@ -539,7 +544,7 @@ fn get_or_fetch_bot_id() -> Option<String> {
 
     let response = channel_host::http_request(
         "GET",
-        "https://discord.com/api/v10/users/@me",
+        &format!("{DISCORD_API_BASE}/users/@me"),
         &discord_auth_headers_json(false),
         None,
         Some(10_000),
@@ -659,7 +664,7 @@ fn poll_channel_mentions(channel_id: &str, bot_id: &str) {
 
 fn fetch_latest_message_id(channel_id: &str) -> Option<String> {
     let url = format!(
-        "https://discord.com/api/v10/channels/{}/messages?limit=1",
+        "{DISCORD_API_BASE}/channels/{}/messages?limit=1",
         channel_id
     );
     let response = channel_host::http_request(
@@ -697,7 +702,7 @@ fn fetch_messages_after_cursor(
 
     for page in 0..MAX_PAGES {
         let url = format!(
-            "https://discord.com/api/v10/channels/{}/messages?limit={}&after={}",
+            "{DISCORD_API_BASE}/channels/{}/messages?limit={}&after={}",
             channel_id, PAGE_LIMIT, after
         );
         let response = match channel_host::http_request(
@@ -986,7 +991,7 @@ fn handle_slash_command(interaction: &DiscordInteraction) -> bool {
             );
             // Attempt to notify user of internal error
             let url = format!(
-                "https://discord.com/api/v10/webhooks/{}/{}",
+                "{DISCORD_API_BASE}/webhooks/{}/{}",
                 interaction.application_id, interaction.token
             );
             let payload = serde_json::json!({
@@ -1106,7 +1111,7 @@ fn check_sender_permission(
     }
 
     let dm_policy =
-        channel_host::workspace_read(DM_POLICY_PATH).unwrap_or_else(|| default_dm_policy());
+        channel_host::workspace_read(DM_POLICY_PATH).unwrap_or_else(default_dm_policy);
     if dm_policy == "open" {
         return true;
     }
@@ -1161,7 +1166,7 @@ fn check_sender_permission(
 /// Send a pairing code as an ephemeral Discord followup message.
 fn send_pairing_reply(ctx: &PairingReplyCtx, code: &str) -> Result<(), String> {
     let url = format!(
-        "https://discord.com/api/v10/webhooks/{}/{}",
+        "{DISCORD_API_BASE}/webhooks/{}/{}",
         ctx.application_id, ctx.token
     );
     let payload = serde_json::json!({
@@ -1194,6 +1199,57 @@ fn send_pairing_reply(ctx: &PairingReplyCtx, code: &str) -> Result<(), String> {
     }
 }
 
+/// Send a broadcast message to a Discord user via DM.
+///
+/// Creates a DM channel with the user (Discord caches this, so repeated calls
+/// for the same user reuse the existing channel) and then posts the message.
+fn broadcast_dm(user_id: &str, content: &str) -> Result<(), String> {
+    // Validate user_id is a plausible Discord snowflake (numeric, 17-20 digits)
+    // to avoid injecting arbitrary strings into API URLs.
+    if user_id.is_empty()
+        || !user_id.chars().all(|c| c.is_ascii_digit())
+        || user_id.len() < 17
+        || user_id.len() > 20
+    {
+        return Err(format!("Invalid Discord user ID: '{}'", user_id));
+    }
+
+    // Step 1: Open (or reuse) a DM channel with the target user.
+    let create_dm_payload = serde_json::json!({ "recipient_id": user_id });
+    let create_dm_bytes = serde_json::to_vec(&create_dm_payload)
+        .map_err(|e| format!("Failed to serialize DM channel request: {}", e))?;
+
+    let dm_response = channel_host::http_request(
+        "POST",
+        &format!("{DISCORD_API_BASE}/users/@me/channels"),
+        &discord_auth_headers_json(true),
+        Some(&create_dm_bytes),
+        Some(10_000),
+    )
+    .map_err(|e| format!("Failed to create DM channel: {}", e))?;
+
+    if !(200..300).contains(&dm_response.status) {
+        let body = String::from_utf8_lossy(&dm_response.body);
+        return Err(format!(
+            "Discord create-DM failed: {} - {}",
+            dm_response.status, body
+        ));
+    }
+
+    #[derive(Deserialize)]
+    struct DmChannelResponse {
+        id: String,
+    }
+    let dm_channel: DmChannelResponse = serde_json::from_slice(&dm_response.body)
+        .map_err(|e| format!("Failed to parse DM channel response: {}", e))?;
+    let channel_id = &dm_channel.id;
+
+    // Step 2: Send the message to the DM channel.
+    let truncated = truncate_message(content);
+    let payload = serde_json::json!({ "content": truncated });
+    send_channel_message(channel_id, payload)
+}
+
 fn json_response(status: u16, value: serde_json::Value) -> OutgoingHttpResponse {
     let body = serde_json::to_vec(&value).unwrap_or_default();
     let headers = serde_json::json!({"Content-Type": "application/json"});
@@ -1593,4 +1649,43 @@ mod tests {
         assert_eq!(interaction.interaction_type, 2);
         assert!(interaction.data.is_some());
     }
+
+    #[test]
+    fn test_broadcast_dm_payload_format() {
+        // Verify the DM channel creation payload is well-formed JSON that
+        // Discord's API expects.
+        let user_id = "123456789012345678";
+        let payload = serde_json::json!({ "recipient_id": user_id });
+        let serialized = serde_json::to_vec(&payload).unwrap();
+        let parsed: serde_json::Value = serde_json::from_slice(&serialized).unwrap();
+        assert_eq!(
+            parsed.get("recipient_id").and_then(|v| v.as_str()),
+            Some(user_id)
+        );
+    }
+
+    #[test]
+    fn test_broadcast_message_truncation() {
+        // Broadcast uses truncate_message, verify it handles content within
+        // Discord's 2000-char limit for DMs.
+        let short = "Hello from broadcast";
+        assert_eq!(truncate_message(short), short);
+
+        let long = "x".repeat(2500);
+        let result = truncate_message(&long);
+        assert!(result.len() <= 2006); // 1990 content + 16 suffix
+        assert!(result.ends_with("\n... (truncated)"));
+    }
+
+    #[test]
+    fn test_broadcast_dm_validates_snowflake() {
+        // broadcast_dm rejects invalid Discord snowflake IDs before making
+        // any API calls. We can call it directly since invalid IDs are
+        // rejected before any host function is invoked.
+        assert!(broadcast_dm("", "hi").is_err());
+        assert!(broadcast_dm("abc", "hi").is_err());
+        assert!(broadcast_dm("12345", "hi").is_err()); // too short
+        assert!(broadcast_dm("123456789012345678901", "hi").is_err()); // too long
+        assert!(broadcast_dm("12345678901234567x", "hi").is_err()); // non-digit
+    }
 }

migrations/V15__document_versions.sql

@@ -0,0 +1,23 @@
+-- Document version history for workspace files.
+-- Every content update saves the previous content as a version,
+-- enabling rollback and audit trails.
+
+CREATE TABLE memory_document_versions (
+    id UUID PRIMARY KEY DEFAULT gen_random_uuid(),
+    document_id UUID NOT NULL REFERENCES memory_documents(id) ON DELETE CASCADE,
+    version INTEGER NOT NULL,
+    content TEXT NOT NULL,
+    content_hash TEXT NOT NULL,
+    created_at TIMESTAMPTZ NOT NULL DEFAULT NOW(),
+    changed_by TEXT,
+    UNIQUE(document_id, version)
+);
+
+CREATE INDEX idx_doc_versions_lookup
+    ON memory_document_versions(document_id, version DESC);
+
+-- GIN index on metadata for JSON path queries (used by hygiene to find
+-- .config documents with hygiene.enabled). The metadata column already
+-- exists (V1) but was never indexed.
+CREATE INDEX idx_memory_documents_metadata
+    ON memory_documents USING GIN (metadata jsonb_path_ops);

src/agent/heartbeat.rs

@@ -276,8 +276,8 @@ impl HeartbeatRunner {
                         .await;
                 if report.had_work() {
                     tracing::info!(
-                        daily_logs_deleted = report.daily_logs_deleted,
-                        conversation_docs_deleted = report.conversation_docs_deleted,
+                        directories_cleaned = ?report.directories_cleaned,
+                        versions_pruned = report.versions_pruned,
                         "heartbeat: memory hygiene deleted stale documents"
                     );
                 }
@@ -590,6 +590,23 @@ pub fn spawn_multi_user_heartbeat(
 
                 let workspace = Arc::new(Workspace::new_with_db(user_id, Arc::clone(store.db())));
 
+                // Run memory hygiene per user (same as single-user heartbeat).
+                let hygiene_ws = Arc::clone(&workspace);
+                let hygiene_cfg = hygiene_config.clone();
+                let hygiene_user = user_id.clone();
+                tokio::spawn(async move {
+                    let report =
+                        crate::workspace::hygiene::run_if_due(&hygiene_ws, &hygiene_cfg).await;
+                    if report.had_work() {
+                        tracing::info!(
+                            user_id = hygiene_user,
+                            directories_cleaned = ?report.directories_cleaned,
+                            versions_pruned = report.versions_pruned,
+                            "multi-user heartbeat: memory hygiene deleted stale documents"
+                        );
+                    }
+                });
+
                 // Drain completed tasks to stay within the concurrency cap.
                 while join_set.len() >= MAX_CONCURRENT_HEARTBEATS {
                     if let Some(join_result) = join_set.join_next().await {
@@ -616,8 +633,8 @@ pub fn spawn_multi_user_heartbeat(
                     if report.had_work() {
                         tracing::info!(
                             user_id = uid,
-                            daily_logs_deleted = report.daily_logs_deleted,
-                            conversation_docs_deleted = report.conversation_docs_deleted,
+                            directories_cleaned = ?report.directories_cleaned,
+                            versions_pruned = report.versions_pruned,
                             "multi-user heartbeat: memory hygiene deleted stale documents"
                         );
                     }

src/channels/web/handlers/jobs.rs

@@ -15,6 +15,14 @@ use crate::channels::web::auth::AuthenticatedUser;
 use crate::channels::web::server::GatewayState;
 use crate::channels::web::types::*;
 
+fn db_error(context: &str, e: impl std::fmt::Display) -> (StatusCode, String) {
+    tracing::error!(%e, context, "Database error in jobs handler");
+    (
+        StatusCode::INTERNAL_SERVER_ERROR,
+        "Internal database error".to_string(),
+    )
+}
+
 pub async fn jobs_list_handler(
     State(state): State<Arc<GatewayState>>,
     AuthenticatedUser(user): AuthenticatedUser,
@@ -213,10 +221,7 @@ pub async fn jobs_detail_handler(
         }
         Ok(None) => {}
         Err(e) => {
-            return Err((
-                StatusCode::INTERNAL_SERVER_ERROR,
-                format!("Database error: {}", e),
-            ));
+            return Err(db_error("jobs_handler", e));
         }
     }
 
@@ -257,10 +262,7 @@ pub async fn jobs_detail_handler(
             }))
         }
         Ok(None) => Err((StatusCode::NOT_FOUND, "Job not found".to_string())),
-        Err(e) => Err((
-            StatusCode::INTERNAL_SERVER_ERROR,
-            format!("Database error: {}", e),
-        )),
+        Err(e) => Err(db_error("jobs_handler", e)),
     }
 }
 
@@ -304,10 +306,7 @@ pub async fn jobs_cancel_handler(
             }
             Ok(None) => {}
             Err(e) => {
-                return Err((
-                    StatusCode::INTERNAL_SERVER_ERROR,
-                    format!("Database error: {}", e),
-                ));
+                return Err(db_error("jobs_handler", e));
             }
         }
     }
@@ -350,10 +349,7 @@ pub async fn jobs_cancel_handler(
             }
             Ok(None) => {}
             Err(e) => {
-                return Err((
-                    StatusCode::INTERNAL_SERVER_ERROR,
-                    format!("Database error: {}", e),
-                ));
+                return Err(db_error("jobs_handler", e));
             }
         }
     }
@@ -471,10 +467,7 @@ pub async fn jobs_restart_handler(
         }
         Ok(None) => {}
         Err(e) => {
-            return Err((
-                StatusCode::INTERNAL_SERVER_ERROR,
-                format!("Database error: {}", e),
-            ));
+            return Err(db_error("jobs_handler", e));
         }
     }
 
@@ -530,10 +523,7 @@ pub async fn jobs_restart_handler(
             })))
         }
         Ok(None) => Err((StatusCode::NOT_FOUND, "Job not found".to_string())),
-        Err(e) => Err((
-            StatusCode::INTERNAL_SERVER_ERROR,
-            format!("Database error: {}", e),
-        )),
+        Err(e) => Err(db_error("jobs_handler", e)),
     }
 }
 
@@ -609,10 +599,7 @@ pub async fn jobs_prompt_handler(
                 return Err((StatusCode::NOT_FOUND, "Job not found".to_string()));
             }
             Err(e) => {
-                return Err((
-                    StatusCode::INTERNAL_SERVER_ERROR,
-                    format!("Database error: {}", e),
-                ));
+                return Err(db_error("jobs_handler", e));
             }
         }
     }
@@ -667,10 +654,7 @@ pub async fn jobs_events_handler(
             return Err((StatusCode::NOT_FOUND, "Job not found".to_string()));
         }
         Err(e) => {
-            return Err((
-                StatusCode::INTERNAL_SERVER_ERROR,
-                format!("Database error: {}", e),
-            ));
+            return Err(db_error("jobs_handler", e));
         }
     }
 
@@ -823,3 +807,17 @@ pub async fn job_files_read_handler(
         content,
     }))
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_db_error_does_not_leak_details() {
+        let (status, body) = db_error("test_context", "relation \"jobs\" does not exist");
+        assert_eq!(status, StatusCode::INTERNAL_SERVER_ERROR);
+        assert_eq!(body, "Internal database error");
+        assert!(!body.contains("relation"));
+        assert!(!body.contains("does not exist"));
+    }
+}

src/cli/oauth_defaults.rs

@@ -569,6 +569,42 @@ pub async fn sweep_expired_flows(registry: &PendingOAuthRegistry) {
 const HOSTED_STATE_PREFIX: &str = "ic2";
 const HOSTED_STATE_CHECKSUM_BYTES: usize = 12;
 
+/// Maximum length for a legacy flow ID or instance name.
+const LEGACY_STATE_MAX_LEN: usize = 128;
+/// Minimum length for a legacy flow ID.
+const LEGACY_STATE_MIN_LEN: usize = 8;
+
+/// Validate that a legacy state component (flow_id or instance_name) contains
+/// only safe characters: alphanumeric, dash, underscore.
+fn is_valid_legacy_state_component(s: &str) -> bool {
+    !s.is_empty()
+        && s.len() <= LEGACY_STATE_MAX_LEN
+        && s.bytes()
+            .all(|b| b.is_ascii_alphanumeric() || b == b'-' || b == b'_')
+}
+
+fn validate_legacy_flow_id(flow_id: &str) -> Result<(), String> {
+    if flow_id.len() < LEGACY_STATE_MIN_LEN {
+        return Err(format!(
+            "Legacy OAuth flow_id too short ({} chars, minimum {LEGACY_STATE_MIN_LEN})",
+            flow_id.len()
+        ));
+    }
+    if flow_id.len() > LEGACY_STATE_MAX_LEN {
+        return Err(format!(
+            "Legacy OAuth flow_id too long ({} chars, maximum {LEGACY_STATE_MAX_LEN})",
+            flow_id.len()
+        ));
+    }
+    if !flow_id
+        .bytes()
+        .all(|b| b.is_ascii_alphanumeric() || b == b'-' || b == b'_')
+    {
+        return Err("Legacy OAuth flow_id contains invalid characters".to_string());
+    }
+    Ok(())
+}
+
 #[derive(Debug, Clone, PartialEq, Eq)]
 pub struct DecodedHostedOAuthState {
     pub flow_id: String,
@@ -653,6 +689,17 @@ pub fn decode_hosted_oauth_state(state: &str) -> Result<DecodedHostedOAuthState,
         if flow_id.is_empty() {
             return Err("Hosted OAuth legacy state is missing flow_id".to_string());
         }
+        validate_legacy_flow_id(flow_id)?;
+        if !instance_name.is_empty() && !is_valid_legacy_state_component(instance_name) {
+            return Err(format!(
+                "Legacy OAuth instance name contains invalid characters or exceeds max length ({LEGACY_STATE_MAX_LEN})"
+            ));
+        }
+        tracing::debug!(
+            flow_id,
+            instance_name,
+            "Decoded legacy prefixed OAuth state"
+        );
         return Ok(DecodedHostedOAuthState {
             flow_id: flow_id.to_string(),
             instance_name: if instance_name.is_empty() {
@@ -668,6 +715,9 @@ pub fn decode_hosted_oauth_state(state: &str) -> Result<DecodedHostedOAuthState,
         return Err("Hosted OAuth state is empty".to_string());
     }
 
+    validate_legacy_flow_id(state)?;
+    tracing::debug!(flow_id = state, "Decoded legacy raw OAuth state");
+
     Ok(DecodedHostedOAuthState {
         flow_id: state.to_string(),
         instance_name: None,
@@ -1734,13 +1784,13 @@ mod tests {
     fn test_decode_hosted_oauth_state_accepts_legacy_formats() {
         use crate::cli::oauth_defaults::decode_hosted_oauth_state;
 
-        let decoded = decode_hosted_oauth_state("kind-deer:abc123").expect("legacy prefixed");
-        assert_eq!(decoded.flow_id, "abc123");
+        let decoded = decode_hosted_oauth_state("kind-deer:abc12345").expect("legacy prefixed");
+        assert_eq!(decoded.flow_id, "abc12345");
         assert_eq!(decoded.instance_name.as_deref(), Some("kind-deer"));
         assert!(decoded.is_legacy);
 
-        let decoded = decode_hosted_oauth_state("abc123").expect("legacy raw");
-        assert_eq!(decoded.flow_id, "abc123");
+        let decoded = decode_hosted_oauth_state("abc12345").expect("legacy raw");
+        assert_eq!(decoded.flow_id, "abc12345");
         assert_eq!(decoded.instance_name, None);
         assert!(decoded.is_legacy);
     }
@@ -1864,4 +1914,72 @@ mod tests {
         assert_eq!(decoded_no_instance.instance_name, None);
         assert!(!decoded_no_instance.is_legacy);
     }
+
+    /// Legacy flow IDs that are too short must be rejected (#1443).
+    #[test]
+    fn test_legacy_state_rejects_short_flow_id() {
+        use crate::cli::oauth_defaults::decode_hosted_oauth_state;
+
+        let err = decode_hosted_oauth_state("abc").expect_err("short raw flow_id");
+        assert!(err.contains("too short"), "unexpected error: {err}");
+
+        let err = decode_hosted_oauth_state("inst:abc").expect_err("short prefixed flow_id");
+        assert!(err.contains("too short"), "unexpected error: {err}");
+    }
+
+    /// Legacy flow IDs with invalid characters must be rejected (#1443).
+    #[test]
+    fn test_legacy_state_rejects_invalid_characters() {
+        use crate::cli::oauth_defaults::decode_hosted_oauth_state;
+
+        let err = decode_hosted_oauth_state("flow id with spaces!").expect_err("spaces in flow_id");
+        assert!(
+            err.contains("invalid characters"),
+            "unexpected error: {err}"
+        );
+
+        let err = decode_hosted_oauth_state("inst:flow/id?bad=yes")
+            .expect_err("special chars in prefixed flow_id");
+        assert!(
+            err.contains("invalid characters"),
+            "unexpected error: {err}"
+        );
+    }
+
+    /// Legacy instance names with invalid characters must be rejected (#1444).
+    #[test]
+    fn test_legacy_state_rejects_invalid_instance_name() {
+        use crate::cli::oauth_defaults::decode_hosted_oauth_state;
+
+        let err = decode_hosted_oauth_state("bad instance!:valid-flow-id-12345")
+            .expect_err("invalid instance name");
+        assert!(err.contains("instance name"), "unexpected error: {err}");
+    }
+
+    /// Excessively long legacy flow IDs must be rejected (#1443).
+    #[test]
+    fn test_legacy_state_rejects_oversized_flow_id() {
+        use crate::cli::oauth_defaults::decode_hosted_oauth_state;
+
+        let long_id = "a".repeat(200);
+        let err = decode_hosted_oauth_state(&long_id).expect_err("oversized flow_id");
+        assert!(err.contains("too long"), "unexpected error: {err}");
+    }
+
+    /// Valid legacy flow IDs at boundary lengths are accepted.
+    #[test]
+    fn test_legacy_state_accepts_boundary_lengths() {
+        use crate::cli::oauth_defaults::decode_hosted_oauth_state;
+
+        // Exactly 8 chars (minimum)
+        let decoded = decode_hosted_oauth_state("abcd1234").expect("8-char flow_id");
+        assert_eq!(decoded.flow_id, "abcd1234");
+        assert!(decoded.is_legacy);
+
+        // Exactly 128 chars (maximum)
+        let max_id = "a".repeat(128);
+        let decoded = decode_hosted_oauth_state(&max_id).expect("128-char flow_id");
+        assert_eq!(decoded.flow_id, max_id);
+        assert!(decoded.is_legacy);
+    }
 }

src/config/hygiene.rs

@@ -10,10 +10,8 @@ use crate::error::ConfigError;
 pub struct HygieneConfig {
     /// Whether hygiene is enabled. Env: `MEMORY_HYGIENE_ENABLED` (default: true).
     pub enabled: bool,
-    /// Days before `daily/` documents are deleted. Env: `MEMORY_HYGIENE_DAILY_RETENTION_DAYS` (default: 30).
-    pub daily_retention_days: u32,
-    /// Days before `conversations/` documents are deleted. Env: `MEMORY_HYGIENE_CONVERSATION_RETENTION_DAYS` (default: 7).
-    pub conversation_retention_days: u32,
+    /// Maximum versions to keep per document. Env: `MEMORY_HYGIENE_VERSION_KEEP_COUNT` (default: 50).
+    pub version_keep_count: u32,
     /// Minimum hours between hygiene passes. Env: `MEMORY_HYGIENE_CADENCE_HOURS` (default: 12).
     pub cadence_hours: u32,
 }
@@ -22,8 +20,7 @@ impl Default for HygieneConfig {
     fn default() -> Self {
         Self {
             enabled: true,
-            daily_retention_days: 30,
-            conversation_retention_days: 7,
+            version_keep_count: 50,
             cadence_hours: 12,
         }
     }
@@ -33,11 +30,7 @@ impl HygieneConfig {
     pub(crate) fn resolve() -> Result<Self, ConfigError> {
         Ok(Self {
             enabled: parse_bool_env("MEMORY_HYGIENE_ENABLED", true)?,
-            daily_retention_days: parse_optional_env("MEMORY_HYGIENE_DAILY_RETENTION_DAYS", 30)?,
-            conversation_retention_days: parse_optional_env(
-                "MEMORY_HYGIENE_CONVERSATION_RETENTION_DAYS",
-                7,
-            )?,
+            version_keep_count: parse_optional_env("MEMORY_HYGIENE_VERSION_KEEP_COUNT", 50)?,
             cadence_hours: parse_optional_env("MEMORY_HYGIENE_CADENCE_HOURS", 12)?,
         })
     }
@@ -47,8 +40,7 @@ impl HygieneConfig {
     pub fn to_workspace_config(&self) -> crate::workspace::hygiene::HygieneConfig {
         crate::workspace::hygiene::HygieneConfig {
             enabled: self.enabled,
-            daily_retention_days: self.daily_retention_days,
-            conversation_retention_days: self.conversation_retention_days,
+            version_keep_count: self.version_keep_count,
             cadence_hours: self.cadence_hours,
             state_dir: ironclaw_base_dir(),
         }

src/db/libsql/mod.rs

@@ -17,7 +17,6 @@ mod workspace;
 
 use std::path::Path;
 use std::sync::Arc;
-use std::sync::atomic::{AtomicBool, Ordering};
 
 use async_trait::async_trait;
 use chrono::{DateTime, NaiveDateTime, Utc};
@@ -34,8 +33,6 @@ use crate::workspace::MemoryDocument;
 
 use crate::db::libsql_migrations;
 
-static NAIVE_TIMESTAMP_LOGGED: AtomicBool = AtomicBool::new(false);
-
 /// Explicit column list for routines table (matches positional access in `row_to_routine_libsql`).
 pub(crate) const ROUTINE_COLUMNS: &str = "\
     id, name, description, user_id, enabled, \
@@ -167,13 +164,11 @@ impl LibSqlBackend {
 ///
 /// Returns an error if none of the formats match.
 pub(crate) fn parse_timestamp(s: &str) -> Result<DateTime<Utc>, String> {
-    let log_naive_timestamp_once = || {
-        if !NAIVE_TIMESTAMP_LOGGED.swap(true, Ordering::Relaxed) {
-            tracing::debug!(
-                timestamp = %s,
-                "parsed naive timestamp without timezone; assuming UTC for backward compatibility"
-            );
-        }
+    let log_naive_timestamp = || {
+        tracing::warn!(
+            timestamp = %s,
+            "parsed naive timestamp, assuming UTC — consider migrating to RFC 3339"
+        );
     };
 
     // RFC 3339 (our canonical write format)
@@ -182,12 +177,12 @@ pub(crate) fn parse_timestamp(s: &str) -> Result<DateTime<Utc>, String> {
     }
     // Naive with fractional seconds (legacy or SQLite datetime() output)
     if let Ok(ndt) = NaiveDateTime::parse_from_str(s, "%Y-%m-%d %H:%M:%S%.f") {
-        log_naive_timestamp_once();
+        log_naive_timestamp();
         return Ok(ndt.and_utc());
     }
     // Naive without fractional seconds (legacy format)
     if let Ok(ndt) = NaiveDateTime::parse_from_str(s, "%Y-%m-%d %H:%M:%S") {
-        log_naive_timestamp_once();
+        log_naive_timestamp();
         return Ok(ndt.and_utc());
     }
     Err(format!("unparseable timestamp: {:?}", s))
@@ -439,7 +434,7 @@ mod tests {
     use chrono::{TimeZone, Utc};
 
     use crate::db::Database;
-    use crate::db::libsql::{LibSqlBackend, normalize_notify_user, parse_timestamp};
+    use crate::db::libsql::{LibSqlBackend, fmt_ts, normalize_notify_user, parse_timestamp};
 
     #[test]
     fn test_normalize_notify_user_treats_legacy_default_as_missing() {
@@ -468,6 +463,15 @@ mod tests {
         assert_eq!(naive_without_millis, expected);
     }
 
+    #[test]
+    fn test_fmt_ts_roundtrips_through_parse_timestamp() {
+        let original = Utc.with_ymd_and_hms(2026, 6, 15, 8, 30, 45).unwrap()
+            + chrono::Duration::milliseconds(123);
+        let formatted = fmt_ts(&original);
+        let parsed = parse_timestamp(&formatted).unwrap();
+        assert_eq!(parsed, original);
+    }
+
     #[tokio::test]
     async fn test_libsql_now_format_is_rfc3339_and_parseable() {
         let backend = LibSqlBackend::new_memory().await.unwrap();

src/db/libsql/workspace.rs

@@ -13,8 +13,8 @@ use super::{
 use crate::db::WorkspaceStore;
 use crate::error::{DatabaseError, WorkspaceError};
 use crate::workspace::{
-    MemoryChunk, MemoryDocument, RankedResult, SearchConfig, SearchResult, WorkspaceEntry,
-    fuse_results,
+    DocumentVersion, MemoryChunk, MemoryDocument, RankedResult, SearchConfig, SearchResult,
+    VersionSummary, WorkspaceEntry, fuse_results,
 };
 
 use chrono::Utc;
@@ -840,6 +840,330 @@ impl WorkspaceStore for LibSqlBackend {
 
         Ok(fuse_results(fts_results, vector_results, config))
     }
+
+    // ==================== Metadata ====================
+
+    async fn update_document_metadata(
+        &self,
+        id: Uuid,
+        metadata: &serde_json::Value,
+    ) -> Result<(), WorkspaceError> {
+        let conn = self
+            .connect()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: e.to_string(),
+            })?;
+        let now = fmt_ts(&Utc::now());
+        let meta_str =
+            serde_json::to_string(metadata).map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to serialize metadata: {e}"),
+            })?;
+        conn.execute(
+            "UPDATE memory_documents SET metadata = ?2, updated_at = ?3 WHERE id = ?1",
+            params![id.to_string(), meta_str, now],
+        )
+        .await
+        .map_err(|e| WorkspaceError::SearchFailed {
+            reason: format!("Failed to update metadata: {e}"),
+        })?;
+        Ok(())
+    }
+
+    async fn find_config_documents(
+        &self,
+        user_id: &str,
+        agent_id: Option<Uuid>,
+    ) -> Result<Vec<MemoryDocument>, WorkspaceError> {
+        let conn = self
+            .connect()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: e.to_string(),
+            })?;
+        let agent_str = agent_id.map(|a| a.to_string());
+        let mut rows = conn
+            .query(
+                r#"
+                SELECT id, user_id, agent_id, path, content,
+                       created_at, updated_at, metadata
+                FROM memory_documents
+                WHERE user_id = ?1 AND agent_id IS ?2
+                  AND (path LIKE '%/.config' OR path = '.config')
+                ORDER BY path
+                "#,
+                params![user_id, agent_str],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to find config documents: {e}"),
+            })?;
+
+        let mut docs = Vec::new();
+        while let Some(row) = rows
+            .next()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to read config document row: {e}"),
+            })?
+        {
+            docs.push(row_to_memory_document(&row));
+        }
+        Ok(docs)
+    }
+
+    // ==================== Versioning ====================
+
+    async fn save_version(
+        &self,
+        document_id: Uuid,
+        content: &str,
+        content_hash: &str,
+        changed_by: Option<&str>,
+    ) -> Result<i32, WorkspaceError> {
+        let conn = self
+            .connect()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: e.to_string(),
+            })?;
+        let id = Uuid::new_v4().to_string();
+        let doc_id = document_id.to_string();
+        let now = fmt_ts(&Utc::now());
+
+        // Use a transaction to prevent race conditions: the SELECT and INSERT
+        // must be atomic so concurrent writers don't allocate the same version.
+        let tx = conn
+            .transaction()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to start transaction: {e}"),
+            })?;
+
+        // Get next version number (inside transaction — serializes writers)
+        let mut rows = tx
+            .query(
+                "SELECT COALESCE(MAX(version), 0) + 1 FROM memory_document_versions WHERE document_id = ?1",
+                params![doc_id.clone()],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to get next version number: {e}"),
+            })?;
+
+        let next_version = if let Some(row) =
+            rows.next()
+                .await
+                .map_err(|e| WorkspaceError::SearchFailed {
+                    reason: format!("Failed to read version number: {e}"),
+                })? {
+            get_i64(&row, 0) as i32
+        } else {
+            1
+        };
+        drop(rows);
+
+        tx.execute(
+            r#"
+            INSERT INTO memory_document_versions
+                (id, document_id, version, content, content_hash, created_at, changed_by)
+            VALUES (?1, ?2, ?3, ?4, ?5, ?6, ?7)
+            "#,
+            params![
+                id,
+                doc_id,
+                next_version as i64,
+                content,
+                content_hash,
+                now,
+                changed_by
+            ],
+        )
+        .await
+        .map_err(|e| WorkspaceError::SearchFailed {
+            reason: format!("Failed to save version: {e}"),
+        })?;
+
+        tx.commit()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to commit version: {e}"),
+            })?;
+
+        Ok(next_version)
+    }
+
+    async fn get_version(
+        &self,
+        document_id: Uuid,
+        version: i32,
+    ) -> Result<DocumentVersion, WorkspaceError> {
+        let conn = self
+            .connect()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: e.to_string(),
+            })?;
+        let mut rows = conn
+            .query(
+                r#"
+                SELECT id, document_id, version, content, content_hash,
+                       created_at, changed_by
+                FROM memory_document_versions
+                WHERE document_id = ?1 AND version = ?2
+                "#,
+                params![document_id.to_string(), version as i64],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to get version: {e}"),
+            })?;
+
+        let row = rows
+            .next()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to read version row: {e}"),
+            })?
+            .ok_or(WorkspaceError::VersionNotFound {
+                document_id,
+                version,
+            })?;
+
+        Ok(DocumentVersion {
+            id: get_text(&row, 0)
+                .parse()
+                .map_err(|e| WorkspaceError::SearchFailed {
+                    reason: format!("Invalid version UUID: {e}"),
+                })?,
+            document_id: get_text(&row, 1)
+                .parse()
+                .map_err(|e| WorkspaceError::SearchFailed {
+                    reason: format!("Invalid document UUID: {e}"),
+                })?,
+            version: get_i64(&row, 2) as i32,
+            content: get_text(&row, 3),
+            content_hash: get_text(&row, 4),
+            created_at: get_ts(&row, 5),
+            changed_by: get_opt_text(&row, 6),
+        })
+    }
+
+    async fn list_versions(
+        &self,
+        document_id: Uuid,
+        limit: i64,
+    ) -> Result<Vec<VersionSummary>, WorkspaceError> {
+        let conn = self
+            .connect()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: e.to_string(),
+            })?;
+        let mut rows = conn
+            .query(
+                r#"
+                SELECT version, content_hash, created_at, changed_by
+                FROM memory_document_versions
+                WHERE document_id = ?1
+                ORDER BY version DESC
+                LIMIT ?2
+                "#,
+                params![document_id.to_string(), limit],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to list versions: {e}"),
+            })?;
+
+        let mut versions = Vec::new();
+        while let Some(row) = rows
+            .next()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to read version row: {e}"),
+            })?
+        {
+            versions.push(VersionSummary {
+                version: get_i64(&row, 0) as i32,
+                content_hash: get_text(&row, 1),
+                created_at: get_ts(&row, 2),
+                changed_by: get_opt_text(&row, 3),
+            });
+        }
+        Ok(versions)
+    }
+
+    async fn get_latest_version_number(
+        &self,
+        document_id: Uuid,
+    ) -> Result<Option<i32>, WorkspaceError> {
+        let conn = self
+            .connect()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: e.to_string(),
+            })?;
+        let mut rows = conn
+            .query(
+                "SELECT MAX(version) FROM memory_document_versions WHERE document_id = ?1",
+                params![document_id.to_string()],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to get latest version number: {e}"),
+            })?;
+
+        if let Some(row) = rows
+            .next()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to read version number: {e}"),
+            })?
+        {
+            // MAX returns NULL if no rows — libsql returns Null for the value
+            let val = row.get::<libsql::Value>(0).ok();
+            match val {
+                Some(libsql::Value::Integer(v)) => Ok(Some(v as i32)),
+                _ => Ok(None),
+            }
+        } else {
+            Ok(None)
+        }
+    }
+
+    async fn prune_versions(
+        &self,
+        document_id: Uuid,
+        keep_count: i32,
+    ) -> Result<u64, WorkspaceError> {
+        let conn = self
+            .connect()
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: e.to_string(),
+            })?;
+        let doc_id = document_id.to_string();
+        let result = conn
+            .execute(
+                r#"
+                DELETE FROM memory_document_versions
+                WHERE document_id = ?1
+                  AND version NOT IN (
+                      SELECT version FROM memory_document_versions
+                      WHERE document_id = ?1
+                      ORDER BY version DESC
+                      LIMIT ?2
+                  )
+                "#,
+                params![doc_id, keep_count as i64],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to prune versions: {e}"),
+            })?;
+        Ok(result)
+    }
 }
 
 #[cfg(test)]

src/db/libsql_migrations.rs

@@ -785,6 +785,25 @@ CREATE TABLE IF NOT EXISTS api_tokens (
 );
 CREATE INDEX IF NOT EXISTS idx_api_tokens_user ON api_tokens(user_id);
 CREATE INDEX IF NOT EXISTS idx_api_tokens_hash ON api_tokens(token_hash);
+"#,
+    ),
+    (
+        15,
+        "document_versions",
+        r#"
+CREATE TABLE IF NOT EXISTS memory_document_versions (
+    id TEXT PRIMARY KEY,
+    document_id TEXT NOT NULL REFERENCES memory_documents(id) ON DELETE CASCADE,
+    version INTEGER NOT NULL,
+    content TEXT NOT NULL,
+    content_hash TEXT NOT NULL,
+    created_at TEXT NOT NULL DEFAULT (strftime('%Y-%m-%dT%H:%M:%fZ', 'now')),
+    changed_by TEXT,
+    UNIQUE(document_id, version)
+);
+
+CREATE INDEX IF NOT EXISTS idx_doc_versions_lookup
+    ON memory_document_versions(document_id, version DESC);
 "#,
     ),
 ];

src/db/mod.rs

@@ -700,6 +700,67 @@ pub trait WorkspaceStore: Send + Sync {
         config: &SearchConfig,
     ) -> Result<Vec<SearchResult>, WorkspaceError>;
 
+    // ==================== Metadata ====================
+
+    /// Update the metadata JSON field on a document (full replacement).
+    async fn update_document_metadata(
+        &self,
+        id: Uuid,
+        metadata: &serde_json::Value,
+    ) -> Result<(), WorkspaceError>;
+
+    /// Find all `.config` documents in the workspace.
+    ///
+    /// Returns documents whose path ends with `/.config` or equals `.config`.
+    /// Used by the hygiene system to discover metadata-driven cleanup targets.
+    async fn find_config_documents(
+        &self,
+        user_id: &str,
+        agent_id: Option<Uuid>,
+    ) -> Result<Vec<MemoryDocument>, WorkspaceError>;
+
+    // ==================== Versioning ====================
+
+    /// Save the current content of a document as a new version.
+    ///
+    /// Returns the new version number (1-based, monotonically increasing).
+    async fn save_version(
+        &self,
+        document_id: Uuid,
+        content: &str,
+        content_hash: &str,
+        changed_by: Option<&str>,
+    ) -> Result<i32, WorkspaceError>;
+
+    /// Get a specific version of a document.
+    async fn get_version(
+        &self,
+        document_id: Uuid,
+        version: i32,
+    ) -> Result<crate::workspace::DocumentVersion, WorkspaceError>;
+
+    /// List versions of a document (newest first).
+    async fn list_versions(
+        &self,
+        document_id: Uuid,
+        limit: i64,
+    ) -> Result<Vec<crate::workspace::VersionSummary>, WorkspaceError>;
+
+    /// Get the latest version number for a document, or `None` if no versions exist.
+    async fn get_latest_version_number(
+        &self,
+        document_id: Uuid,
+    ) -> Result<Option<i32>, WorkspaceError>;
+
+    /// Delete old versions, keeping only the most recent `keep_count`.
+    ///
+    /// Returns the number of versions deleted.
+    async fn prune_versions(
+        &self,
+        document_id: Uuid,
+        keep_count: i32,
+    ) -> Result<u64, WorkspaceError>;
+
     // ==================== Multi-scope read methods ====================
     //
     // Default implementations loop over user_ids calling single-scope methods,

src/db/postgres.rs

@@ -25,7 +25,8 @@ use crate::history::{
     LlmCallRecord, SandboxJobRecord, SandboxJobSummary, SettingRow, Store,
 };
 use crate::workspace::{
-    MemoryChunk, MemoryDocument, Repository, SearchConfig, SearchResult, WorkspaceEntry,
+    DocumentVersion, MemoryChunk, MemoryDocument, Repository, SearchConfig, SearchResult,
+    VersionSummary, WorkspaceEntry,
 };
 
 /// PostgreSQL database backend.
@@ -785,6 +786,69 @@ impl WorkspaceStore for PgBackend {
             .list_directory_multi(user_ids, agent_id, directory)
             .await
     }
+
+    // ==================== Metadata ====================
+
+    async fn update_document_metadata(
+        &self,
+        id: Uuid,
+        metadata: &serde_json::Value,
+    ) -> Result<(), WorkspaceError> {
+        self.repo.update_document_metadata(id, metadata).await
+    }
+
+    async fn find_config_documents(
+        &self,
+        user_id: &str,
+        agent_id: Option<Uuid>,
+    ) -> Result<Vec<MemoryDocument>, WorkspaceError> {
+        self.repo.find_config_documents(user_id, agent_id).await
+    }
+
+    // ==================== Versioning ====================
+
+    async fn save_version(
+        &self,
+        document_id: Uuid,
+        content: &str,
+        content_hash: &str,
+        changed_by: Option<&str>,
+    ) -> Result<i32, WorkspaceError> {
+        self.repo
+            .save_version(document_id, content, content_hash, changed_by)
+            .await
+    }
+
+    async fn get_version(
+        &self,
+        document_id: Uuid,
+        version: i32,
+    ) -> Result<DocumentVersion, WorkspaceError> {
+        self.repo.get_version(document_id, version).await
+    }
+
+    async fn list_versions(
+        &self,
+        document_id: Uuid,
+        limit: i64,
+    ) -> Result<Vec<VersionSummary>, WorkspaceError> {
+        self.repo.list_versions(document_id, limit).await
+    }
+
+    async fn get_latest_version_number(
+        &self,
+        document_id: Uuid,
+    ) -> Result<Option<i32>, WorkspaceError> {
+        self.repo.get_latest_version_number(document_id).await
+    }
+
+    async fn prune_versions(
+        &self,
+        document_id: Uuid,
+        keep_count: i32,
+    ) -> Result<u64, WorkspaceError> {
+        self.repo.prune_versions(document_id, keep_count).await
+    }
 }
 
 // ==================== UserStore ====================

src/error.rs

@@ -315,6 +315,12 @@ pub enum WorkspaceError {
 
     #[error("Write rejected for '{path}': prompt injection detected ({reason})")]
     InjectionRejected { path: String, reason: String },
+
+    #[error("Version not found: document {document_id} version {version}")]
+    VersionNotFound { document_id: Uuid, version: i32 },
+
+    #[error("Patch failed for '{path}': {reason}")]
+    PatchFailed { path: String, reason: String },
 }
 
 /// Orchestrator errors (internal API, container management).

src/extensions/manager.rs

@@ -53,6 +53,38 @@ struct HostedOAuthFlowStart {
     flow: crate::cli::oauth_defaults::PendingOAuthFlow,
 }
 
+#[derive(Debug, Default)]
+struct SecretCleanupPlan {
+    base_secrets: HashSet<String>,
+    companion_secrets: HashMap<String, HashSet<String>>,
+}
+
+impl SecretCleanupPlan {
+    fn add_base_secret(&mut self, secret_name: impl AsRef<str>) {
+        self.base_secrets
+            .insert(secret_name.as_ref().to_lowercase());
+    }
+
+    fn add_companion_secret(
+        &mut self,
+        base_secret_name: impl AsRef<str>,
+        companion_secret_name: impl AsRef<str>,
+    ) {
+        self.companion_secrets
+            .entry(base_secret_name.as_ref().to_lowercase())
+            .or_default()
+            .insert(companion_secret_name.as_ref().to_lowercase());
+    }
+}
+
+fn oauth_refresh_secret_name(secret_name: &str) -> String {
+    format!("{}_refresh_token", secret_name.to_lowercase())
+}
+
+fn oauth_scopes_secret_name(secret_name: &str) -> String {
+    format!("{}_scopes", secret_name.to_lowercase())
+}
+
 fn normalize_oauth_callback_path(path: &str) -> String {
     let trimmed_path = path.trim_end_matches('/');
     if trimmed_path.is_empty() {
@@ -1602,6 +1634,10 @@ impl ExtensionManager {
 
         match kind {
             ExtensionKind::McpServer => {
+                let cleanup_plan = self
+                    .collect_secret_cleanup_plan(name, kind, user_id)
+                    .await?;
+
                 // Unregister tools with this server's prefix
                 let tool_names: Vec<String> = self
                     .tool_registry
@@ -1623,6 +1659,9 @@ impl ExtensionManager {
                     .await
                     .map_err(|e| ExtensionError::Config(e.to_string()))?;
 
+                self.cleanup_uninstalled_extension_secrets(cleanup_plan, user_id)
+                    .await;
+
                 Ok(format!(
                     "Removed MCP server '{}' and {} tool(s)",
                     name,
@@ -1630,6 +1669,10 @@ impl ExtensionManager {
                 ))
             }
             ExtensionKind::WasmTool => {
+                let cleanup_plan = self
+                    .collect_secret_cleanup_plan(name, kind, user_id)
+                    .await?;
+
                 // Unregister from tool registry
                 self.tool_registry.unregister(name).await;
 
@@ -1674,9 +1717,16 @@ impl ExtensionManager {
                     let _ = tokio::fs::remove_file(&cap_path).await;
                 }
 
+                self.cleanup_uninstalled_extension_secrets(cleanup_plan, user_id)
+                    .await;
+
                 Ok(format!("Removed WASM tool '{}'", name))
             }
             ExtensionKind::WasmChannel => {
+                let cleanup_plan = self
+                    .collect_secret_cleanup_plan(name, kind, user_id)
+                    .await?;
+
                 // Remove from active set and persist
                 self.active_channel_names.write().await.remove(name);
                 self.persist_active_channels(user_id).await;
@@ -1702,6 +1752,9 @@ impl ExtensionManager {
                     let _ = tokio::fs::remove_file(&cap_path).await;
                 }
 
+                self.cleanup_uninstalled_extension_secrets(cleanup_plan, user_id)
+                    .await;
+
                 Ok(format!(
                     "Removed channel '{}'. Restart IronClaw for the change to take effect.",
                     name
@@ -2999,6 +3052,258 @@ impl ExtensionManager {
         crate::tools::wasm::CapabilitiesFile::from_bytes(&cap_bytes).ok()
     }
 
+    async fn load_channel_capabilities(
+        &self,
+        name: &str,
+    ) -> Option<crate::channels::wasm::ChannelCapabilitiesFile> {
+        let cap_path = self
+            .wasm_channels_dir
+            .join(format!("{}.capabilities.json", name));
+        let cap_bytes = tokio::fs::read(&cap_path).await.ok()?;
+        crate::channels::wasm::ChannelCapabilitiesFile::from_bytes(&cap_bytes).ok()
+    }
+
+    async fn collect_secret_cleanup_plan(
+        &self,
+        name: &str,
+        kind: ExtensionKind,
+        user_id: &str,
+    ) -> Result<SecretCleanupPlan, ExtensionError> {
+        let mut plan = SecretCleanupPlan::default();
+
+        match kind {
+            ExtensionKind::WasmTool => {
+                if let Some(cap) = self.load_tool_capabilities(name).await {
+                    for secret_name in Self::tool_secret_names(&cap) {
+                        plan.add_base_secret(secret_name);
+                    }
+
+                    if let Some(auth) = cap.auth {
+                        plan.add_base_secret(&auth.secret_name);
+                        plan.add_companion_secret(
+                            &auth.secret_name,
+                            oauth_refresh_secret_name(&auth.secret_name),
+                        );
+                        plan.add_companion_secret(
+                            &auth.secret_name,
+                            oauth_scopes_secret_name(&auth.secret_name),
+                        );
+                    }
+                }
+            }
+            ExtensionKind::WasmChannel => {
+                if let Some(cap) = self.load_channel_capabilities(name).await {
+                    for secret_name in Self::channel_secret_names(&cap) {
+                        plan.add_base_secret(secret_name);
+                    }
+                }
+            }
+            ExtensionKind::McpServer => {
+                let server = self
+                    .get_mcp_server(name, user_id)
+                    .await
+                    .map_err(|e| ExtensionError::Config(e.to_string()))?;
+                let token_secret_name = server.token_secret_name();
+                plan.add_base_secret(&token_secret_name);
+                plan.add_base_secret(server.client_id_secret_name());
+                // MCP OAuth can persist companion secrets through two paths:
+                // the MCP auth helper uses `mcp_<name>_refresh_token`, while the
+                // hosted gateway callback stores companions alongside the access
+                // token secret (`<token_secret>_refresh_token` / `_scopes`).
+                plan.add_companion_secret(&token_secret_name, server.refresh_token_secret_name());
+                plan.add_companion_secret(
+                    &token_secret_name,
+                    oauth_refresh_secret_name(&token_secret_name),
+                );
+                plan.add_companion_secret(
+                    &token_secret_name,
+                    oauth_scopes_secret_name(&token_secret_name),
+                );
+            }
+            ExtensionKind::ChannelRelay => {}
+        }
+
+        Ok(plan)
+    }
+
+    async fn cleanup_uninstalled_extension_secrets(&self, plan: SecretCleanupPlan, user_id: &str) {
+        let referenced_secrets = match self.collect_referenced_secret_names(user_id).await {
+            Ok(secret_names) => secret_names,
+            Err(error) => {
+                tracing::warn!(
+                    user_id,
+                    error,
+                    "Failed to determine which secrets are still referenced; keeping secrets"
+                );
+                return;
+            }
+        };
+
+        for base_secret in &plan.base_secrets {
+            if referenced_secrets.contains(base_secret) {
+                continue;
+            }
+
+            self.delete_secret_best_effort(user_id, base_secret).await;
+
+            if let Some(companion_secrets) = plan.companion_secrets.get(base_secret) {
+                for companion_secret in companion_secrets {
+                    if !referenced_secrets.contains(companion_secret) {
+                        self.delete_secret_best_effort(user_id, companion_secret)
+                            .await;
+                    }
+                }
+            }
+        }
+    }
+
+    async fn delete_secret_best_effort(&self, user_id: &str, secret_name: &str) {
+        if let Err(error) = self.secrets.delete(user_id, secret_name).await {
+            tracing::warn!(
+                user_id,
+                secret_name,
+                error = %error,
+                "Failed to delete secret while uninstalling extension"
+            );
+        }
+    }
+
+    async fn collect_referenced_secret_names(
+        &self,
+        user_id: &str,
+    ) -> Result<HashSet<String>, String> {
+        let mut referenced_secret_names = HashSet::new();
+
+        let tools = discover_tools(&self.wasm_tools_dir)
+            .await
+            .map_err(|e| format!("discover tools: {e}"))?;
+        for (tool_name, discovered_tool) in &tools {
+            let cap = self
+                .load_tool_capabilities(tool_name)
+                .await
+                .ok_or_else(|| {
+                    let path = discovered_tool
+                        .capabilities_path
+                        .as_ref()
+                        .map(|path| path.display().to_string())
+                        .unwrap_or_else(|| format!("{} (missing)", tool_name));
+                    format!("load tool capabilities for {tool_name}: {path}")
+                })?;
+            referenced_secret_names.extend(Self::tool_secret_names(&cap));
+        }
+
+        let channels = crate::channels::wasm::discover_channels(&self.wasm_channels_dir)
+            .await
+            .map_err(|e| format!("discover channels: {e}"))?;
+        for (channel_name, discovered_channel) in &channels {
+            let cap = self
+                .load_channel_capabilities(channel_name)
+                .await
+                .ok_or_else(|| {
+                    let path = discovered_channel
+                        .capabilities_path
+                        .as_ref()
+                        .map(|path| path.display().to_string())
+                        .unwrap_or_else(|| format!("{} (missing)", channel_name));
+                    format!("load channel capabilities for {channel_name}: {path}")
+                })?;
+            referenced_secret_names.extend(Self::channel_secret_names(&cap));
+        }
+
+        let mcp_servers = self
+            .load_mcp_servers(user_id)
+            .await
+            .map_err(|e| format!("load MCP servers: {e}"))?;
+        for server in &mcp_servers.servers {
+            referenced_secret_names.extend(Self::mcp_server_secret_names(server));
+        }
+
+        Ok(referenced_secret_names)
+    }
+
+    fn tool_secret_names(cap: &crate::tools::wasm::CapabilitiesFile) -> HashSet<String> {
+        let mut names = HashSet::new();
+
+        if let Some(auth) = &cap.auth {
+            names.insert(auth.secret_name.to_lowercase());
+        }
+        if let Some(setup) = &cap.setup {
+            names.extend(
+                setup
+                    .required_secrets
+                    .iter()
+                    .map(|secret| secret.name.to_lowercase()),
+            );
+        }
+        if let Some(http) = &cap.http {
+            names.extend(
+                http.credentials
+                    .values()
+                    .map(|credential| credential.secret_name.to_lowercase()),
+            );
+        }
+        if let Some(webhook) = &cap.webhook {
+            if let Some(secret_name) = &webhook.secret_name {
+                names.insert(secret_name.to_lowercase());
+            }
+            if let Some(secret_name) = &webhook.signature_key_secret_name {
+                names.insert(secret_name.to_lowercase());
+            }
+            if let Some(secret_name) = &webhook.hmac_secret_name {
+                names.insert(secret_name.to_lowercase());
+            }
+        }
+
+        names
+    }
+
+    fn channel_secret_names(
+        cap: &crate::channels::wasm::ChannelCapabilitiesFile,
+    ) -> HashSet<String> {
+        let mut names: HashSet<String> = cap
+            .setup
+            .required_secrets
+            .iter()
+            .map(|secret| secret.name.to_lowercase())
+            .collect();
+
+        if let Some(http) = cap.capabilities.tool.http.as_ref() {
+            names.extend(
+                http.credentials
+                    .values()
+                    .map(|credential| credential.secret_name.to_lowercase()),
+            );
+        }
+
+        if let Some(webhook) = cap
+            .capabilities
+            .channel
+            .as_ref()
+            .and_then(|channel| channel.webhook.as_ref())
+        {
+            if webhook.secret_header.is_some() || webhook.secret_name.is_some() {
+                names.insert(cap.webhook_secret_name().to_lowercase());
+            }
+            if let Some(secret_name) = cap.signature_key_secret_name() {
+                names.insert(secret_name.to_lowercase());
+            }
+            if let Some(secret_name) = cap.hmac_secret_name() {
+                names.insert(secret_name.to_lowercase());
+            }
+        }
+
+        names
+    }
+
+    fn mcp_server_secret_names(server: &McpServerConfig) -> HashSet<String> {
+        [
+            server.token_secret_name().to_lowercase(),
+            server.client_id_secret_name().to_lowercase(),
+        ]
+        .into_iter()
+        .collect()
+    }
+
     /// Collect merged OAuth scopes from all installed tools sharing the same secret_name.
     ///
     /// When multiple tools share an OAuth provider (e.g., google-calendar and google-drive
@@ -6033,6 +6338,8 @@ mod tests {
         ExtensionError, ExtensionKind, ExtensionSource, InstallResult, VerificationChallenge,
     };
     use crate::pairing::PairingStore;
+    use crate::secrets::CreateSecretParams;
+    use crate::tools::mcp::McpServerConfig;
 
     fn require(condition: bool, message: impl Into<String>) -> Result<(), String> {
         if condition {
@@ -6353,6 +6660,38 @@ mod tests {
         tools_dir
     }
 
+    fn write_test_channel(
+        dir: &std::path::Path,
+        name: &str,
+        capabilities_json: &str,
+    ) -> std::path::PathBuf {
+        let channels_dir = dir.join("channels");
+        std::fs::create_dir_all(&channels_dir).expect("channels dir");
+        std::fs::write(
+            channels_dir.join(format!("{name}.wasm")),
+            b"not-a-real-wasm",
+        )
+        .expect("wasm");
+        std::fs::write(
+            channels_dir.join(format!("{name}.capabilities.json")),
+            capabilities_json,
+        )
+        .expect("capabilities");
+        channels_dir
+    }
+
+    async fn store_test_secret(
+        manager: &crate::extensions::manager::ExtensionManager,
+        name: &str,
+        value: &str,
+    ) {
+        manager
+            .secrets
+            .create("test", CreateSecretParams::new(name, value))
+            .await
+            .expect("store secret");
+    }
+
     #[test]
     fn test_setting_value_is_present() {
         assert!(
@@ -7423,7 +7762,13 @@ mod tests {
         // Regression: remove() only checked channel_runtime for shutdown, missing
         // relay-only mode where only relay_channel_manager is set.
         let dir = tempfile::tempdir().expect("temp dir");
-        let mgr = make_test_manager(None, dir.path().to_path_buf());
+        let (store, _db_dir) = make_test_store().await;
+        let mgr = make_test_manager_with_dirs(
+            None,
+            dir.path().join("tools"),
+            dir.path().join("channels"),
+            Some(store),
+        );
 
         // Set up relay channel manager with a stub channel
         let cm = Arc::new(crate::channels::ChannelManager::new());
@@ -7450,6 +7795,8 @@ mod tests {
                 .await
                 .expect("store team_id");
         }
+        store_test_secret(&mgr, "relay:slack-relay:oauth_state", "nonce").await;
+        store_test_secret(&mgr, "relay:slack-relay:stream_token", "legacy-token").await;
 
         // Verify channel exists before removal
         assert!(cm.get_channel("slack-relay").await.is_some());
@@ -7478,6 +7825,30 @@ mod tests {
             cm.get_channel("slack-relay").await.is_none(),
             "relay channel should be removed from the channel manager"
         );
+        assert!(
+            !mgr.secrets
+                .exists("test", "relay:slack-relay:oauth_state")
+                .await
+                .expect("oauth state exists query"),
+            "relay oauth_state secret should be removed"
+        );
+        assert!(
+            !mgr.secrets
+                .exists("test", "relay:slack-relay:stream_token")
+                .await
+                .expect("stream token exists query"),
+            "relay legacy stream token should be removed"
+        );
+        assert_eq!(
+            mgr.store
+                .as_ref()
+                .expect("store")
+                .get_setting("test", "relay:slack-relay:team_id")
+                .await
+                .expect("team_id query"),
+            None,
+            "relay team_id setting should be removed"
+        );
     }
 
     #[tokio::test]
@@ -7585,6 +7956,185 @@ mod tests {
         );
     }
 
+    #[tokio::test]
+    async fn test_remove_wasm_tool_deletes_unique_secrets() {
+        let dir = tempfile::tempdir().expect("temp dir");
+        let tools_dir = write_test_tool(
+            dir.path(),
+            "github",
+            r#"{
+                "name": "github",
+                "auth": { "secret_name": "github_token" },
+                "setup": {
+                    "required_secrets": [
+                        { "name": "github_client_secret", "prompt": "GitHub client secret for testing cleanup behavior." }
+                    ]
+                },
+                "http": {
+                    "credentials": {
+                        "service_token": {
+                            "secret_name": "github_service_token",
+                            "location": { "type": "bearer" }
+                        }
+                    }
+                },
+                "webhook": {
+                    "hmac_secret_name": "github_webhook_secret"
+                }
+            }"#,
+        );
+        let mgr = make_test_manager_with_dirs(None, tools_dir, dir.path().join("channels"), None);
+
+        store_test_secret(&mgr, "github_token", "access-token").await;
+        store_test_secret(&mgr, "github_token_refresh_token", "refresh-token").await;
+        store_test_secret(&mgr, "github_token_scopes", "repo workflow").await;
+        store_test_secret(&mgr, "github_client_secret", "client-secret").await;
+        store_test_secret(&mgr, "github_service_token", "service-token").await;
+        store_test_secret(&mgr, "github_webhook_secret", "webhook-secret").await;
+
+        mgr.remove("github", "test")
+            .await
+            .expect("remove should succeed");
+
+        for secret_name in [
+            "github_token",
+            "github_token_refresh_token",
+            "github_token_scopes",
+            "github_client_secret",
+            "github_service_token",
+            "github_webhook_secret",
+        ] {
+            assert!(
+                !mgr.secrets
+                    .exists("test", secret_name)
+                    .await
+                    .expect("exists query"),
+                "secret {secret_name} should be deleted"
+            );
+        }
+    }
+
+    #[tokio::test]
+    async fn test_remove_wasm_tool_keeps_secrets_when_other_tool_capabilities_missing() {
+        let dir = tempfile::tempdir().expect("temp dir");
+        let tools_dir = write_test_tool(
+            dir.path(),
+            "github",
+            r#"{
+                "name": "github",
+                "auth": { "secret_name": "shared_token" }
+            }"#,
+        );
+        std::fs::write(tools_dir.join("broken.wasm"), b"fake-tool").expect("write tool");
+
+        let mgr = make_test_manager_with_dirs(None, tools_dir, dir.path().join("channels"), None);
+        store_test_secret(&mgr, "shared_token", "access-token").await;
+        store_test_secret(&mgr, "shared_token_refresh_token", "refresh-token").await;
+        store_test_secret(&mgr, "shared_token_scopes", "repo").await;
+
+        mgr.remove("github", "test")
+            .await
+            .expect("remove should succeed");
+
+        for secret_name in [
+            "shared_token",
+            "shared_token_refresh_token",
+            "shared_token_scopes",
+        ] {
+            assert!(
+                mgr.secrets
+                    .exists("test", secret_name)
+                    .await
+                    .expect("exists query"),
+                "secret {secret_name} should be retained when reference detection is uncertain"
+            );
+        }
+    }
+
+    #[tokio::test]
+    async fn test_remove_wasm_tool_keeps_shared_secrets_until_last_extension() {
+        let dir = tempfile::tempdir().expect("temp dir");
+        write_test_tool(
+            dir.path(),
+            "google-calendar",
+            r#"{
+                "name": "google-calendar",
+                "auth": { "secret_name": "google_oauth_token" },
+                "setup": {
+                    "required_secrets": [
+                        { "name": "google_oauth_client_id", "prompt": "Google OAuth client id for cleanup testing." },
+                        { "name": "google_oauth_client_secret", "prompt": "Google OAuth client secret for cleanup testing." }
+                    ]
+                }
+            }"#,
+        );
+        let tools_dir = write_test_tool(
+            dir.path(),
+            "google-drive",
+            r#"{
+                "name": "google-drive",
+                "auth": { "secret_name": "google_oauth_token" },
+                "setup": {
+                    "required_secrets": [
+                        { "name": "google_oauth_client_id", "prompt": "Google OAuth client id for cleanup testing." },
+                        { "name": "google_oauth_client_secret", "prompt": "Google OAuth client secret for cleanup testing." }
+                    ]
+                }
+            }"#,
+        );
+        let mgr = make_test_manager_with_dirs(None, tools_dir, dir.path().join("channels"), None);
+
+        for (secret_name, value) in [
+            ("google_oauth_token", "access-token"),
+            ("google_oauth_token_refresh_token", "refresh-token"),
+            ("google_oauth_token_scopes", "calendar drive"),
+            ("google_oauth_client_id", "client-id"),
+            ("google_oauth_client_secret", "client-secret"),
+        ] {
+            store_test_secret(&mgr, secret_name, value).await;
+        }
+
+        mgr.remove("google-calendar", "test")
+            .await
+            .expect("first remove should succeed");
+
+        for secret_name in [
+            "google_oauth_token",
+            "google_oauth_token_refresh_token",
+            "google_oauth_token_scopes",
+            "google_oauth_client_id",
+            "google_oauth_client_secret",
+        ] {
+            assert!(
+                mgr.secrets
+                    .exists("test", secret_name)
+                    .await
+                    .expect("exists query"),
+                "shared secret {secret_name} should remain while google-drive is still installed"
+            );
+        }
+
+        mgr.remove("google-drive", "test")
+            .await
+            .expect("second remove should succeed");
+
+        for secret_name in [
+            "google_oauth_token",
+            "google_oauth_token_refresh_token",
+            "google_oauth_token_scopes",
+            "google_oauth_client_id",
+            "google_oauth_client_secret",
+        ] {
+            assert!(
+                !mgr.secrets
+                    .exists("test", secret_name)
+                    .await
+                    .expect("exists query"),
+                "shared secret {secret_name} should be deleted after the last tool is removed"
+            );
+        }
+    }
+
     #[tokio::test]
     async fn test_remove_wasm_channel_clears_activation_error_and_deletes_files() {
         let dir = tempfile::tempdir().expect("temp dir");
@@ -7619,6 +8169,104 @@ mod tests {
         );
     }
 
+    #[tokio::test]
+    async fn test_remove_wasm_channel_deletes_setup_secrets() {
+        let dir = tempfile::tempdir().expect("temp dir");
+        let channels_dir = write_test_channel(
+            dir.path(),
+            "telegram",
+            r#"{
+                "type": "channel",
+                "name": "telegram",
+                "setup": {
+                    "required_secrets": [
+                        {
+                            "name": "telegram_bot_token",
+                            "prompt": "Telegram bot token used to verify uninstall cleanup behavior."
+                        }
+                    ]
+                },
+                "capabilities": {
+                    "http": {
+                        "credentials": {
+                            "tenant_token": {
+                                "secret_name": "telegram_service_token",
+                                "location": { "type": "bearer" }
+                            }
+                        }
+                    },
+                    "channel": {
+                        "webhook": {
+                            "secret_header": "X-Telegram-Bot-Api-Secret-Token",
+                            "secret_name": "telegram_webhook_secret"
+                        }
+                    }
+                }
+            }"#,
+        );
+        let mgr = make_test_manager_with_dirs(None, dir.path().join("tools"), channels_dir, None);
+
+        store_test_secret(&mgr, "telegram_bot_token", "123:telegram-token").await;
+        store_test_secret(&mgr, "telegram_service_token", "tenant-service-token").await;
+        store_test_secret(&mgr, "telegram_webhook_secret", "webhook-secret").await;
+
+        mgr.remove("telegram", "test")
+            .await
+            .expect("remove should succeed");
+
+        for secret_name in [
+            "telegram_bot_token",
+            "telegram_service_token",
+            "telegram_webhook_secret",
+        ] {
+            assert!(
+                !mgr.secrets
+                    .exists("test", secret_name)
+                    .await
+                    .expect("exists query"),
+                "channel secret {secret_name} should be deleted"
+            );
+        }
+    }
+
+    #[tokio::test]
+    async fn test_remove_mcp_server_deletes_stored_secrets() {
+        let dir = tempfile::tempdir().expect("temp dir");
+        let (store, _db_dir) = make_test_store().await;
+        let mgr = make_test_manager_with_dirs(
+            None,
+            dir.path().join("tools"),
+            dir.path().join("channels"),
+            Some(Arc::clone(&store)),
+        );
+        let server = McpServerConfig::new("notion", "https://example.com/mcp");
+        mgr.add_mcp_server(server.clone(), "test")
+            .await
+            .expect("add mcp server");
+
+        store_test_secret(&mgr, &server.token_secret_name(), "access-token").await;
+        store_test_secret(&mgr, &server.refresh_token_secret_name(), "refresh-token").await;
+        store_test_secret(&mgr, &server.client_id_secret_name(), "client-id").await;
+
+        mgr.remove("notion", "test")
+            .await
+            .expect("remove should succeed");
+
+        for secret_name in [
+            server.token_secret_name(),
+            server.refresh_token_secret_name(),
+            server.client_id_secret_name(),
+        ] {
+            assert!(
+                !mgr.secrets
+                    .exists("test", &secret_name)
+                    .await
+                    .expect("exists query"),
+                "MCP secret {secret_name} should be deleted"
+            );
+        }
+    }
+
     #[test]
     fn test_sanitize_url_with_query_params() {
         let url = "https://api.example.com/path?api_key=secret123&token=abc";

src/llm/circuit_breaker.rs

@@ -234,6 +234,7 @@ fn is_transient(err: &LlmError) -> bool {
         LlmError::RequestFailed { .. }
             | LlmError::RateLimited { .. }
             | LlmError::InvalidResponse { .. }
+            | LlmError::EmptyResponse { .. }
             | LlmError::SessionExpired { .. }
             | LlmError::SessionRenewalFailed { .. }
             | LlmError::Http(_)

src/llm/error.rs

@@ -17,6 +17,9 @@ pub enum LlmError {
     #[error("Invalid response from {provider}: {reason}")]
     InvalidResponse { provider: String, reason: String },
 
+    #[error("Empty response from {provider}: no content returned")]
+    EmptyResponse { provider: String },
+
     #[error("Context length exceeded: {used} tokens used, {limit} allowed")]
     ContextLengthExceeded { used: usize, limit: usize },
 

src/llm/github_copilot.rs

@@ -231,9 +231,8 @@ impl LlmProvider for GithubCopilotProvider {
                 .choices
                 .into_iter()
                 .next()
-                .ok_or_else(|| LlmError::InvalidResponse {
+                .ok_or_else(|| LlmError::EmptyResponse {
                     provider: "github_copilot".to_string(),
-                    reason: "No choices in response".to_string(),
                 })?;
 
         let (content, _tool_calls) = extract_choice_content(&choice);
@@ -309,9 +308,8 @@ impl LlmProvider for GithubCopilotProvider {
                 .choices
                 .into_iter()
                 .next()
-                .ok_or_else(|| LlmError::InvalidResponse {
+                .ok_or_else(|| LlmError::EmptyResponse {
                     provider: "github_copilot".to_string(),
-                    reason: "No choices in response".to_string(),
                 })?;
 
         let (content, tool_calls) = extract_choice_content(&choice);

src/llm/nearai_chat.rs

@@ -490,9 +490,8 @@ impl LlmProvider for NearAiChatProvider {
                 .choices
                 .into_iter()
                 .next()
-                .ok_or_else(|| LlmError::InvalidResponse {
+                .ok_or_else(|| LlmError::EmptyResponse {
                     provider: "nearai_chat".to_string(),
-                    reason: "No choices in response".to_string(),
                 })?;
 
         // Fall back to reasoning_content when content is null (same as
@@ -570,9 +569,8 @@ impl LlmProvider for NearAiChatProvider {
                 .choices
                 .into_iter()
                 .next()
-                .ok_or_else(|| LlmError::InvalidResponse {
+                .ok_or_else(|| LlmError::EmptyResponse {
                     provider: "nearai_chat".to_string(),
-                    reason: "No choices in response".to_string(),
                 })?;
 
         let tool_calls: Vec<ToolCall> = choice

src/llm/retry.rs

@@ -48,6 +48,7 @@ pub(crate) fn is_retryable(err: &LlmError) -> bool {
         LlmError::RequestFailed { .. }
             | LlmError::RateLimited { .. }
             | LlmError::InvalidResponse { .. }
+            | LlmError::EmptyResponse { .. }
             | LlmError::SessionRenewalFailed { .. }
             | LlmError::Http(_)
             | LlmError::Io(_)

src/tools/builtin/memory.rs

@@ -246,9 +246,26 @@ impl Tool for MemoryWriteTool {
                     "type": "boolean",
                     "description": "Skip privacy classification and write directly to the specified layer without redirect. Use when you're certain the content belongs in the target layer.",
                     "default": false
+                },
+                "metadata": {
+                    "type": "object",
+                    "description": "Optional metadata to set on the document (e.g., {\"skip_indexing\": true, \"hygiene\": {\"enabled\": true, \"retention_days\": 7}})"
+                },
+                "old_string": {
+                    "type": "string",
+                    "description": "When present, switches to patch mode: finds and replaces this exact string in the document. Requires target to be a path (not 'memory' or 'daily_log')."
+                },
+                "new_string": {
+                    "type": "string",
+                    "description": "Replacement string (required when old_string is present)."
+                },
+                "replace_all": {
+                    "type": "boolean",
+                    "description": "If true, replace all occurrences of old_string. Default: false.",
+                    "default": false
                 }
             },
-            "required": ["content"]
+            "required": []
         })
     }
 
@@ -259,7 +276,9 @@ impl Tool for MemoryWriteTool {
     ) -> Result<ToolOutput, ToolError> {
         let start = std::time::Instant::now();
 
-        let content = require_str(&params, "content")?;
+        // In patch mode (old_string present), content is not required.
+        let is_patch_mode = params.get("old_string").and_then(|v| v.as_str()).is_some();
+        let content = params.get("content").and_then(|v| v.as_str()).unwrap_or("");
 
         let target = params
             .get("target")
@@ -299,9 +318,9 @@ impl Tool for MemoryWriteTool {
             return Ok(ToolOutput::success(output, start.elapsed()));
         }
 
-        if content.trim().is_empty() {
+        if !is_patch_mode && content.trim().is_empty() {
             return Err(ToolError::InvalidParameters(
-                "content cannot be empty".to_string(),
+                "content cannot be empty (use old_string/new_string for patch mode)".to_string(),
             ));
         }
 
@@ -330,6 +349,46 @@ impl Tool for MemoryWriteTool {
             path => path.to_string(),
         };
 
+        // Patch mode: if old_string is provided, do search-and-replace instead of write/append.
+        let old_string = params.get("old_string").and_then(|v| v.as_str());
+        if let Some(old_str) = old_string {
+            let new_str = params
+                .get("new_string")
+                .and_then(|v| v.as_str())
+                .ok_or_else(|| {
+                    ToolError::InvalidParameters(
+                        "new_string is required when old_string is provided".to_string(),
+                    )
+                })?;
+            let replace_all = params
+                .get("replace_all")
+                .and_then(|v| v.as_bool())
+                .unwrap_or(false);
+
+            let result = workspace
+                .patch(&resolved_path, old_str, new_str, replace_all)
+                .await
+                .map_err(map_write_err)?;
+
+            // Apply metadata if provided
+            if let Some(meta) = params.get("metadata")
+                && meta.is_object()
+            {
+                workspace
+                    .update_metadata(result.document.id, meta)
+                    .await
+                    .map_err(map_write_err)?;
+            }
+
+            let output = serde_json::json!({
+                "status": "patched",
+                "path": resolved_path,
+                "replacements": result.replacements,
+                "content_length": result.document.content.len(),
+            });
+            return Ok(ToolOutput::success(output, start.elapsed()));
+        }
+
         // When a layer is specified, route through layer-aware methods for ALL targets.
         // Otherwise, use default workspace methods (which include injection scanning).
         let layer_result = if let Some(layer_name) = layer {
@@ -433,6 +492,24 @@ impl Tool for MemoryWriteTool {
             }
         }
 
+        // Apply metadata if provided (after write/append, works for all targets).
+        // We read the document once to get its ID — this is a hot read right
+        // after the write, so it's effectively free (same DB connection/cache).
+        if let Some(meta) = params.get("metadata")
+            && meta.is_object()
+        {
+            match workspace.read(&resolved_path).await {
+                Ok(doc) => {
+                    if let Err(e) = workspace.update_metadata(doc.id, meta).await {
+                        tracing::warn!(path = %resolved_path, "failed to update metadata: {e}");
+                    }
+                }
+                Err(e) => {
+                    tracing::warn!(path = %resolved_path, "failed to read doc for metadata update: {e}");
+                }
+            }
+        }
+
         let mut output = serde_json::json!({
             "status": "written",
             "path": resolved_path,
@@ -501,6 +578,15 @@ impl Tool for MemoryReadTool {
                 "path": {
                     "type": "string",
                     "description": "Path to the file (e.g., 'MEMORY.md', 'daily/2024-01-15.md', 'projects/alpha/notes.md')"
+                },
+                "version": {
+                    "type": "integer",
+                    "description": "Read a specific historical version of the document (omit for current content)"
+                },
+                "list_versions": {
+                    "type": "boolean",
+                    "description": "If true, return version history instead of file content",
+                    "default": false
                 }
             },
             "required": ["path"]
@@ -525,11 +611,61 @@ impl Tool for MemoryReadTool {
         }
 
         let workspace = self.resolver.resolve(&ctx.user_id).await;
+
+        let list_versions = params
+            .get("list_versions")
+            .and_then(|v| v.as_bool())
+            .unwrap_or(false);
+        let version = params
+            .get("version")
+            .and_then(|v| v.as_i64())
+            .map(|v| v as i32);
+
+        // Read the document first (needed for document_id in all version operations)
         let doc = workspace
             .read(path)
             .await
             .map_err(|e| ToolError::ExecutionFailed(format!("Read failed: {}", e)))?;
 
+        // List versions mode
+        if list_versions {
+            let versions = workspace
+                .list_versions(doc.id, 50)
+                .await
+                .map_err(|e| ToolError::ExecutionFailed(format!("List versions failed: {}", e)))?;
+
+            let output = serde_json::json!({
+                "path": doc.path,
+                "versions": versions.iter().map(|v| serde_json::json!({
+                    "version": v.version,
+                    "content_hash": v.content_hash,
+                    "created_at": v.created_at.to_rfc3339(),
+                    "changed_by": v.changed_by,
+                })).collect::<Vec<_>>(),
+                "version_count": versions.len(),
+            });
+            return Ok(ToolOutput::success(output, start.elapsed()));
+        }
+
+        // Specific version mode
+        if let Some(ver) = version {
+            let version_doc = workspace
+                .get_version(doc.id, ver)
+                .await
+                .map_err(|e| ToolError::ExecutionFailed(format!("Get version failed: {}", e)))?;
+
+            let output = serde_json::json!({
+                "path": doc.path,
+                "version": version_doc.version,
+                "content": version_doc.content,
+                "content_hash": version_doc.content_hash,
+                "created_at": version_doc.created_at.to_rfc3339(),
+                "changed_by": version_doc.changed_by,
+            });
+            return Ok(ToolOutput::success(output, start.elapsed()));
+        }
+
+        // Normal read
         let output = serde_json::json!({
             "path": doc.path,
             "content": doc.content,

src/tools/wasm/loader.rs

@@ -124,8 +124,10 @@ impl WasmToolLoader {
         let wasm_bytes = fs::read(wasm_path).await?;
 
         // Read capabilities (optional) and extract OAuth refresh config
-        // and tool description. Parameter schema is auto-derived from the
-        // WASM module's schema() export (see WasmToolSchemas::compact_schema).
+        // and tool description. Parameter schema is NOT read from the
+        // capabilities file — it is auto-derived from the WASM module's
+        // schema() export at prepare time (see WasmToolSchemas::compact_schema),
+        // so no schema override is needed here.
         let (capabilities, oauth_refresh, description) = if let Some(cap_path) = capabilities_path {
             if cap_path.exists() {
                 let cap_bytes = fs::read(cap_path).await?;

src/tools/wasm/wrapper.rs

@@ -759,14 +759,31 @@ impl WasmToolSchemas {
         }
 
         let kept: serde_json::Map<String, serde_json::Value> = all_properties
-            .into_iter()
+            .iter()
             .filter(|(name, prop)| {
-                required.contains(name) || prop.get("enum").is_some() || prop.get("const").is_some()
+                required.contains(name.as_str())
+                    || prop.get("enum").is_some()
+                    || prop.get("const").is_some()
             })
+            .map(|(k, v)| (k.clone(), v.clone()))
             .collect();
 
         if kept.is_empty() {
-            return Self::permissive_schema();
+            // When the schema has typed properties but none survived the
+            // required/enum filter, include all typed properties so the LLM
+            // sees meaningful parameter hints instead of permissive `{}`.
+            let typed: serde_json::Map<String, serde_json::Value> = all_properties
+                .into_iter()
+                .filter(|(_, prop)| schema_is_typed_property(prop))
+                .collect();
+            if typed.is_empty() {
+                return Self::permissive_schema();
+            }
+            return serde_json::json!({
+                "type": "object",
+                "properties": typed,
+                "additionalProperties": true,
+            });
         }
 
         let kept_required: Vec<serde_json::Value> = required
@@ -1991,6 +2008,58 @@ mod tests {
         );
     }
 
+    #[tokio::test]
+    async fn test_typed_schema_without_required_is_advertised() {
+        // Regression test for #1303: when a WASM tool exports a typed schema
+        // with no required/enum fields, the advertised schema should still
+        // contain the typed properties instead of falling back to permissive {}.
+        let discovery_schema = serde_json::json!({
+            "type": "object",
+            "properties": {
+                "query": { "type": "string" },
+                "limit": { "type": "integer" }
+            }
+        });
+
+        let runtime = Arc::new(WasmToolRuntime::new(WasmRuntimeConfig::for_testing()).unwrap());
+        let prepared = runtime
+            .prepare("typed_search", b"\0asm\x0d\0\x01\0", None)
+            .await
+            .unwrap();
+        let mut wrapper =
+            super::WasmToolWrapper::new(Arc::clone(&runtime), prepared, Capabilities::default());
+        wrapper.schemas = super::WasmToolSchemas::new(discovery_schema.clone());
+        wrapper.description = "Typed search tool".to_string();
+
+        let advertised = wrapper.parameters_schema();
+        let props = advertised["properties"].as_object().unwrap();
+
+        // Both typed properties should be preserved in the advertised schema
+        assert!(
+            props.contains_key("query"),
+            "advertised schema should contain 'query' property"
+        );
+        assert!(
+            props.contains_key("limit"),
+            "advertised schema should contain 'limit' property"
+        );
+        assert_eq!(props.len(), 2);
+
+        // The schema should NOT be permissive
+        assert!(
+            !super::WasmToolSchemas::is_permissive_schema(&advertised),
+            "advertised schema should not be permissive when typed properties exist"
+        );
+
+        // No tool_info hint needed since typed properties are visible
+        let schema = wrapper.schema();
+        assert!(
+            !schema.description.contains("tool_info"),
+            "description should not contain tool_info hint: {}",
+            schema.description
+        );
+    }
+
     #[test]
     fn test_compact_schema_keeps_required_and_enum_properties() {
         let schema = serde_json::json!({
@@ -2028,8 +2097,8 @@ mod tests {
     }
 
     #[test]
-    fn test_compact_schema_falls_back_to_permissive_when_empty() {
-        // No required, no enum → permissive fallback
+    fn test_compact_schema_preserves_typed_properties_when_no_required() {
+        // No required, no enum, but typed properties → keep all typed props
         let schema = serde_json::json!({
             "type": "object",
             "properties": {
@@ -2038,6 +2107,24 @@ mod tests {
             }
         });
 
+        let compacted = super::WasmToolSchemas::compact_schema(&schema);
+        let props = compacted["properties"].as_object().unwrap();
+        assert_eq!(props.len(), 2);
+        assert!(props.contains_key("query"));
+        assert!(props.contains_key("limit"));
+        assert_eq!(compacted["additionalProperties"], true);
+    }
+
+    #[test]
+    fn test_compact_schema_falls_back_to_permissive_when_no_typed_properties() {
+        // Properties with no type info → permissive fallback
+        let schema = serde_json::json!({
+            "type": "object",
+            "properties": {
+                "data": {}
+            }
+        });
+
         let compacted = super::WasmToolSchemas::compact_schema(&schema);
         assert!(compacted["properties"].as_object().unwrap().is_empty());
     }

src/worker/claude_bridge.rs

@@ -31,6 +31,7 @@ use std::time::Duration;
 
 use serde::{Deserialize, Serialize};
 use tokio::io::{AsyncBufReadExt, BufReader};
+#[cfg(not(unix))]
 use tokio::process::Command;
 use uuid::Uuid;
 
@@ -340,6 +341,11 @@ impl ClaudeBridgeRuntime {
 
     /// Spawn a `claude` CLI process and stream its output.
     ///
+    /// Uses a PTY on Unix so Node.js line-buffers stdout instead of
+    /// full-buffering (which causes the bridge to hang on non-TTY pipes).
+    /// Arguments are passed via `execve` (no shell) — injection-safe by
+    /// construction.
+    ///
     /// Returns the session_id if captured from the `system` init message.
     async fn run_claude_session(
         &self,
@@ -347,47 +353,102 @@ impl ClaudeBridgeRuntime {
         resume_session_id: Option<&str>,
         extra_env: &std::collections::HashMap<String, String>,
     ) -> Result<Option<String>, WorkerError> {
-        let mut cmd = Command::new("claude");
-        cmd.arg("-p")
-            .arg(prompt)
-            .arg("--output-format")
-            .arg("stream-json")
-            .arg("--verbose")
-            .arg("--max-turns")
-            .arg(self.config.max_turns.to_string())
-            .arg("--model")
-            .arg(&self.config.model);
+        let max_turns_str = self.config.max_turns.to_string();
 
-        if let Some(sid) = resume_session_id {
-            cmd.arg("--resume").arg(sid);
-        }
-
-        // Inject credentials into the child process environment without
-        // mutating the global process env (which is unsafe in multi-threaded programs).
-        cmd.envs(extra_env);
-
-        cmd.current_dir("/workspace")
-            .stdout(std::process::Stdio::piped())
-            .stderr(std::process::Stdio::piped());
-
-        let mut child = cmd.spawn().map_err(|e| WorkerError::ExecutionFailed {
-            reason: format!("failed to spawn claude: {}", e),
-        })?;
-
-        let stdout = child
-            .stdout
-            .take()
-            .ok_or_else(|| WorkerError::ExecutionFailed {
-                reason: "failed to capture claude stdout".to_string(),
+        // Spawn with PTY on Unix to fix Node.js stdout buffering.
+        // All arguments are passed individually via execve — never through
+        // a shell interpreter. This eliminates shell injection by construction.
+        #[cfg(unix)]
+        let (mut child, stdout, stderr) = {
+            let (pty, pts) = pty_process::open().map_err(|e| WorkerError::ExecutionFailed {
+                reason: format!("failed to allocate PTY: {}", e),
             })?;
 
-        let stderr = child
-            .stderr
-            .take()
-            .ok_or_else(|| WorkerError::ExecutionFailed {
-                reason: "failed to capture claude stderr".to_string(),
+            let mut cmd = pty_process::Command::new("claude");
+            cmd = cmd
+                .arg("-p")
+                .arg(prompt)
+                .arg("--output-format")
+                .arg("stream-json")
+                .arg("--verbose")
+                .arg("--max-turns")
+                .arg(&max_turns_str)
+                .arg("--model")
+                .arg(&self.config.model);
+
+            if let Some(sid) = resume_session_id {
+                cmd = cmd.arg("--resume").arg(sid);
+            }
+
+            cmd = cmd.envs(extra_env.iter());
+            cmd = cmd.current_dir("/workspace");
+            // Keep stderr on a separate pipe — pty-process attaches the PTY
+            // to all fds by default, which would merge stderr into the PTY
+            // stream and break NDJSON parsing.
+            cmd = cmd.stderr(std::process::Stdio::piped());
+
+            let mut child = cmd.spawn(pts).map_err(|e| WorkerError::ExecutionFailed {
+                reason: format!("failed to spawn claude with PTY: {}", e),
             })?;
 
+            let stderr = child
+                .stderr
+                .take()
+                .ok_or_else(|| WorkerError::ExecutionFailed {
+                    reason: "failed to capture claude stderr".to_string(),
+                })?;
+
+            // stdout comes from the PTY master, which implements AsyncRead
+            let stdout: Box<dyn tokio::io::AsyncRead + Unpin + Send> = Box::new(pty);
+            (child, stdout, stderr)
+        };
+
+        // Non-Unix fallback (Windows CI) — no PTY, direct spawn.
+        // Claude bridge only runs in Linux Docker containers, so this path
+        // exists solely for compilation on Windows targets.
+        #[cfg(not(unix))]
+        let (mut child, stdout, stderr) = {
+            let mut cmd = Command::new("claude");
+            cmd.arg("-p")
+                .arg(prompt)
+                .arg("--output-format")
+                .arg("stream-json")
+                .arg("--verbose")
+                .arg("--max-turns")
+                .arg(&max_turns_str)
+                .arg("--model")
+                .arg(&self.config.model);
+
+            if let Some(sid) = resume_session_id {
+                cmd.arg("--resume").arg(sid);
+            }
+
+            cmd.envs(extra_env);
+            cmd.current_dir("/workspace")
+                .stdout(std::process::Stdio::piped())
+                .stderr(std::process::Stdio::piped());
+
+            let mut child = cmd.spawn().map_err(|e| WorkerError::ExecutionFailed {
+                reason: format!("failed to spawn claude: {}", e),
+            })?;
+
+            let stdout_pipe = child
+                .stdout
+                .take()
+                .ok_or_else(|| WorkerError::ExecutionFailed {
+                    reason: "failed to capture claude stdout".to_string(),
+                })?;
+            let stderr = child
+                .stderr
+                .take()
+                .ok_or_else(|| WorkerError::ExecutionFailed {
+                    reason: "failed to capture claude stderr".to_string(),
+                })?;
+
+            let stdout: Box<dyn tokio::io::AsyncRead + Unpin + Send> = Box::new(stdout_pipe);
+            (child, stdout, stderr)
+        };
+
         // Spawn stderr reader that forwards lines as log events
         let client_for_stderr = Arc::clone(&self.client);
         let job_id = self.config.job_id;
@@ -1027,4 +1088,51 @@ mod tests {
         let copied = copy_dir_recursive(nonexistent, dst.path()).unwrap();
         assert_eq!(copied, 0);
     }
+
+    /// Regression test: arguments are passed individually (not via shell string),
+    /// so shell metacharacters in prompt/model/session_id are harmless.
+    #[test]
+    fn command_args_no_shell_interpretation() {
+        // Prompt, model, and session_id may contain shell metacharacters from
+        // user-supplied task descriptions or LLM output. Since we use
+        // Command::arg() (execve), these are passed as literal strings.
+        let prompt = "Fix the user's bug; echo $HOME && rm -rf /";
+        let model = "claude-3-opus-20240229";
+        let session_id = "'; DROP TABLE jobs; --";
+
+        let max_turns = 10u32;
+        let max_turns_str = max_turns.to_string();
+        let args: Vec<&str> = vec![
+            "-p",
+            prompt,
+            "--output-format",
+            "stream-json",
+            "--verbose",
+            "--max-turns",
+            &max_turns_str,
+            "--model",
+            model,
+            "--resume",
+            session_id,
+        ];
+
+        // All values present as literal strings — no shell interpretation
+        // ["-p", prompt, "--output-format", "stream-json", "--verbose",
+        //  "--max-turns", "10", "--model", model, "--resume", session_id]
+        assert_eq!(args[1], prompt);
+        assert_eq!(args[8], model);
+        assert_eq!(args[10], session_id);
+        // Shell metacharacters preserved, not expanded
+        assert!(args[1].contains("$HOME"));
+        assert!(args[1].contains("&&"));
+        assert!(args[10].contains("'; DROP TABLE"));
+    }
+
+    /// Verify PTY is available on Unix platforms.
+    #[cfg(unix)]
+    #[tokio::test]
+    async fn pty_opens_successfully() {
+        let result = pty_process::open();
+        assert!(result.is_ok(), "PTY allocation should succeed on Unix");
+    }
 }

src/worker/job.rs

@@ -391,6 +391,7 @@ Report when the job is complete or if you encounter issues you cannot resolve."#
             worker: self,
             rx: tokio::sync::Mutex::new(rx),
             consecutive_rate_limits: std::sync::atomic::AtomicUsize::new(0),
+            has_text_response: std::sync::atomic::AtomicBool::new(false),
         };
 
         let config = AgenticLoopConfig {
@@ -1101,6 +1102,15 @@ fn store_fallback_in_metadata(
 }
 
 /// Job delegate: implements `LoopDelegate` for the background job context.
+/// Whether an LLM error represents a completion-eligible empty response.
+///
+/// Only `EmptyResponse` (provider returned no choices/content) qualifies.
+/// Infrastructure errors (`AuthFailed`, `Http`, `Io`, etc.) never qualify —
+/// they must propagate even if prior text output was produced.
+fn is_completion_eligible_error(error: &crate::error::LlmError) -> bool {
+    matches!(error, crate::error::LlmError::EmptyResponse { .. })
+}
+
 ///
 /// Handles: signal channel (stop/ping/user messages), cancellation checks,
 /// rate-limit retry, parallel tool execution, DB persistence, SSE broadcasting.
@@ -1109,6 +1119,10 @@ struct JobDelegate<'a> {
     rx: tokio::sync::Mutex<&'a mut mpsc::Receiver<WorkerMessage>>,
     /// Tracks consecutive rate-limit errors to fail fast instead of burning iterations.
     consecutive_rate_limits: std::sync::atomic::AtomicUsize,
+    /// Whether a substantive (non-empty) text response has been produced.
+    /// When true, an empty follow-up response is treated as job completion
+    /// rather than a retry signal (prevents spurious failures in routines).
+    has_text_response: std::sync::atomic::AtomicBool,
 }
 
 impl<'a> JobDelegate<'a> {
@@ -1161,6 +1175,53 @@ impl<'a> JobDelegate<'a> {
             finish_reason: crate::llm::FinishReason::Stop,
         })
     }
+
+    /// Mark the job as completed, logging a warning on failure.
+    async fn mark_completed_or_warn(&self, context: &str) {
+        if let Err(e) = self.worker.mark_completed().await {
+            tracing::warn!(
+                job_id = %self.worker.job_id,
+                error = %e,
+                "Failed to mark job completed ({context})"
+            );
+        }
+    }
+
+    /// If a substantive text response was already produced and the error
+    /// indicates the LLM simply returned nothing, treat it as successful
+    /// completion rather than a fatal failure.
+    ///
+    /// Only swallows `EmptyResponse` — infrastructure errors (`AuthFailed`,
+    /// `ContextLengthExceeded`, `Http`, `Io`, etc.) always propagate.
+    ///
+    /// Returns `Some(empty RespondOutput)` when the error should be swallowed,
+    /// `None` when it should propagate normally.
+    async fn try_complete_on_error(
+        &self,
+        context: &str,
+        error: &crate::error::LlmError,
+    ) -> Option<crate::llm::RespondOutput> {
+        if !is_completion_eligible_error(error) {
+            return None;
+        }
+        if !self
+            .has_text_response
+            .load(std::sync::atomic::Ordering::Relaxed)
+        {
+            return None;
+        }
+        tracing::info!(
+            job_id = %self.worker.job_id,
+            error = %error,
+            "{context} empty response after text output — treating as completion"
+        );
+        self.mark_completed_or_warn(context).await;
+        Some(crate::llm::RespondOutput {
+            result: RespondResult::Text(String::new()),
+            usage: crate::llm::TokenUsage::default(),
+            finish_reason: crate::llm::FinishReason::Stop,
+        })
+    }
 }
 
 #[async_trait]
@@ -1291,7 +1352,12 @@ impl<'a> LoopDelegate for JobDelegate<'a> {
             Err(crate::error::LlmError::RateLimited { retry_after, .. }) => {
                 return self.handle_rate_limit(retry_after, "tool selection").await;
             }
-            Err(e) => return Err(e.into()),
+            Err(e) => {
+                if let Some(output) = self.try_complete_on_error("select_tools", &e).await {
+                    return Ok(output);
+                }
+                return Err(e.into());
+            }
         };
 
         // Fall back to respond_with_tools
@@ -1321,7 +1387,12 @@ impl<'a> LoopDelegate for JobDelegate<'a> {
                 self.handle_rate_limit(retry_after, "respond_with_tools")
                     .await
             }
-            Err(e) => Err(e.into()),
+            Err(e) => {
+                if let Some(output) = self.try_complete_on_error("respond_with_tools", &e).await {
+                    return Ok(output);
+                }
+                Err(e.into())
+            }
         }
     }
 
@@ -1330,9 +1401,22 @@ impl<'a> LoopDelegate for JobDelegate<'a> {
         text: &str,
         reason_ctx: &mut ReasoningContext,
     ) -> TextAction {
-        // Empty text from rate-limit backoff retry — skip processing and let the
-        // loop proceed to the next iteration which will re-call the LLM.
+        // Empty text after a substantive response means the LLM has finished.
+        // Treat as successful completion rather than continuing the loop (which
+        // would produce "Response contained no message or tool call (empty)").
         if text.is_empty() {
+            if self
+                .has_text_response
+                .load(std::sync::atomic::Ordering::Relaxed)
+            {
+                tracing::debug!(
+                    job_id = %self.worker.job_id,
+                    "Empty response after text output — treating as completion"
+                );
+                self.mark_completed_or_warn("empty text response").await;
+                return TextAction::Return(LoopOutcome::Response(String::new()));
+            }
+            // No prior text response — this is likely a rate-limit backoff retry.
             return TextAction::Continue;
         }
 
@@ -1348,6 +1432,10 @@ impl<'a> LoopDelegate for JobDelegate<'a> {
             return TextAction::Return(LoopOutcome::Response(text.to_string()));
         }
 
+        // Track that a substantive response has been produced.
+        self.has_text_response
+            .store(true, std::sync::atomic::Ordering::Relaxed);
+
         // Add assistant response to context
         reason_ctx.messages.push(ChatMessage::assistant(text));
 
@@ -2285,4 +2373,60 @@ mod tests {
         assert_eq!(telegram[0].0, "owner-scope");
         assert_eq!(telegram[0].1.content, "hello from routine");
     }
+
+    /// Regression test: only `EmptyResponse` errors are eligible for
+    /// completion-swallowing. Infrastructure errors must always propagate.
+    #[test]
+    fn is_completion_eligible_only_matches_empty_response() {
+        use crate::error::LlmError;
+
+        // EmptyResponse is eligible
+        assert!(super::is_completion_eligible_error(
+            &LlmError::EmptyResponse {
+                provider: "test".to_string(),
+            }
+        ));
+
+        // All other variants are NOT eligible
+        assert!(!super::is_completion_eligible_error(
+            &LlmError::InvalidResponse {
+                provider: "test".to_string(),
+                reason: "parse error".to_string(),
+            }
+        ));
+        assert!(!super::is_completion_eligible_error(
+            &LlmError::AuthFailed {
+                provider: "test".to_string(),
+            }
+        ));
+        assert!(!super::is_completion_eligible_error(
+            &LlmError::ContextLengthExceeded {
+                used: 100_000,
+                limit: 50_000,
+            }
+        ));
+        assert!(!super::is_completion_eligible_error(
+            &LlmError::ModelNotAvailable {
+                provider: "test".to_string(),
+                model: "gpt-4".to_string(),
+            }
+        ));
+        assert!(!super::is_completion_eligible_error(
+            &LlmError::RequestFailed {
+                provider: "test".to_string(),
+                reason: "timeout".to_string(),
+            }
+        ));
+        assert!(!super::is_completion_eligible_error(
+            &LlmError::SessionExpired {
+                provider: "test".to_string(),
+            }
+        ));
+        assert!(!super::is_completion_eligible_error(
+            &LlmError::SessionRenewalFailed {
+                provider: "test".to_string(),
+                reason: "timeout".to_string(),
+            }
+        ));
+    }
 }

src/workspace/document.rs

@@ -2,6 +2,7 @@
 
 use chrono::{DateTime, Utc};
 use serde::{Deserialize, Serialize};
+use sha2::{Digest, Sha256};
 use uuid::Uuid;
 
 /// Well-known document paths.
@@ -37,6 +38,139 @@ pub mod paths {
     pub const ASSISTANT_DIRECTIVES: &str = "context/assistant-directives.md";
 }
 
+/// Name of the folder-level configuration document.
+///
+/// A document at `{directory}/.config` carries metadata flags that apply
+/// as defaults to all documents in that directory (e.g., `skip_indexing`,
+/// `hygiene` settings). Individual document metadata overrides folder defaults.
+pub const CONFIG_FILE_NAME: &str = ".config";
+
+/// Typed overlay for the `metadata` JSON field on [`MemoryDocument`].
+///
+/// Fields use `Option` so that only explicitly set flags participate in
+/// the merge chain (document metadata → folder `.config` → system defaults).
+/// Unknown fields are preserved via `serde(flatten)`.
+#[derive(Debug, Clone, Default, Serialize, Deserialize, PartialEq)]
+pub struct DocumentMetadata {
+    /// When `true`, skip chunking and embedding for this document/folder.
+    #[serde(default, skip_serializing_if = "Option::is_none")]
+    pub skip_indexing: Option<bool>,
+
+    /// When `true`, skip automatic versioning for this document/folder.
+    #[serde(default, skip_serializing_if = "Option::is_none")]
+    pub skip_versioning: Option<bool>,
+
+    /// Hygiene (auto-cleanup) configuration for this folder.
+    #[serde(default, skip_serializing_if = "Option::is_none")]
+    pub hygiene: Option<HygieneMetadata>,
+
+    /// Preserve unknown fields for forward compatibility.
+    #[serde(flatten)]
+    pub extra: serde_json::Map<String, serde_json::Value>,
+}
+
+impl DocumentMetadata {
+    /// Parse from a raw JSON [`serde_json::Value`].
+    ///
+    /// Returns [`Default`] if the value is not an object or cannot be parsed.
+    pub fn from_value(value: &serde_json::Value) -> Self {
+        serde_json::from_value(value.clone()).unwrap_or_default()
+    }
+
+    /// Convert to a JSON [`serde_json::Value`].
+    pub fn to_value(&self) -> serde_json::Value {
+        serde_json::to_value(self).unwrap_or(serde_json::json!({}))
+    }
+
+    /// Merge two metadata values: `overlay` keys win over `base` keys.
+    ///
+    /// This is a shallow merge at the top-level keys — nested objects are
+    /// replaced wholesale, not recursively merged. This keeps the semantics
+    /// simple and predictable across both PostgreSQL and libSQL.
+    pub fn merge(base: &serde_json::Value, overlay: &serde_json::Value) -> serde_json::Value {
+        let mut merged = match base {
+            serde_json::Value::Object(map) => map.clone(),
+            _ => serde_json::Map::new(),
+        };
+        if let serde_json::Value::Object(over) = overlay {
+            for (k, v) in over {
+                merged.insert(k.clone(), v.clone());
+            }
+        }
+        serde_json::Value::Object(merged)
+    }
+}
+
+/// Hygiene (auto-cleanup) settings for a folder.
+#[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
+pub struct HygieneMetadata {
+    /// Whether this folder is a hygiene target.
+    pub enabled: bool,
+
+    /// Delete documents older than this many days.
+    #[serde(default = "default_retention_days")]
+    pub retention_days: u32,
+}
+
+fn default_retention_days() -> u32 {
+    30
+}
+
+/// A historical version of a workspace document.
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct DocumentVersion {
+    /// Version record ID.
+    pub id: Uuid,
+    /// Parent document ID.
+    pub document_id: Uuid,
+    /// Version number (1-based, monotonically increasing per document).
+    pub version: i32,
+    /// Full document content at this version.
+    pub content: String,
+    /// SHA-256 hash of `content` (hex-encoded, prefixed with `sha256:`).
+    pub content_hash: String,
+    /// When this version was created.
+    pub created_at: DateTime<Utc>,
+    /// Who/what created this version (e.g. `"agent"`, `"user:alice"`).
+    pub changed_by: Option<String>,
+}
+
+/// Summary of a document version (without full content).
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct VersionSummary {
+    /// Version number.
+    pub version: i32,
+    /// SHA-256 hash of the version's content.
+    pub content_hash: String,
+    /// When this version was created.
+    pub created_at: DateTime<Utc>,
+    /// Who/what created this version.
+    pub changed_by: Option<String>,
+}
+
+/// Result of a workspace patch operation.
+#[derive(Debug, Clone)]
+pub struct PatchResult {
+    /// The updated document.
+    pub document: MemoryDocument,
+    /// Number of replacements made.
+    pub replacements: usize,
+}
+
+/// Compute a SHA-256 hash of content, returned as `"sha256:{hex}"`.
+pub fn content_sha256(content: &str) -> String {
+    let mut hasher = Sha256::new();
+    hasher.update(content.as_bytes());
+    let result = hasher.finalize();
+    format!("sha256:{:x}", result)
+}
+
+/// Check if a path refers to a `.config` document.
+pub fn is_config_path(path: &str) -> bool {
+    let file_name = path.rsplit('/').next().unwrap_or(path);
+    file_name == CONFIG_FILE_NAME
+}
+
 /// Paths treated as identity documents for multi-scope isolation.
 ///
 /// These files are always read from the primary scope only — never from
@@ -360,6 +494,120 @@ mod tests {
         assert_eq!(result[0].updated_at, Some(ts));
     }
 
+    #[test]
+    fn test_document_metadata_default_is_empty() {
+        let meta = DocumentMetadata::default();
+        assert_eq!(meta.skip_indexing, None);
+        assert_eq!(meta.skip_versioning, None);
+        assert_eq!(meta.hygiene, None);
+        assert!(meta.extra.is_empty());
+    }
+
+    #[test]
+    fn test_document_metadata_from_value_full() {
+        let value = serde_json::json!({
+            "skip_indexing": true,
+            "skip_versioning": false,
+            "hygiene": { "enabled": true, "retention_days": 7 }
+        });
+        let meta = DocumentMetadata::from_value(&value);
+        assert_eq!(meta.skip_indexing, Some(true));
+        assert_eq!(meta.skip_versioning, Some(false));
+        let hygiene = meta.hygiene.unwrap();
+        assert!(hygiene.enabled);
+        assert_eq!(hygiene.retention_days, 7);
+    }
+
+    #[test]
+    fn test_document_metadata_from_value_partial() {
+        let value = serde_json::json!({"skip_indexing": true});
+        let meta = DocumentMetadata::from_value(&value);
+        assert_eq!(meta.skip_indexing, Some(true));
+        assert_eq!(meta.hygiene, None);
+    }
+
+    #[test]
+    fn test_document_metadata_from_value_invalid() {
+        let meta = DocumentMetadata::from_value(&serde_json::json!("not an object"));
+        assert_eq!(meta, DocumentMetadata::default());
+    }
+
+    #[test]
+    fn test_document_metadata_preserves_unknown_fields() {
+        let value = serde_json::json!({
+            "skip_indexing": true,
+            "custom_field": "hello"
+        });
+        let meta = DocumentMetadata::from_value(&value);
+        assert_eq!(meta.skip_indexing, Some(true));
+        assert_eq!(
+            meta.extra.get("custom_field").and_then(|v| v.as_str()),
+            Some("hello")
+        );
+
+        // Round-trip preserves the field
+        let back = meta.to_value();
+        assert_eq!(
+            back.get("custom_field").and_then(|v| v.as_str()),
+            Some("hello")
+        );
+    }
+
+    #[test]
+    fn test_document_metadata_merge() {
+        let base = serde_json::json!({"skip_indexing": false, "hygiene": {"enabled": true, "retention_days": 30}});
+        let overlay = serde_json::json!({"skip_indexing": true, "skip_versioning": true});
+        let merged = DocumentMetadata::merge(&base, &overlay);
+        let meta = DocumentMetadata::from_value(&merged);
+        // Overlay wins
+        assert_eq!(meta.skip_indexing, Some(true));
+        assert_eq!(meta.skip_versioning, Some(true));
+        // Base preserved when not overridden
+        assert!(meta.hygiene.is_some());
+    }
+
+    #[test]
+    fn test_document_metadata_merge_empty_base() {
+        let base = serde_json::json!({});
+        let overlay = serde_json::json!({"skip_indexing": true});
+        let merged = DocumentMetadata::merge(&base, &overlay);
+        let meta = DocumentMetadata::from_value(&merged);
+        assert_eq!(meta.skip_indexing, Some(true));
+    }
+
+    #[test]
+    fn test_hygiene_metadata_default_retention() {
+        let value = serde_json::json!({"enabled": true});
+        let hygiene: HygieneMetadata = serde_json::from_value(value).unwrap();
+        assert!(hygiene.enabled);
+        assert_eq!(hygiene.retention_days, 30);
+    }
+
+    #[test]
+    fn test_content_sha256_deterministic() {
+        let hash1 = content_sha256("hello world");
+        let hash2 = content_sha256("hello world");
+        assert_eq!(hash1, hash2);
+        assert!(hash1.starts_with("sha256:"));
+    }
+
+    #[test]
+    fn test_content_sha256_different_content() {
+        let hash1 = content_sha256("hello");
+        let hash2 = content_sha256("world");
+        assert_ne!(hash1, hash2);
+    }
+
+    #[test]
+    fn test_is_config_path() {
+        assert!(is_config_path(".config"));
+        assert!(is_config_path("daily/.config"));
+        assert!(is_config_path("frontend/widgets/.config"));
+        assert!(!is_config_path("daily/2024-01-15.md"));
+        assert!(!is_config_path("MEMORY.md"));
+        assert!(!is_config_path(".config.bak"));
+    }
+
     #[test]
     fn test_merge_workspace_entries_sorted_by_path() {
         let entries = vec![

src/workspace/hygiene.rs

@@ -1,8 +1,10 @@
 //! Memory hygiene: automatic cleanup of stale workspace documents.
 //!
-//! Runs on a configurable cadence and deletes daily log entries and conversation
-//! documents older than their respective retention periods. Identity files
-//! (`IDENTITY.md`, `SOUL.md`, etc.) are never touched.
+//! Runs on a configurable cadence and discovers which directories have hygiene
+//! enabled by reading `.config` metadata documents. This is a **metadata-driven**
+//! approach: instead of hardcoding `daily/` and `conversations/`, the system
+//! respects `hygiene.enabled` and `hygiene.retention_days` set on each folder's
+//! `.config` document.
 //!
 //! A global [`AtomicBool`] guard prevents concurrent hygiene passes, which
 //! avoids TOCTOU races on the state file and Windows file-locking errors
@@ -10,18 +12,16 @@
 //! pass completes.
 //!
 //! ```text
-//! ┌─────────────────────────────────────────────┐
-//! │               Hygiene Pass                   │
-//! │                                              │
-//! │  0. Acquire RUNNING guard (skip if held)     │
-//! │  1. Check cadence (skip if ran recently)     │
-//! │  2. Save state (claim the cadence window)    │
-//! │  3. List daily/ documents                    │
-//! │  4. Delete those older than daily_retention  │
-//! │  5. List conversations/ documents            │
-//! │  6. Delete those older than conversation_ret │
-//! │  7. Log summary                              │
-//! └─────────────────────────────────────────────┘
+//! ┌──────────────────────────────────────────────────┐
+//! │               Hygiene Pass                        │
+//! │                                                   │
+//! │  0. Acquire RUNNING guard (skip if held)          │
+//! │  1. Check cadence (skip if ran recently)          │
+//! │  2. Save state (claim the cadence window)         │
+//! │  3. Discover .config docs with hygiene.enabled    │
+//! │  4. For each: cleanup_directory(parent, retention)│
+//! │  5. Log summary                                   │
+//! └──────────────────────────────────────────────────┘
 //! ```
 
 use std::path::PathBuf;
@@ -31,46 +31,22 @@ use chrono::{DateTime, Utc};
 use serde::{Deserialize, Serialize};
 
 use crate::bootstrap::ironclaw_base_dir;
-use crate::workspace::Workspace;
+use crate::workspace::{DocumentMetadata, Workspace, is_config_path};
 
 /// Global guard preventing concurrent hygiene passes.
 static RUNNING: AtomicBool = AtomicBool::new(false);
 
-/// Paths that must never be deleted by hygiene, regardless of age.
-const IDENTITY_PATHS: &[&str] = &[
-    crate::workspace::document::paths::MEMORY,
-    crate::workspace::document::paths::IDENTITY,
-    crate::workspace::document::paths::SOUL,
-    crate::workspace::document::paths::AGENTS,
-    crate::workspace::document::paths::USER,
-    crate::workspace::document::paths::HEARTBEAT,
-    crate::workspace::document::paths::README,
-    crate::workspace::document::paths::TOOLS,
-    crate::workspace::document::paths::BOOTSTRAP,
-];
-
-/// Check if a document path is an identity document that must never be deleted.
-///
-/// Performs case-insensitive comparison to handle case-insensitive filesystems
-/// (Windows, macOS) and prevent accidental deletion of identity docs with
-/// different casing (e.g., memory.md, MEMORY.MD, Memory.md).
-fn is_identity_path(path: &str) -> bool {
-    let file_name = path.rsplit('/').next().unwrap_or(path);
-    let file_name_lower = file_name.to_lowercase();
-    IDENTITY_PATHS
-        .iter()
-        .any(|&p| p.to_lowercase() == file_name_lower)
-}
-
 /// Configuration for workspace hygiene.
 #[derive(Debug, Clone)]
 pub struct HygieneConfig {
     /// Whether hygiene is enabled at all.
     pub enabled: bool,
-    /// Documents in `daily/` older than this many days are deleted.
-    pub daily_retention_days: u32,
-    /// Documents in `conversations/` older than this many days are deleted.
-    pub conversation_retention_days: u32,
+    /// Maximum number of versions to keep per document.
+    ///
+    /// TODO: Wire up global version pruning once per-document iteration
+    /// is efficient (e.g., via a dedicated DB query). For now this field
+    /// is stored in config but not actively enforced during hygiene passes.
+    pub version_keep_count: u32,
     /// Minimum hours between hygiene passes.
     pub cadence_hours: u32,
     /// Directory to store state file (default: `~/.ironclaw`).
@@ -81,8 +57,7 @@ impl Default for HygieneConfig {
     fn default() -> Self {
         Self {
             enabled: true,
-            daily_retention_days: 30,
-            conversation_retention_days: 7,
+            version_keep_count: 50,
             cadence_hours: 12,
             state_dir: ironclaw_base_dir(),
         }
@@ -98,10 +73,10 @@ struct HygieneState {
 /// Summary of what a hygiene pass cleaned up.
 #[derive(Debug, Default)]
 pub struct HygieneReport {
-    /// Number of daily log documents deleted.
-    pub daily_logs_deleted: u32,
-    /// Number of conversation documents deleted.
-    pub conversation_docs_deleted: u32,
+    /// Per-directory cleanup results: `(directory_path, deleted_count)`.
+    pub directories_cleaned: Vec<(String, u32)>,
+    /// Number of document versions pruned across all documents.
+    pub versions_pruned: u64,
     /// Whether the run was skipped (cadence not yet elapsed).
     pub skipped: bool,
 }
@@ -109,7 +84,7 @@ pub struct HygieneReport {
 impl HygieneReport {
     /// True if any cleanup work was done.
     pub fn had_work(&self) -> bool {
-        self.daily_logs_deleted > 0 || self.conversation_docs_deleted > 0
+        self.directories_cleaned.iter().any(|(_, n)| *n > 0) || self.versions_pruned > 0
     }
 }
 
@@ -168,30 +143,51 @@ pub async fn run_if_due(workspace: &Workspace, config: &HygieneConfig) -> Hygien
     // TOCTOU races where another task reads stale state.
     save_state(&state_file);
 
-    tracing::info!(
-        daily_retention_days = config.daily_retention_days,
-        conversation_retention_days = config.conversation_retention_days,
-        "memory hygiene: starting cleanup pass"
-    );
+    tracing::info!("memory hygiene: starting cleanup pass");
 
     let mut report = HygieneReport::default();
 
-    // Delete old daily logs
-    match cleanup_daily_logs(workspace, config.daily_retention_days).await {
-        Ok(count) => report.daily_logs_deleted = count,
-        Err(e) => tracing::warn!("memory hygiene: failed to clean daily logs: {e}"),
-    }
+    // Discover directories that have hygiene enabled via .config metadata.
+    let config_docs = match workspace.find_config_documents().await {
+        Ok(docs) => docs,
+        Err(e) => {
+            tracing::warn!("memory hygiene: failed to discover .config documents: {e}");
+            return report;
+        }
+    };
 
-    // Delete old conversation documents
-    match cleanup_conversation_docs(workspace, config.conversation_retention_days).await {
-        Ok(count) => report.conversation_docs_deleted = count,
-        Err(e) => tracing::warn!("memory hygiene: failed to clean conversation docs: {e}"),
+    for doc in &config_docs {
+        let meta = DocumentMetadata::from_value(&doc.metadata);
+        let Some(hygiene) = meta.hygiene else {
+            continue;
+        };
+        if !hygiene.enabled {
+            continue;
+        }
+
+        // Derive the parent directory from the .config path.
+        let directory = match doc.path.rsplit_once('/') {
+            Some((dir, _)) => format!("{dir}/"),
+            None => continue, // root-level .config — skip
+        };
+
+        match cleanup_directory(workspace, &directory, hygiene.retention_days).await {
+            Ok(deleted) => {
+                if deleted > 0 {
+                    tracing::info!(directory, deleted, "memory hygiene: cleaned directory");
+                }
+                report.directories_cleaned.push((directory, deleted));
+            }
+            Err(e) => {
+                tracing::warn!(directory, "memory hygiene: failed to clean directory: {e}");
+            }
+        }
     }
 
     if report.had_work() {
         tracing::info!(
-            daily_logs_deleted = report.daily_logs_deleted,
-            conversation_docs_deleted = report.conversation_docs_deleted,
+            directories_cleaned = ?report.directories_cleaned,
+            versions_pruned = report.versions_pruned,
             "memory hygiene: cleanup complete"
         );
     } else {
@@ -210,88 +206,41 @@ impl Drop for RunningGuard {
     }
 }
 
-/// Delete daily log documents older than `retention_days`.
-async fn cleanup_daily_logs(
+/// Delete documents in `directory` that are older than `retention_days`.
+///
+/// Skips directories and `.config` files (which must never be deleted by
+/// hygiene). Returns the number of documents deleted.
+async fn cleanup_directory(
     workspace: &Workspace,
+    directory: &str,
     retention_days: u32,
 ) -> Result<u32, anyhow::Error> {
     let cutoff = Utc::now() - chrono::Duration::days(i64::from(retention_days));
-    let entries = workspace.list("daily/").await?;
-
+    let entries = workspace.list(directory).await?;
     let mut deleted = 0u32;
     for entry in entries {
         if entry.is_directory {
             continue;
         }
-
-        // Never delete identity documents
-        if is_identity_path(&entry.path) {
+        if is_config_path(&entry.path) {
             continue;
         }
-
-        // Check if the document is old enough to delete
         if let Some(updated_at) = entry.updated_at
             && updated_at < cutoff
         {
-            let path = if entry.path.starts_with("daily/") {
+            let path = if entry.path.starts_with(directory) {
                 entry.path.clone()
             } else {
-                format!("daily/{}", entry.path)
+                format!("{}{}", directory, entry.path)
             };
-
             if let Err(e) = workspace.delete(&path).await {
                 tracing::warn!(path, "memory hygiene: failed to delete: {e}");
             } else {
-                tracing::debug!(path, "memory hygiene: deleted old daily log");
+                tracing::debug!(path, "memory hygiene: deleted stale document");
                 deleted += 1;
             }
         }
     }
-
-    Ok(deleted)
-}
-
-/// Delete conversation documents older than `retention_days`.
-async fn cleanup_conversation_docs(
-    workspace: &Workspace,
-    retention_days: u32,
-) -> Result<u32, anyhow::Error> {
-    let cutoff = Utc::now() - chrono::Duration::days(i64::from(retention_days));
-    let entries = workspace.list("conversations/").await?;
-
-    let mut deleted = 0u32;
-    for entry in entries {
-        if entry.is_directory {
-            continue;
-        }
-
-        // Never delete identity documents
-        if is_identity_path(&entry.path) {
-            continue;
-        }
-
-        // Check if the document is old enough to delete
-        if let Some(updated_at) = entry.updated_at
-            && updated_at < cutoff
-        {
-            let path = if entry.path.starts_with("conversations/") {
-                entry.path.clone()
-            } else {
-                format!("conversations/{}", entry.path)
-            };
-
-            if let Err(e) = workspace.delete(&path).await {
-                tracing::warn!(
-                    path,
-                    "memory hygiene: failed to delete conversation doc: {e}"
-                );
-            } else {
-                tracing::debug!(path, "memory hygiene: deleted old conversation doc");
-                deleted += 1;
-            }
-        }
-    }
-
     Ok(deleted)
 }
 
@@ -349,8 +298,7 @@ mod tests {
     fn default_config_is_reasonable() {
         let cfg = HygieneConfig::default();
         assert!(cfg.enabled);
-        assert_eq!(cfg.daily_retention_days, 30);
-        assert_eq!(cfg.conversation_retention_days, 7);
+        assert_eq!(cfg.version_keep_count, 50);
         assert_eq!(cfg.cadence_hours, 12);
     }
 
@@ -362,84 +310,33 @@ mod tests {
     }
 
     #[test]
-    fn report_had_work_when_deleted() {
+    fn report_had_work_when_directories_cleaned() {
         let report = HygieneReport {
-            daily_logs_deleted: 3,
-            conversation_docs_deleted: 0,
+            directories_cleaned: vec![("daily/".to_string(), 3)],
+            versions_pruned: 0,
             skipped: false,
         };
         assert!(report.had_work());
     }
 
     #[test]
-    fn report_had_work_when_conversation_deleted() {
+    fn report_had_work_when_versions_pruned() {
         let report = HygieneReport {
-            daily_logs_deleted: 0,
-            conversation_docs_deleted: 2,
+            directories_cleaned: vec![],
+            versions_pruned: 5,
             skipped: false,
         };
         assert!(report.had_work());
     }
 
     #[test]
-    fn is_identity_path_excludes_sacred_docs() {
-        for name in [
-            "MEMORY.md",
-            "IDENTITY.md",
-            "SOUL.md",
-            "AGENTS.md",
-            "USER.md",
-            "HEARTBEAT.md",
-            "README.md",
-            "TOOLS.md",
-            "BOOTSTRAP.md",
-        ] {
-            assert!(is_identity_path(name), "{name} should be excluded");
-            assert!(
-                is_identity_path(&format!("conversations/{name}")),
-                "conversations/{name} should be excluded via path"
-            );
-        }
-    }
-
-    #[test]
-    fn is_identity_path_case_insensitive() {
-        // Verify case-insensitive matching for case-insensitive filesystems
-        assert!(
-            is_identity_path("memory.md"),
-            "lowercase memory.md should be excluded"
-        );
-        assert!(
-            is_identity_path("Memory.md"),
-            "mixed case Memory.md should be excluded"
-        );
-        assert!(
-            is_identity_path("MEMORY.MD"),
-            "uppercase MEMORY.MD should be excluded"
-        );
-        assert!(
-            is_identity_path("identity.md"),
-            "lowercase identity.md should be excluded"
-        );
-        assert!(
-            is_identity_path("conversations/soul.md"),
-            "conversations/soul.md should be excluded"
-        );
-        assert!(
-            is_identity_path("conversations/SOUL.MD"),
-            "conversations/SOUL.MD should be excluded"
-        );
-    }
-
-    #[test]
-    fn is_identity_path_allows_normal_docs() {
-        for path in [
-            "daily/2024-01-01.md",
-            "conversations/chat-abc.md",
-            "notes.md",
-        ] {
-            assert!(!is_identity_path(path), "{path} should not be excluded");
-        }
+    fn report_no_work_when_zero_deletions() {
+        let report = HygieneReport {
+            directories_cleaned: vec![("daily/".to_string(), 0)],
+            versions_pruned: 0,
+            skipped: false,
+        };
+        assert!(!report.had_work());
     }
 
     #[test]
@@ -552,61 +449,105 @@ mod tests {
             Arc::new(Workspace::new_with_db("default", db.clone()))
         }
 
-        #[tokio::test]
-        async fn cleanup_daily_logs_preserves_identity_documents() {
-            let (db, _tmp) = create_test_db().await;
-            let ws = create_workspace(&db);
-
-            // Write several regular documents (non-identity)
-            ws.write("daily/2024-01-15.md", "Old log")
+        /// Helper to seed a .config document with hygiene metadata on a directory.
+        async fn seed_hygiene_config(workspace: &Workspace, directory: &str, retention_days: u32) {
+            let config_path = format!("{}.config", directory);
+            // Create the .config document with empty content
+            workspace
+                .write(&config_path, "")
                 .await
-                .expect("write log 1");
-            ws.write("daily/2024-01-20.md", "Another log")
+                .expect("write .config");
+            // Read back to get the document ID
+            let doc = workspace
+                .read(&config_path)
                 .await
-                .expect("write log 2");
-
-            // Write an identity document
-            ws.write("MEMORY.md", "Long-term curated memory")
+                .expect("read .config doc");
+            // Set hygiene metadata
+            workspace
+                .update_metadata(
+                    doc.id,
+                    &serde_json::json!({
+                        "hygiene": {"enabled": true, "retention_days": retention_days},
+                        "skip_versioning": true
+                    }),
+                )
                 .await
-                .expect("write identity");
-
-            // List before cleanup
-            let before = ws.list("daily/").await.expect("list before");
-            let daily_count_before = before.iter().filter(|e| !e.is_directory).count();
-            assert!(daily_count_before >= 2, "should have at least 2 daily logs");
-
-            // Run cleanup with 0-day retention (deletes everything old)
-            // This tests that even with aggressive cleanup, identity docs survive
-            let deleted = cleanup_daily_logs(&ws, 0)
-                .await
-                .expect("cleanup_daily_logs");
-
-            // Should have deleted some documents (the daily logs)
-            assert!(deleted > 0, "should have deleted old daily documents");
-
-            // Verify identity doc still exists
-            let identity = db
-                .get_document_by_path("default", None, "MEMORY.md")
-                .await
-                .expect("get identity doc");
-            assert_eq!(identity.path, "MEMORY.md");
-            assert_eq!(identity.content, "Long-term curated memory");
+                .expect("set metadata");
         }
 
         #[tokio::test]
-        async fn cleanup_conversation_docs_handles_empty_directory() {
+        async fn cleanup_directory_skips_config_files() {
             let (db, _tmp) = create_test_db().await;
             let ws = create_workspace(&db);
 
-            // Run cleanup on an empty directory (conversations/ doesn't exist)
-            let deleted = cleanup_conversation_docs(&ws, 7)
+            // Write documents including a .config
+            ws.write("daily/2024-01-15.md", "Old log")
                 .await
-                .expect("cleanup_conversation_docs");
+                .expect("write log");
+            ws.write("daily/.config", "").await.expect("write config");
+
+            // Run cleanup with 0-day retention (deletes everything old)
+            let deleted = cleanup_directory(&ws, "daily/", 0)
+                .await
+                .expect("cleanup_directory");
+
+            // Should have deleted the log but not the .config
+            assert!(deleted > 0, "should have deleted old daily documents");
+
+            // Verify .config still exists
+            let config_doc = db
+                .get_document_by_path("default", None, "daily/.config")
+                .await
+                .expect("get .config doc");
+            assert_eq!(config_doc.path, "daily/.config");
+        }
+
+        #[tokio::test]
+        async fn cleanup_directory_handles_empty_directory() {
+            let (db, _tmp) = create_test_db().await;
+            let ws = create_workspace(&db);
+
+            // Run cleanup on an empty directory
+            let deleted = cleanup_directory(&ws, "conversations/", 7)
+                .await
+                .expect("cleanup_directory");
 
-            // Should delete 0 (nothing to delete)
             assert_eq!(deleted, 0, "should delete 0 from empty directory");
         }
 
+        #[tokio::test]
+        async fn metadata_driven_cleanup_discovers_directories() {
+            let (db, _tmp) = create_test_db().await;
+            let ws = create_workspace(&db);
+
+            // Seed .config with hygiene enabled on daily/
+            seed_hygiene_config(&ws, "daily/", 0).await;
+
+            // Write some documents
+            ws.write("daily/log1.md", "content 1")
+                .await
+                .expect("write doc 1");
+            ws.write("daily/log2.md", "content 2")
+                .await
+                .expect("write doc 2");
+
+            let config = HygieneConfig {
+                enabled: true,
+                version_keep_count: 50,
+                cadence_hours: 12,
+                state_dir: _tmp.path().to_path_buf(),
+            };
+
+            // First run should discover daily/ and clean it
+            let report = run_if_due(&ws, &config).await;
+            assert!(!report.skipped, "first run should not be skipped");
+            assert!(report.had_work(), "should have cleaned documents");
+            assert!(
+                !report.directories_cleaned.is_empty(),
+                "should have at least one directory cleaned"
+            );
+        }
+
         #[tokio::test]
         async fn cleanup_respects_cadence_prevents_concurrent_runs() {
             let (db, _tmp) = create_test_db().await;
@@ -614,8 +555,7 @@ mod tests {
 
             let config = HygieneConfig {
                 enabled: true,
-                daily_retention_days: 30,
-                conversation_retention_days: 7,
+                version_keep_count: 50,
                 cadence_hours: 12,
                 state_dir: _tmp.path().to_path_buf(),
             };
@@ -627,13 +567,6 @@ mod tests {
             // Second run immediately should be skipped (cadence not elapsed)
             let report2 = run_if_due(&ws, &config).await;
             assert!(report2.skipped, "second run should be skipped by cadence");
-
-            // Report structure should be correct
-            assert_eq!(
-                report1.daily_logs_deleted + report1.conversation_docs_deleted,
-                0,
-                "first run should have clean counts"
-            );
         }
 
         #[tokio::test]
@@ -641,6 +574,10 @@ mod tests {
             let (db, _tmp) = create_test_db().await;
             let ws = create_workspace(&db);
 
+            // Seed hygiene on both directories
+            seed_hygiene_config(&ws, "daily/", 0).await;
+            seed_hygiene_config(&ws, "conversations/", 0).await;
+
             // Write some documents
             ws.write("daily/log1.md", "content 1")
                 .await
@@ -652,35 +589,34 @@ mod tests {
                 .await
                 .expect("write doc 3");
 
-            // Run with 0-day retention to delete everything non-identity
-            let deleted_daily = cleanup_daily_logs(&ws, 0).await.expect("cleanup daily");
-            let deleted_conv = cleanup_conversation_docs(&ws, 0)
+            // Run with 0-day retention via direct cleanup_directory calls
+            let deleted_daily = cleanup_directory(&ws, "daily/", 0)
+                .await
+                .expect("cleanup daily");
+            let deleted_conv = cleanup_directory(&ws, "conversations/", 0)
                 .await
                 .expect("cleanup conversations");
 
-            // Both should report deletions
             assert!(deleted_daily > 0, "should report deleted daily logs");
             assert_eq!(deleted_conv, 1, "should report 1 deleted conversation doc");
 
-            // Create a HygieneReport and verify aggregation works
+            // Verify HygieneReport aggregation
             let report = HygieneReport {
-                daily_logs_deleted: deleted_daily,
-                conversation_docs_deleted: deleted_conv,
+                directories_cleaned: vec![
+                    ("daily/".to_string(), deleted_daily),
+                    ("conversations/".to_string(), deleted_conv),
+                ],
+                versions_pruned: 0,
                 skipped: false,
             };
 
-            // Verify HygieneReport structure
             assert!(!report.skipped, "should not be skipped");
             assert!(report.had_work(), "report should indicate work was done");
-            assert!(
-                report.daily_logs_deleted > 0 || report.conversation_docs_deleted > 0,
-                "report should have at least one deletion count > 0"
-            );
 
-            // Verify had_work() correctly combines both counts
+            // Verify had_work() correctly checks directory counts
             let no_work = HygieneReport {
-                daily_logs_deleted: 0,
-                conversation_docs_deleted: 0,
+                directories_cleaned: vec![],
+                versions_pruned: 0,
                 skipped: false,
             };
             assert!(!no_work.had_work(), "empty report should indicate no work");

src/workspace/mod.rs

@@ -53,8 +53,9 @@ mod search;
 
 pub use chunker::{ChunkConfig, chunk_document};
 pub use document::{
-    IDENTITY_PATHS, MemoryChunk, MemoryDocument, WorkspaceEntry, is_identity_path,
-    merge_workspace_entries, paths,
+    CONFIG_FILE_NAME, DocumentMetadata, DocumentVersion, HygieneMetadata, IDENTITY_PATHS,
+    MemoryChunk, MemoryDocument, PatchResult, VersionSummary, WorkspaceEntry, content_sha256,
+    is_config_path, is_identity_path, merge_workspace_entries, paths,
 };
 pub use embedding_cache::{CachedEmbeddingProvider, EmbeddingCacheConfig};
 pub use embeddings::{
@@ -366,6 +367,101 @@ impl WorkspaceStorage {
             }
         }
     }
+
+    // ==================== Metadata ====================
+
+    async fn update_document_metadata(
+        &self,
+        id: Uuid,
+        metadata: &serde_json::Value,
+    ) -> Result<(), WorkspaceError> {
+        match self {
+            #[cfg(feature = "postgres")]
+            Self::Repo(repo) => repo.update_document_metadata(id, metadata).await,
+            Self::Db(db) => db.update_document_metadata(id, metadata).await,
+        }
+    }
+
+    async fn find_config_documents(
+        &self,
+        user_id: &str,
+        agent_id: Option<Uuid>,
+    ) -> Result<Vec<MemoryDocument>, WorkspaceError> {
+        match self {
+            #[cfg(feature = "postgres")]
+            Self::Repo(repo) => repo.find_config_documents(user_id, agent_id).await,
+            Self::Db(db) => db.find_config_documents(user_id, agent_id).await,
+        }
+    }
+
+    // ==================== Versioning ====================
+
+    async fn save_version(
+        &self,
+        document_id: Uuid,
+        content: &str,
+        content_hash: &str,
+        changed_by: Option<&str>,
+    ) -> Result<i32, WorkspaceError> {
+        match self {
+            #[cfg(feature = "postgres")]
+            Self::Repo(repo) => {
+                repo.save_version(document_id, content, content_hash, changed_by)
+                    .await
+            }
+            Self::Db(db) => {
+                db.save_version(document_id, content, content_hash, changed_by)
+                    .await
+            }
+        }
+    }
+
+    async fn get_version(
+        &self,
+        document_id: Uuid,
+        version: i32,
+    ) -> Result<DocumentVersion, WorkspaceError> {
+        match self {
+            #[cfg(feature = "postgres")]
+            Self::Repo(repo) => repo.get_version(document_id, version).await,
+            Self::Db(db) => db.get_version(document_id, version).await,
+        }
+    }
+
+    async fn list_versions(
+        &self,
+        document_id: Uuid,
+        limit: i64,
+    ) -> Result<Vec<VersionSummary>, WorkspaceError> {
+        match self {
+            #[cfg(feature = "postgres")]
+            Self::Repo(repo) => repo.list_versions(document_id, limit).await,
+            Self::Db(db) => db.list_versions(document_id, limit).await,
+        }
+    }
+
+    async fn get_latest_version_number(
+        &self,
+        document_id: Uuid,
+    ) -> Result<Option<i32>, WorkspaceError> {
+        match self {
+            #[cfg(feature = "postgres")]
+            Self::Repo(repo) => repo.get_latest_version_number(document_id).await,
+            Self::Db(db) => db.get_latest_version_number(document_id).await,
+        }
+    }
+
+    async fn prune_versions(
+        &self,
+        document_id: Uuid,
+        keep_count: i32,
+    ) -> Result<u64, WorkspaceError> {
+        match self {
+            #[cfg(feature = "postgres")]
+            Self::Repo(repo) => repo.prune_versions(document_id, keep_count).await,
+            Self::Db(db) => db.prune_versions(document_id, keep_count).await,
+        }
+    }
 }
 
 /// Default template seeded into HEARTBEAT.md on first access.
@@ -696,10 +792,199 @@ impl Workspace {
             .await
     }
 
+    // ==================== Metadata ====================
+
+    /// Update the metadata JSON on a document by ID (full replacement).
+    pub async fn update_metadata(
+        &self,
+        id: Uuid,
+        metadata: &serde_json::Value,
+    ) -> Result<(), WorkspaceError> {
+        self.storage.update_document_metadata(id, metadata).await
+    }
+
+    /// Prune old versions for a document, keeping only the most recent `keep_count`.
+    ///
+    /// Returns the number of versions deleted.
+    pub async fn prune_versions(
+        &self,
+        document_id: Uuid,
+        keep_count: i32,
+    ) -> Result<u64, WorkspaceError> {
+        self.storage.prune_versions(document_id, keep_count).await
+    }
+
+    /// Find all `.config` documents in this workspace scope.
+    pub async fn find_config_documents(&self) -> Result<Vec<MemoryDocument>, WorkspaceError> {
+        self.storage
+            .find_config_documents(&self.user_id, self.agent_id)
+            .await
+    }
+
+    /// Resolve effective metadata for a document path.
+    ///
+    /// Resolution chain: document's own metadata → nearest ancestor `.config` → defaults.
+    pub async fn resolve_metadata(&self, path: &str) -> DocumentMetadata {
+        // 1. Document's own metadata
+        let doc_meta = self
+            .storage
+            .get_document_by_path(&self.user_id, self.agent_id, path)
+            .await
+            .ok()
+            .map(|d| d.metadata);
+
+        // 2. Walk up parent directories looking for .config
+        let mut config_meta = None;
+        let normalized = normalize_path(path);
+        let mut current = normalized.as_str();
+        while let Some(slash_pos) = current.rfind('/') {
+            let parent = &current[..slash_pos];
+            let config_path = format!("{}/{CONFIG_FILE_NAME}", parent);
+            if let Ok(doc) = self
+                .storage
+                .get_document_by_path(&self.user_id, self.agent_id, &config_path)
+                .await
+            {
+                config_meta = Some(doc.metadata);
+                break;
+            }
+            current = parent;
+        }
+        // Also check root-level .config
+        if config_meta.is_none()
+            && let Ok(doc) = self
+                .storage
+                .get_document_by_path(&self.user_id, self.agent_id, CONFIG_FILE_NAME)
+                .await
+        {
+            config_meta = Some(doc.metadata);
+        }
+
+        // 3. Merge: config as base, document metadata as overlay
+        let base = config_meta.unwrap_or(serde_json::json!({}));
+        let overlay = doc_meta.unwrap_or(serde_json::json!({}));
+        let merged = DocumentMetadata::merge(&base, &overlay);
+        DocumentMetadata::from_value(&merged)
+    }
+
+    // ==================== Versioning ====================
+
+    /// List versions of a document (newest first).
+    pub async fn list_versions(
+        &self,
+        document_id: Uuid,
+        limit: i64,
+    ) -> Result<Vec<VersionSummary>, WorkspaceError> {
+        self.storage.list_versions(document_id, limit).await
+    }
+
+    /// Get a specific version of a document.
+    pub async fn get_version(
+        &self,
+        document_id: Uuid,
+        version: i32,
+    ) -> Result<DocumentVersion, WorkspaceError> {
+        self.storage.get_version(document_id, version).await
+    }
+
+    /// Save the current content as a version if it differs from the latest.
+    ///
+    /// Returns the new version number, or `None` if skipped (empty content,
+    /// identical hash, or versioning disabled via metadata).
+    async fn maybe_save_version(
+        &self,
+        document_id: Uuid,
+        current_content: &str,
+        path: &str,
+        changed_by: Option<&str>,
+    ) -> Result<Option<i32>, WorkspaceError> {
+        // Don't version empty documents
+        if current_content.is_empty() {
+            return Ok(None);
+        }
+
+        // Check metadata for skip_versioning flag
+        let metadata = self.resolve_metadata(path).await;
+        if metadata.skip_versioning == Some(true) {
+            return Ok(None);
+        }
+
+        let hash = content_sha256(current_content);
+
+        // Check if latest version already has this hash (skip duplicate saves)
+        if let Ok(Some(latest)) = self.storage.get_latest_version_number(document_id).await
+            && let Ok(ver) = self.storage.get_version(document_id, latest).await
+            && ver.content_hash == hash
+        {
+            return Ok(None);
+        }
+
+        let version = self
+            .storage
+            .save_version(document_id, current_content, &hash, changed_by)
+            .await?;
+        Ok(Some(version))
+    }
+
+    // ==================== Patch ====================
+
+    /// Apply a search-and-replace patch to a workspace document.
+    ///
+    /// Finds `old_string` in the document and replaces it with `new_string`.
+    /// If `replace_all` is true, replaces all occurrences; otherwise only the first.
+    /// Auto-versions before applying the patch.
+    pub async fn patch(
+        &self,
+        path: &str,
+        old_string: &str,
+        new_string: &str,
+        replace_all: bool,
+    ) -> Result<PatchResult, WorkspaceError> {
+        let path = normalize_path(path);
+        let doc = self
+            .storage
+            .get_document_by_path(&self.user_id, self.agent_id, &path)
+            .await?;
+
+        if !doc.content.contains(old_string) {
+            return Err(WorkspaceError::PatchFailed {
+                path,
+                reason: "old_string not found in document".to_string(),
+            });
+        }
+
+        let (new_content, count) = if replace_all {
+            let count = doc.content.matches(old_string).count();
+            (doc.content.replace(old_string, new_string), count)
+        } else {
+            (doc.content.replacen(old_string, new_string, 1), 1)
+        };
+
+        // Injection scan for system prompt files
+        if is_system_prompt_file(&path) && !new_content.is_empty() {
+            reject_if_injected(&path, &new_content)?;
+        }
+
+        // Auto-version before updating
+        let _ = self
+            .maybe_save_version(doc.id, &doc.content, &path, None)
+            .await;
+
+        self.storage.update_document(doc.id, &new_content).await?;
+        self.reindex_document(doc.id).await?;
+
+        let updated = self.storage.get_document_by_id(doc.id).await?;
+        Ok(PatchResult {
+            document: updated,
+            replacements: count,
+        })
+    }
+
     /// Write (create or update) a file.
     ///
     /// Creates parent directories implicitly (they're virtual in the DB).
     /// Re-indexes the document for search after writing.
+    /// Auto-versions the previous content before overwriting.
     ///
     /// # Example
     /// ```ignore
@@ -715,6 +1000,12 @@ impl Workspace {
             .storage
             .get_or_create_document_by_path(&self.user_id, self.agent_id, &path)
             .await?;
+
+        // Auto-version previous content before overwriting
+        let _ = self
+            .maybe_save_version(doc.id, &doc.content, &path, None)
+            .await;
+
         self.storage.update_document(doc.id, content).await?;
         self.reindex_document(doc.id).await?;
 
@@ -754,6 +1045,11 @@ impl Workspace {
             reject_if_injected(&path, &new_content)?;
         }
 
+        // Auto-version previous content before appending
+        let _ = self
+            .maybe_save_version(doc.id, &doc.content, &path, None)
+            .await;
+
         self.storage.update_document(doc.id, &new_content).await?;
         self.reindex_document(doc.id).await?;
         Ok(())
@@ -1585,6 +1881,14 @@ impl Workspace {
         // Get the document
         let doc = self.storage.get_document_by_id(document_id).await?;
 
+        // Check metadata for skip_indexing flag
+        let metadata = self.resolve_metadata(&doc.path).await;
+        if metadata.skip_indexing == Some(true) {
+            // Delete any existing chunks and skip indexing
+            self.storage.delete_chunks(document_id).await?;
+            return Ok(());
+        }
+
         // Chunk the content
         let chunks = chunk_document(&doc.content, ChunkConfig::default());
 
@@ -1670,6 +1974,51 @@ impl Workspace {
             }
         }
 
+        // Seed folder-level .config documents for hygiene defaults.
+        let config_seeds: &[(&str, serde_json::Value)] = &[
+            (
+                "daily/.config",
+                serde_json::json!({
+                    "hygiene": {"enabled": true, "retention_days": 30},
+                    "skip_versioning": true
+                }),
+            ),
+            (
+                "conversations/.config",
+                serde_json::json!({
+                    "hygiene": {"enabled": true, "retention_days": 7},
+                    "skip_versioning": true
+                }),
+            ),
+        ];
+
+        for (config_path, metadata_value) in config_seeds {
+            match self.read_primary(config_path).await {
+                Ok(_) => continue, // Already exists, don't overwrite
+                Err(WorkspaceError::DocumentNotFound { .. }) => {}
+                Err(e) => {
+                    tracing::debug!("Failed to check {}: {}", config_path, e);
+                    continue;
+                }
+            }
+            // Create empty document with metadata
+            if let Ok(doc) = self
+                .storage
+                .get_or_create_document_by_path(&self.user_id, self.agent_id, config_path)
+                .await
+            {
+                if let Err(e) = self
+                    .storage
+                    .update_document_metadata(doc.id, metadata_value)
+                    .await
+                {
+                    tracing::debug!("Failed to set metadata on {}: {}", config_path, e);
+                } else {
+                    count += 1;
+                }
+            }
+        }
+
         // BOOTSTRAP.md is only seeded on truly fresh workspaces (no identity
         // files existed before seeding) AND when no profile exists yet (the user
         // may already have a profile from a previous install and doesn't need

src/workspace/repository.rs

@@ -11,7 +11,9 @@ use uuid::Uuid;
 
 use crate::error::WorkspaceError;
 
-use crate::workspace::document::{MemoryChunk, MemoryDocument, WorkspaceEntry};
+use crate::workspace::document::{
+    DocumentVersion, MemoryChunk, MemoryDocument, VersionSummary, WorkspaceEntry,
+};
 use crate::workspace::search::{RankedResult, SearchConfig, SearchResult, fuse_results};
 
 /// Database repository for workspace operations.
@@ -702,4 +704,192 @@ impl Repository {
         }
         Ok(crate::workspace::merge_workspace_entries(all_entries))
     }
+
+    // ==================== Metadata ====================
+
+    pub async fn update_document_metadata(
+        &self,
+        id: Uuid,
+        metadata: &serde_json::Value,
+    ) -> Result<(), WorkspaceError> {
+        let conn = self.conn().await?;
+        conn.execute(
+            "UPDATE memory_documents SET metadata = $2, updated_at = NOW() WHERE id = $1",
+            &[&id, &metadata],
+        )
+        .await
+        .map_err(|e| WorkspaceError::SearchFailed {
+            reason: format!("Failed to update metadata: {e}"),
+        })?;
+        Ok(())
+    }
+
+    pub async fn find_config_documents(
+        &self,
+        user_id: &str,
+        agent_id: Option<Uuid>,
+    ) -> Result<Vec<MemoryDocument>, WorkspaceError> {
+        let conn = self.conn().await?;
+        let rows = conn
+            .query(
+                r#"
+                SELECT id, user_id, agent_id, path, content,
+                       created_at, updated_at, metadata
+                FROM memory_documents
+                WHERE user_id = $1 AND agent_id IS NOT DISTINCT FROM $2
+                  AND (path LIKE '%/.config' OR path = '.config')
+                ORDER BY path
+                "#,
+                &[&user_id, &agent_id],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to find config documents: {e}"),
+            })?;
+        Ok(rows.iter().map(|r| self.row_to_document(r)).collect())
+    }
+
+    // ==================== Versioning ====================
+
+    pub async fn save_version(
+        &self,
+        document_id: Uuid,
+        content: &str,
+        content_hash: &str,
+        changed_by: Option<&str>,
+    ) -> Result<i32, WorkspaceError> {
+        let conn = self.conn().await?;
+        let row = conn
+            .query_one(
+                r#"
+                INSERT INTO memory_document_versions
+                    (id, document_id, version, content, content_hash, changed_by)
+                VALUES (
+                    gen_random_uuid(),
+                    $1,
+                    (SELECT COALESCE(MAX(version), 0) + 1
+                     FROM memory_document_versions WHERE document_id = $1),
+                    $2, $3, $4
+                )
+                RETURNING version
+                "#,
+                &[&document_id, &content, &content_hash, &changed_by],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to save version: {e}"),
+            })?;
+        Ok(row.get(0))
+    }
+
+    pub async fn get_version(
+        &self,
+        document_id: Uuid,
+        version: i32,
+    ) -> Result<DocumentVersion, WorkspaceError> {
+        let conn = self.conn().await?;
+        let row = conn
+            .query_opt(
+                r#"
+                SELECT id, document_id, version, content, content_hash,
+                       created_at, changed_by
+                FROM memory_document_versions
+                WHERE document_id = $1 AND version = $2
+                "#,
+                &[&document_id, &version],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to get version: {e}"),
+            })?
+            .ok_or(WorkspaceError::VersionNotFound {
+                document_id,
+                version,
+            })?;
+        Ok(DocumentVersion {
+            id: row.get(0),
+            document_id: row.get(1),
+            version: row.get(2),
+            content: row.get(3),
+            content_hash: row.get(4),
+            created_at: row.get(5),
+            changed_by: row.get(6),
+        })
+    }
+
+    pub async fn list_versions(
+        &self,
+        document_id: Uuid,
+        limit: i64,
+    ) -> Result<Vec<VersionSummary>, WorkspaceError> {
+        let conn = self.conn().await?;
+        let rows = conn
+            .query(
+                r#"
+                SELECT version, content_hash, created_at, changed_by
+                FROM memory_document_versions
+                WHERE document_id = $1
+                ORDER BY version DESC
+                LIMIT $2
+                "#,
+                &[&document_id, &limit],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to list versions: {e}"),
+            })?;
+        Ok(rows
+            .iter()
+            .map(|row| VersionSummary {
+                version: row.get(0),
+                content_hash: row.get(1),
+                created_at: row.get(2),
+                changed_by: row.get(3),
+            })
+            .collect())
+    }
+
+    pub async fn get_latest_version_number(
+        &self,
+        document_id: Uuid,
+    ) -> Result<Option<i32>, WorkspaceError> {
+        let conn = self.conn().await?;
+        let row = conn
+            .query_one(
+                "SELECT MAX(version) FROM memory_document_versions WHERE document_id = $1",
+                &[&document_id],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to get latest version number: {e}"),
+            })?;
+        Ok(row.get(0))
+    }
+
+    pub async fn prune_versions(
+        &self,
+        document_id: Uuid,
+        keep_count: i32,
+    ) -> Result<u64, WorkspaceError> {
+        let conn = self.conn().await?;
+        let result = conn
+            .execute(
+                r#"
+                DELETE FROM memory_document_versions
+                WHERE document_id = $1
+                  AND version NOT IN (
+                      SELECT version FROM memory_document_versions
+                      WHERE document_id = $1
+                      ORDER BY version DESC
+                      LIMIT $2
+                  )
+                "#,
+                &[&document_id, &(keep_count as i64)],
+            )
+            .await
+            .map_err(|e| WorkspaceError::SearchFailed {
+                reason: format!("Failed to prune versions: {e}"),
+            })?;
+        Ok(result)
+    }
 }

tests/e2e/CLAUDE.md

@@ -53,6 +53,7 @@ HEADED=1 pytest scenarios/
 | `test_skills.py` | Skills tab UI visibility, ClawHub search (skipped if registry unreachable), install + remove lifecycle |
 | `test_sse_reconnect.py` | SSE reconnects after programmatic `eventSource.close()` + `connectSSE()`; history is reloaded after reconnect |
 | `test_tool_approval.py` | Approval card appears, buttons disable on approve/deny, parameters toggle via `page.evaluate("showApproval(...)")`; the waiting-approval regression uses a real HTTP tool call |
+| `test_extension_uninstall_cleanup.py` | Real install/setup/remove coverage for WASM tools, WASM channels, OAuth-backed shared Google tools, and MCP servers; verifies uninstall deletes stored secrets from the libSQL `secrets` table while preserving shared credentials until the last referencing extension is removed |
 | `test_oauth_refresh.py` | Hosted Gmail OAuth regression: complete setup via `/oauth/callback`, expire the stored access token in libSQL, trigger a real `gmail` tool call through `/api/chat/send`, and verify refresh goes through the mock `/oauth/refresh` proxy without forwarding `client_secret` |
 
 ## `helpers.py`
@@ -77,6 +78,7 @@ All fixtures are defined in `tests/e2e/conftest.py`. Running `pytest scenarios/`
 | `mock_llm_server` | Starts `mock_llm.py --port 0`, reads the assigned port from stdout, waits for `/v1/models` to return 200. Yields the base URL. |
 | `ironclaw_server` | Starts the ironclaw binary with a minimal env (see below), waits for `/api/health` (timeout 60s). Yields the base URL. On teardown sends **SIGINT** (not SIGTERM) so the tokio ctrl_c handler triggers a graceful shutdown and LLVM coverage data is flushed. |
 | `hosted_oauth_refresh_server` | Starts a second ironclaw instance with a dedicated libSQL DB and `GOOGLE_OAUTH_CLIENT_ID=hosted-google-client-id`, while still pointing `IRONCLAW_OAUTH_EXCHANGE_URL` at `mock_llm.py`. Yields a dict with `base_url`, `db_path`, `gateway_user_id`, and `mock_llm_url` for the hosted refresh regression scenario. |
+| `extension_cleanup_server` | Starts an isolated ironclaw instance with its own temp DB/home/WASM dirs, `SECRETS_MASTER_KEY`, and hosted-style OAuth env so uninstall-cleanup scenarios can inspect the `secrets` table without interfering with the shared E2E server state. |
 | `browser` | Launches a single Chromium instance (headless by default; set `HEADED=1` for headed). Shared across all tests. |
 
 ### Function-scoped fixtures

tests/e2e/conftest.py

@@ -443,6 +443,115 @@ async def hosted_oauth_refresh_server(
         home_tmpdir.cleanup()
 
 
+@pytest.fixture(scope="session")
+async def extension_cleanup_server(
+    ironclaw_binary,
+    mock_llm_server,
+):
+    """Start an isolated ironclaw instance for uninstall secret cleanup E2E tests."""
+    reserved = _reserve_loopback_sockets(2)
+    db_tmpdir = tempfile.TemporaryDirectory(prefix="ironclaw-e2e-cleanup-db-")
+    home_tmpdir = tempfile.TemporaryDirectory(prefix="ironclaw-e2e-cleanup-home-")
+    tools_tmpdir = tempfile.TemporaryDirectory(prefix="ironclaw-e2e-cleanup-tools-")
+    channels_tmpdir = tempfile.TemporaryDirectory(prefix="ironclaw-e2e-cleanup-channels-")
+
+    try:
+        gateway_port = reserved[0].getsockname()[1]
+        http_port = reserved[1].getsockname()[1]
+        for sock in reserved:
+            if sock.fileno() != -1:
+                sock.close()
+
+        db_path = os.path.join(db_tmpdir.name, "extension-cleanup.db")
+        home_dir = home_tmpdir.name
+        env = {
+            "PATH": os.environ.get("PATH", "/usr/bin:/bin"),
+            "HOME": home_dir,
+            "IRONCLAW_BASE_DIR": os.path.join(home_dir, ".ironclaw"),
+            "RUST_LOG": "ironclaw=info",
+            "RUST_BACKTRACE": "1",
+            "IRONCLAW_OWNER_ID": OWNER_SCOPE_ID,
+            "GATEWAY_ENABLED": "true",
+            "GATEWAY_HOST": "127.0.0.1",
+            "GATEWAY_PORT": str(gateway_port),
+            "GATEWAY_AUTH_TOKEN": AUTH_TOKEN,
+            "GATEWAY_USER_ID": OWNER_SCOPE_ID,
+            "HTTP_HOST": "127.0.0.1",
+            "HTTP_PORT": str(http_port),
+            "HTTP_WEBHOOK_SECRET": HTTP_WEBHOOK_SECRET,
+            "CLI_ENABLED": "false",
+            "LLM_BACKEND": "openai_compatible",
+            "LLM_BASE_URL": mock_llm_server,
+            "LLM_MODEL": "mock-model",
+            "DATABASE_BACKEND": "libsql",
+            "LIBSQL_PATH": db_path,
+            "SECRETS_MASTER_KEY": "0123456789abcdef0123456789abcdef0123456789abcdef0123456789abcdef",
+            "SANDBOX_ENABLED": "false",
+            "SKILLS_ENABLED": "true",
+            "ROUTINES_ENABLED": "true",
+            "HEARTBEAT_ENABLED": "false",
+            "EMBEDDING_ENABLED": "false",
+            "WASM_ENABLED": "true",
+            "WASM_TOOLS_DIR": tools_tmpdir.name,
+            "WASM_CHANNELS_DIR": channels_tmpdir.name,
+            "ONBOARD_COMPLETED": "true",
+            "IRONCLAW_OAUTH_CALLBACK_URL": "https://oauth.test.example/oauth/callback",
+            "IRONCLAW_OAUTH_EXCHANGE_URL": mock_llm_server,
+            "GOOGLE_OAUTH_CLIENT_ID": "hosted-google-client-id",
+        }
+        _forward_coverage_env(env)
+
+        proc = await asyncio.create_subprocess_exec(
+            ironclaw_binary, "--no-onboard",
+            stdin=asyncio.subprocess.DEVNULL,
+            stdout=asyncio.subprocess.PIPE,
+            stderr=asyncio.subprocess.PIPE,
+            env=env,
+        )
+        startup_kill_attempted = False
+        base_url = f"http://127.0.0.1:{gateway_port}"
+        try:
+            await wait_for_ready(f"{base_url}/api/health", timeout=60)
+            yield {
+                "base_url": base_url,
+                "db_path": db_path,
+                "gateway_user_id": OWNER_SCOPE_ID,
+                "mock_llm_url": mock_llm_server,
+            }
+        except TimeoutError:
+            if proc.returncode is None:
+                startup_kill_attempted = True
+                await _stop_process(proc, timeout=2)
+            returncode = proc.returncode
+            stderr_bytes = b""
+            if proc.stderr:
+                try:
+                    stderr_bytes = await asyncio.wait_for(proc.stderr.read(8192), timeout=2)
+                except asyncio.TimeoutError:
+                    pass
+            stderr_text = stderr_bytes.decode("utf-8", errors="replace")
+            pytest.fail(
+                f"extension cleanup server failed to start on port {gateway_port} "
+                f"(returncode={returncode}).\nstderr:\n{stderr_text}"
+            )
+        finally:
+            if proc.returncode is None:
+                if startup_kill_attempted:
+                    await _stop_process(proc, timeout=2)
+                else:
+                    await _stop_process(proc, sig=signal.SIGINT, timeout=10)
+                    if proc.returncode is None:
+                        await _stop_process(proc, timeout=2)
+    finally:
+        for sock in reserved:
+            if sock.fileno() != -1:
+                sock.close()
+        db_tmpdir.cleanup()
+        home_tmpdir.cleanup()
+        tools_tmpdir.cleanup()
+        channels_tmpdir.cleanup()
+
+
 @pytest.fixture(scope="session")
 async def http_channel_server(ironclaw_server, server_ports):
     """HTTP webhook channel base URL."""

tests/e2e/scenarios/test_extension_uninstall_cleanup.py

@@ -0,0 +1,266 @@
+"""Extension uninstall secret cleanup E2E tests.
+
+Exercises real install/setup/auth/remove flows and verifies the backing
+secrets table is cleaned up when extensions are uninstalled.
+"""
+
+import sqlite3
+from urllib.parse import parse_qs, urlparse
+
+import httpx
+
+from helpers import api_get, api_post
+
+
+def _extract_state(auth_url: str) -> str:
+    parsed = urlparse(auth_url)
+    state = parse_qs(parsed.query).get("state", [None])[0]
+    assert state, f"auth_url should include state: {auth_url}"
+    return state
+
+
+def _secret_exists(db_path: str, user_id: str, name: str) -> bool:
+    with sqlite3.connect(db_path) as conn:
+        row = conn.execute(
+            "SELECT 1 FROM secrets WHERE user_id = ?1 AND name = ?2 LIMIT 1",
+            (user_id, name),
+        ).fetchone()
+    return row is not None
+
+
+def _secret_names(db_path: str, user_id: str) -> set[str]:
+    with sqlite3.connect(db_path) as conn:
+        rows = conn.execute(
+            "SELECT name FROM secrets WHERE user_id = ?1",
+            (user_id,),
+        ).fetchall()
+    return {row[0] for row in rows}
+
+
+async def _get_extension(base_url: str, name: str) -> dict | None:
+    response = await api_get(base_url, "/api/extensions", timeout=15)
+    response.raise_for_status()
+    for extension in response.json().get("extensions", []):
+        if extension["name"] == name:
+            return extension
+    return None
+
+
+async def _ensure_removed(base_url: str, name: str) -> None:
+    extension = await _get_extension(base_url, name)
+    if extension is not None:
+        response = await api_post(base_url, f"/api/extensions/{name}/remove", timeout=30)
+        assert response.status_code == 200, response.text
+        assert response.json().get("success") is True, response.text
+
+
+async def _install_extension(
+    base_url: str,
+    name: str,
+    *,
+    kind: str | None = None,
+    url: str | None = None,
+) -> None:
+    payload = {"name": name}
+    if kind is not None:
+        payload["kind"] = kind
+    if url is not None:
+        payload["url"] = url
+
+    response = await api_post(
+        base_url,
+        "/api/extensions/install",
+        json=payload,
+        timeout=180,
+    )
+    assert response.status_code == 200, response.text
+    assert response.json().get("success") is True, response.text
+
+
+async def test_remove_wasm_tool_deletes_unique_secret(extension_cleanup_server):
+    server = extension_cleanup_server["base_url"]
+    db_path = extension_cleanup_server["db_path"]
+    user_id = extension_cleanup_server["gateway_user_id"]
+
+    await _ensure_removed(server, "web-search")
+
+    await _install_extension(server, "web-search")
+
+    setup_response = await api_post(
+        server,
+        "/api/extensions/web-search/setup",
+        json={"secrets": {"brave_api_key": "cleanup-test-key"}},
+        timeout=30,
+    )
+    assert setup_response.status_code == 200, setup_response.text
+    assert setup_response.json().get("success") is True, setup_response.text
+    assert _secret_exists(db_path, user_id, "brave_api_key")
+
+    remove_response = await api_post(
+        server,
+        "/api/extensions/web-search/remove",
+        timeout=30,
+    )
+    assert remove_response.status_code == 200, remove_response.text
+    assert remove_response.json().get("success") is True, remove_response.text
+    assert not _secret_exists(db_path, user_id, "brave_api_key")
+
+
+async def test_remove_wasm_channel_deletes_setup_secrets(extension_cleanup_server):
+    server = extension_cleanup_server["base_url"]
+    db_path = extension_cleanup_server["db_path"]
+    user_id = extension_cleanup_server["gateway_user_id"]
+
+    await _ensure_removed(server, "discord")
+
+    await _install_extension(server, "discord", kind="wasm_channel")
+
+    setup_response = await api_post(
+        server,
+        "/api/extensions/discord/setup",
+        json={
+            "secrets": {
+                "discord_bot_token": "cleanup-discord-bot-token",
+                "discord_public_key": "cleanup-discord-public-key",
+            }
+        },
+        timeout=30,
+    )
+    assert setup_response.status_code == 200, setup_response.text
+    assert setup_response.json().get("success") is True, setup_response.text
+    assert _secret_exists(db_path, user_id, "discord_bot_token")
+    assert _secret_exists(db_path, user_id, "discord_public_key")
+
+    remove_response = await api_post(
+        server,
+        "/api/extensions/discord/remove",
+        timeout=30,
+    )
+    assert remove_response.status_code == 200, remove_response.text
+    assert remove_response.json().get("success") is True, remove_response.text
+    assert not _secret_exists(db_path, user_id, "discord_bot_token")
+    assert not _secret_exists(db_path, user_id, "discord_public_key")
+
+
+async def test_remove_shared_google_oauth_secrets_after_last_tool(extension_cleanup_server):
+    server = extension_cleanup_server["base_url"]
+    db_path = extension_cleanup_server["db_path"]
+    user_id = extension_cleanup_server["gateway_user_id"]
+
+    await _ensure_removed(server, "gmail")
+    await _ensure_removed(server, "google-drive")
+
+    await _install_extension(server, "gmail")
+    await _install_extension(server, "google-drive")
+
+    setup_response = await api_post(
+        server,
+        "/api/extensions/gmail/setup",
+        json={"secrets": {}},
+        timeout=30,
+    )
+    assert setup_response.status_code == 200, setup_response.text
+    auth_url = setup_response.json().get("auth_url")
+    assert auth_url, setup_response.text
+
+    async with httpx.AsyncClient() as client:
+        callback_response = await client.get(
+            f"{server}/oauth/callback",
+            params={"code": "mock_auth_code", "state": _extract_state(auth_url)},
+            timeout=30,
+            follow_redirects=True,
+        )
+    assert callback_response.status_code == 200, callback_response.text[:400]
+
+    shared_secrets = [
+        "google_oauth_token",
+        "google_oauth_token_refresh_token",
+        "google_oauth_token_scopes",
+    ]
+    for secret_name in shared_secrets:
+        assert _secret_exists(db_path, user_id, secret_name), f"expected {secret_name} to exist"
+
+    gmail_remove_response = await api_post(
+        server,
+        "/api/extensions/gmail/remove",
+        timeout=30,
+    )
+    assert gmail_remove_response.status_code == 200, gmail_remove_response.text
+    assert gmail_remove_response.json().get("success") is True, gmail_remove_response.text
+    for secret_name in shared_secrets:
+        assert _secret_exists(db_path, user_id, secret_name), (
+            f"{secret_name} should remain while google-drive is still installed"
+        )
+
+    drive_remove_response = await api_post(
+        server,
+        "/api/extensions/google-drive/remove",
+        timeout=30,
+    )
+    assert drive_remove_response.status_code == 200, drive_remove_response.text
+    assert drive_remove_response.json().get("success") is True, drive_remove_response.text
+    for secret_name in shared_secrets:
+        assert not _secret_exists(db_path, user_id, secret_name), (
+            f"{secret_name} should be deleted after the last Google tool is removed"
+        )
+
+
+async def test_remove_mcp_server_deletes_stored_secrets(extension_cleanup_server):
+    server = extension_cleanup_server["base_url"]
+    db_path = extension_cleanup_server["db_path"]
+    user_id = extension_cleanup_server["gateway_user_id"]
+    mcp_url = f"{extension_cleanup_server['mock_llm_url']}/mcp"
+
+    await _ensure_removed(server, "mock-mcp")
+
+    await _install_extension(server, "mock-mcp", kind="mcp_server", url=mcp_url)
+
+    setup_response = await api_post(
+        server,
+        "/api/extensions/mock-mcp/setup",
+        json={"secrets": {}},
+        timeout=30,
+    )
+    assert setup_response.status_code == 200, setup_response.text
+    auth_url = setup_response.json().get("auth_url")
+    if auth_url is None:
+        activate_response = await api_post(
+            server,
+            "/api/extensions/mock-mcp/activate",
+            timeout=30,
+        )
+        assert activate_response.status_code == 200, activate_response.text
+        auth_url = activate_response.json().get("auth_url")
+    assert auth_url, "mock-mcp should require OAuth in E2E"
+
+    async with httpx.AsyncClient() as client:
+        callback_response = await client.get(
+            f"{server}/oauth/callback",
+            params={"code": "mock_mcp_code", "state": _extract_state(auth_url)},
+            timeout=30,
+            follow_redirects=True,
+        )
+    assert callback_response.status_code == 200, callback_response.text[:400]
+
+    expected_mcp_secrets = [
+        "mcp_mock-mcp_access_token",
+        "mcp_mock-mcp_client_id",
+    ]
+    stored_secret_names = _secret_names(db_path, user_id)
+    for secret_name in expected_mcp_secrets:
+        assert secret_name in stored_secret_names, (
+            f"expected {secret_name} to exist; stored secrets were {sorted(stored_secret_names)}"
+        )
+
+    remove_response = await api_post(
+        server,
+        "/api/extensions/mock-mcp/remove",
+        timeout=30,
+    )
+    assert remove_response.status_code == 200, remove_response.text
+    assert remove_response.json().get("success") is True, remove_response.text
+    remaining_secret_names = _secret_names(db_path, user_id)
+    assert not any(name.startswith("mcp_mock-mcp_") for name in remaining_secret_names), (
+        f"mock-mcp secrets should be deleted on remove; remaining secrets were "
+        f"{sorted(remaining_secret_names)}"
+    )

tests/e2e_routine_heartbeat.rs

@@ -955,8 +955,7 @@ mod tests {
 
         let hygiene_config = HygieneConfig {
             enabled: false,
-            daily_retention_days: 30,
-            conversation_retention_days: 7,
+            version_keep_count: 50,
             cadence_hours: 24,
             state_dir: _tmp.path().to_path_buf(),
         };
@@ -1002,8 +1001,7 @@ mod tests {
 
         let hygiene_config = HygieneConfig {
             enabled: false,
-            daily_retention_days: 30,
-            conversation_retention_days: 7,
+            version_keep_count: 50,
             cadence_hours: 24,
             state_dir: _tmp.path().to_path_buf(),
         };