refactor: architecture improvements for contributor velocity (#198)

* refactor: split large files and consolidate test stubs for contributor velocity

- Extract 7 Database sub-traits (ConversationStore, JobStore, SandboxStore,
  RoutineStore, ToolFailureStore, SettingsStore, WorkspaceStore) with Database
  as a supertrait combining them all
- Split libsql_backend.rs (2769 lines) into src/db/libsql/ directory with
  one file per sub-trait implementation
- Split config.rs (1753 lines) into src/config/ directory with 16 domain files
- Consolidate 3 duplicate test LLM stubs into shared StubLlm in src/testing.rs
- Split server.rs handlers into src/channels/web/handlers/ directory
- Extract main.rs init phases into AppBuilder (src/app.rs)
- Add developer setup script (scripts/dev-setup.sh)

Co-Authored-By: Claude Opus 4.6 <[email protected]>

* refactor: move heartbeat test from examples/ to tests/

Convert standalone example binary into a proper #[ignore] integration
test, matching the convention of the other integration tests.

Co-Authored-By: Claude Opus 4.6 <[email protected]>

* style: fix rustfmt formatting for CI

Co-Authored-By: Claude Opus 4.6 <[email protected]>

* fix: address PR review comments from Copilot

- tunnel.rs: replace .ok().flatten() with ? to propagate env var errors
- secrets.rs: remove misleading "process-wide cache" comment
- database.rs: use uppercase "DATABASE_URL" in error key
- testing.rs: gate harness tests with #[cfg(feature = "libsql")]

Co-Authored-By: Claude Opus 4.6 <[email protected]>

---------

Co-authored-by: Illia Polosukhin <[email protected]>
Co-authored-by: Claude Opus 4.6 <[email protected]>

tests/heartbeat_integration.rs

@@ -0,0 +1,124 @@
+#![cfg(feature = "postgres")]
+//! Heartbeat integration test.
+//!
+//! Exercises the heartbeat system in isolation: connects to the real
+//! database, reads the real HEARTBEAT.md, calls the real LLM, and prints
+//! every step so you can see exactly where it breaks.
+//!
+//! Usage:
+//!   cargo test --test heartbeat_integration -- --ignored --nocapture
+
+use std::sync::Arc;
+
+use ironclaw::{
+    agent::HeartbeatRunner,
+    config::Config,
+    history::Store,
+    llm::{SessionConfig, create_llm_provider, create_session_manager},
+    workspace::Workspace,
+};
+
+#[tokio::test]
+#[ignore] // Requires running database and LLM credentials
+async fn test_heartbeat_end_to_end() {
+    // Load .env and set up logging
+    let _ = dotenvy::dotenv();
+    let _ = tracing_subscriber::fmt()
+        .with_env_filter("ironclaw=debug")
+        .try_init();
+
+    println!("=== Heartbeat Integration Test ===\n");
+
+    // 1. Load config
+    let config = Config::from_env().await.expect("Failed to load config");
+    println!("[1/6] Config loaded");
+    println!("  heartbeat.enabled = {}", config.heartbeat.enabled);
+    println!(
+        "  heartbeat.interval_secs = {}",
+        config.heartbeat.interval_secs
+    );
+    println!(
+        "  heartbeat.notify_channel = {:?}",
+        config.heartbeat.notify_channel
+    );
+    println!(
+        "  heartbeat.notify_user = {:?}",
+        config.heartbeat.notify_user
+    );
+
+    // 2. Connect to database
+    let store = Store::new(&config.database)
+        .await
+        .expect("Failed to connect to database");
+    store
+        .run_migrations()
+        .await
+        .expect("Failed to run migrations");
+    println!("[2/6] Database connected");
+
+    // 3. Create workspace
+    let workspace = Arc::new(Workspace::new("default", store.pool()));
+    println!("[3/6] Workspace created");
+
+    // 4. Read HEARTBEAT.md
+    let checklist = workspace.heartbeat_checklist().await;
+    match &checklist {
+        Ok(Some(content)) => {
+            let preview: String = content.chars().take(200).collect();
+            println!("[4/6] HEARTBEAT.md found ({} chars)", content.len());
+            println!("  Preview: {}...", preview);
+        }
+        Ok(None) => {
+            println!("[4/6] HEARTBEAT.md is None (no file, no seed fallback)");
+            println!("  Heartbeat will return Skipped.");
+        }
+        Err(e) => {
+            println!("[4/6] HEARTBEAT.md read error: {}", e);
+        }
+    }
+
+    // Check if the checklist would be considered "effectively empty"
+    if let Ok(Some(_)) = checklist {
+        println!("  (Will verify via runner below)");
+    }
+
+    // 5. Create LLM provider
+    let session = create_session_manager(SessionConfig {
+        auth_base_url: config.llm.nearai.auth_base_url.clone(),
+        session_path: config.llm.nearai.session_path.clone(),
+    })
+    .await;
+    let llm = create_llm_provider(&config.llm, session).expect("Failed to create LLM provider");
+    println!("[5/6] LLM provider created (model: {})", llm.model_name());
+
+    // 6. Run heartbeat check
+    println!("[6/6] Running check_heartbeat()...\n");
+
+    let hb_config = ironclaw::agent::HeartbeatConfig::default();
+    let runner = HeartbeatRunner::new(hb_config, workspace, llm);
+
+    let result = runner.check_heartbeat().await;
+
+    println!("=== Result ===\n");
+    match &result {
+        ironclaw::agent::HeartbeatResult::Ok => {
+            println!("HeartbeatResult::Ok");
+            println!("  LLM responded HEARTBEAT_OK, nothing needs attention.");
+        }
+        ironclaw::agent::HeartbeatResult::NeedsAttention(msg) => {
+            println!("HeartbeatResult::NeedsAttention");
+            println!("  Message:\n{}", msg);
+        }
+        ironclaw::agent::HeartbeatResult::Skipped => {
+            println!("HeartbeatResult::Skipped");
+            println!("  No checklist found, or checklist was effectively empty.");
+            println!("  This means the HEARTBEAT.md either:");
+            println!("    - Does not exist in the workspace database");
+            println!("    - Contains only headers, comments, and empty checkboxes");
+        }
+        ironclaw::agent::HeartbeatResult::Failed(err) => {
+            println!("HeartbeatResult::Failed");
+            println!("  Error: {}", err);
+        }
+    }
+}