fix: persist turns after approval and add agent-level tests (#250)

* fix: persist turns after approval and add agent-level tests

Port relevant changes from PR #112 that were not carried over to #237:

- Add persist_turn calls in process_approval for the response, error,
  and auth-required paths. Previously, turns completed after tool
  approval were never persisted to DB — if the process crashed after
  approval the entire turn (user message + assistant response) was lost.

- Add agent-level unit tests: StaticLlmProvider mock, make_test_agent
  helper, tests for auto-approval logic, destructive shell command
  detection, and PendingApproval backward-compatible deserialization
  (without deferred_tool_calls field).

- Remove unused _thread_state binding in process_approval.

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

* fix: address 14 audit findings in src/agent/

Audit of the agent module found 2 High, 7 Medium, 3 Low, and 2 Nit
severity issues. This commit fixes all of them:

High:
- Remove 4 `.expect()` calls in session.rs (entry API, match, direct
  indexing, if-let) to eliminate panic paths in production
- Add typed RoutineError enum replacing Result<_, String> across
  routine.rs, routine_engine.rs, and callers in history/store.rs and
  db/libsql/mod.rs

Medium:
- Sanitize routine names in path construction to prevent directory
  traversal (routine_engine.rs)
- Log warnings for 5 silently-swallowed errors in scheduler.rs,
  compaction.rs, and worker.rs
- Extract shared handle_auth_intercept helper to deduplicate auth
  interception in thread_ops.rs
- Add session count warning threshold in session_manager.rs
- Make FullJob stub degradation visible via warn-level log and
  prepended warning in output

Low:
- Restrict dead code visibility with #[cfg(test)] on 19 unused items
  in submission.rs, task.rs, and undo.rs
- Narrow pub to pub(crate) on self_repair.rs builder methods
- Remove TaskStatus from mod.rs re-exports (test-only type)

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

* fix: address PR review comments

- Reorder persist_turn before persist_response_chain so the
  conversation row exists before the metadata UPDATE runs
- Add persist_response_chain call to handle_auth_intercept so
  auth-required paths preserve the response chain
- Harden sanitize_routine_name to use allowlist (alphanumeric,
  dash, underscore) instead of denylist replacements
- Fix stale active_thread ID in get_or_create_thread: fall back
  to create_thread() when the stored ID is missing from the map
- Persist turn on approval rejection so user messages survive
  crashes after a tool is rejected

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

---------

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

src/agent/task.rs

@@ -29,6 +29,7 @@ impl TaskOutput {
     }
 
     /// Create a text result.
+    #[cfg(test)]
     pub fn text(text: impl Into<String>, duration: Duration) -> Self {
         Self {
             result: serde_json::Value::String(text.into()),
@@ -37,6 +38,7 @@ impl TaskOutput {
     }
 
     /// Create an empty success result.
+    #[cfg(test)]
     pub fn empty(duration: Duration) -> Self {
         Self {
             result: serde_json::Value::Null,
@@ -130,6 +132,7 @@ impl Task {
     }
 
     /// Create a new Job task with a specific ID.
+    #[cfg(test)]
     pub fn job_with_id(id: Uuid, title: impl Into<String>, description: impl Into<String>) -> Self {
         Self::Job {
             id,
@@ -152,6 +155,7 @@ impl Task {
     }
 
     /// Create a new Background task.
+    #[cfg(test)]
     pub fn background(handler: std::sync::Arc<dyn TaskHandler>) -> Self {
         Self::Background {
             id: Uuid::new_v4(),
@@ -160,6 +164,7 @@ impl Task {
     }
 
     /// Create a new Background task with a specific ID.
+    #[cfg(test)]
     pub fn background_with_id(id: Uuid, handler: std::sync::Arc<dyn TaskHandler>) -> Self {
         Self::Background { id, handler }
     }
@@ -174,6 +179,7 @@ impl Task {
     }
 
     /// Get the parent ID for sub-tasks.
+    #[cfg(test)]
     pub fn parent_id(&self) -> Option<Uuid> {
         match self {
             Self::Job { .. } => None,
@@ -225,6 +231,7 @@ impl fmt::Debug for Task {
 }
 
 /// Status of a scheduled task.
+#[cfg(test)]
 #[derive(Debug, Clone, Copy, PartialEq, Eq)]
 pub enum TaskStatus {
     /// Task is queued waiting for execution.