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/db/libsql/mod.rs

@@ -320,10 +320,10 @@ pub(crate) fn row_to_routine_libsql(row: &libsql::Row) -> Result<Routine, Databa
     let max_concurrent = get_i64(row, 10);
     let dedup_window_secs: Option<i64> = row.get::<i64>(11).ok();
 
-    let trigger =
-        Trigger::from_db(&trigger_type, trigger_config).map_err(DatabaseError::Serialization)?;
+    let trigger = Trigger::from_db(&trigger_type, trigger_config)
+        .map_err(|e| DatabaseError::Serialization(e.to_string()))?;
     let action = RoutineAction::from_db(&action_type, action_config)
-        .map_err(DatabaseError::Serialization)?;
+        .map_err(|e| DatabaseError::Serialization(e.to_string()))?;
 
     Ok(Routine {
         id: get_text(row, 0).parse().unwrap_or_default(),
@@ -359,7 +359,7 @@ pub(crate) fn row_to_routine_run_libsql(row: &libsql::Row) -> Result<RoutineRun,
     let status_str = get_text(row, 5);
     let status: RunStatus = status_str
         .parse()
-        .map_err(|e: String| DatabaseError::Serialization(e))?;
+        .map_err(|e: crate::error::RoutineError| DatabaseError::Serialization(e.to_string()))?;
 
     Ok(RoutineRun {
         id: get_text(row, 0).parse().unwrap_or_default(),