feat(self-repair): wire stuck_threshold, store, and builder (#712)

* feat(self-repair): wire stuck_threshold, store, and builder (#647)

Wire the previously dead-code fields in DefaultSelfRepair:

- stuck_threshold: detect_stuck_jobs() now filters by duration, only
  reporting jobs stuck longer than the configured threshold
- with_store(): wired in agent_loop.rs from AgentDeps.store for
  tool failure tracking via Database trait
- with_builder(): wired from register_builder_tool() return value
  through AppComponents and AgentDeps for automatic tool rebuilding
- tools: passed alongside builder for hot-reload logging

Remove all #[allow(dead_code)] annotations. Add regression tests for
threshold-based filtering (both above and below threshold).

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

* fix: add missing `builder` field to AgentDeps in gateway workflow harness

After rebase onto staging, AgentDeps gained a `builder` field for
self-repair tool rebuilding. The gateway workflow test harness was
missing this field, causing CI compilation failure.

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

* ci: retrigger CI

* fix: force CI refresh after path_routing_tests dedup

* test: add E2E test for stuck job repair and tool rebuild cycle

Tests the full self-repair flow requested in review:
1. Job transitions Pending -> InProgress -> Stuck
2. detect_stuck_jobs() finds it (zero threshold)
3. repair_stuck_job() recovers it back to InProgress
4. A broken tool is repaired via MockBuilder
5. Verify builder was invoked and repair succeeded

Uses a MockBuilder (impl SoftwareBuilder) that returns successful
BuildResult without requiring an LLM or filesystem. Uses libsql
test database for the store (increment_repair_attempts, mark_tool_repaired).

Co-Authored-By: Claude Opus 4.6 (1M context) <[email protected]>

* fix(self-repair): measure stuck_duration from Stuck transition, not started_at

- Use ctx.transitions to find the most recent Stuck transition timestamp
  instead of ctx.started_at (which reflects job start, not stuck time)
- Fix StuckJob.last_activity to use stuck transition timestamp
- Remove misleading "hot-reloaded into registry" log
- Remove stray "// ci fix" comment in memory.rs
- Add regression test: backdated started_at must not inflate stuck_duration

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

* ci: re-trigger CI with latest changes

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

* fix: add type annotation to Ok(()) in test to resolve E0282

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

---------

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

src/agent/agent_loop.rs

@@ -146,6 +146,8 @@ pub struct AgentDeps {
     pub transcription: Option<Arc<crate::transcription::TranscriptionMiddleware>>,
     /// Document text extraction middleware for PDF, DOCX, PPTX, etc.
     pub document_extraction: Option<Arc<crate::document_extraction::DocumentExtractionMiddleware>>,
+    /// Software builder for self-repair tool rebuilding.
+    pub builder: Option<Arc<dyn crate::tools::SoftwareBuilder>>,
 }
 
 /// The main agent that coordinates all components.
@@ -340,11 +342,18 @@ impl Agent {
         let mut message_stream = self.channels.start_all().await?;
 
         // Start self-repair task with notification forwarding
-        let repair = Arc::new(DefaultSelfRepair::new(
+        let mut self_repair = DefaultSelfRepair::new(
             self.context_manager.clone(),
             self.config.stuck_threshold,
             self.config.max_repair_attempts,
-        ));
+        );
+        if let Some(ref store) = self.deps.store {
+            self_repair = self_repair.with_store(Arc::clone(store));
+        }
+        if let Some(ref builder) = self.deps.builder {
+            self_repair = self_repair.with_builder(Arc::clone(builder), Arc::clone(self.tools()));
+        }
+        let repair = Arc::new(self_repair);
         let repair_interval = self.config.repair_check_interval;
         let repair_channels = self.channels.clone();
         let repair_owner_id = self.owner_id().to_string();