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]>

tests/support/gateway_workflow_harness.rs

@@ -257,6 +257,7 @@ impl GatewayWorkflowHarness {
                 http_interceptor: None,
                 transcription: None,
                 document_extraction: None,
+                builder: None,
             },
             channels,
             None,

tests/support/test_rig.rs

@@ -642,6 +642,7 @@ impl TestRigBuilder {
             },
             transcription: None,
             document_extraction: None,
+            builder: None,
         };
 
         // 7. Create TestChannel and ChannelManager.