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/app.rs

@@ -56,6 +56,7 @@ pub struct AppComponents {
     pub session: Arc<SessionManager>,
     pub catalog_entries: Vec<crate::extensions::RegistryEntry>,
     pub dev_loaded_tool_names: Vec<String>,
+    pub builder: Option<Arc<dyn crate::tools::SoftwareBuilder>>,
 }
 
 /// Options that control optional init phases.
@@ -280,6 +281,7 @@ impl AppBuilder {
             Arc<ToolRegistry>,
             Option<Arc<dyn EmbeddingProvider>>,
             Option<Arc<Workspace>>,
+            Option<Arc<dyn crate::tools::SoftwareBuilder>>,
         ),
         anyhow::Error,
     > {
@@ -367,16 +369,19 @@ impl AppBuilder {
         }
 
         // Register builder tool if enabled
-        if self.config.builder.enabled
+        let builder = if self.config.builder.enabled
             && (self.config.agent.allow_local_tools || !self.config.sandbox.enabled)
         {
-            tools
+            let b = tools
                 .register_builder_tool(llm.clone(), Some(self.config.builder.to_builder_config()))
                 .await;
-            tracing::debug!("Builder mode enabled");
-        }
+            tracing::info!("Builder mode enabled");
+            Some(b)
+        } else {
+            None
+        };
 
-        Ok((safety, tools, embeddings, workspace))
+        Ok((safety, tools, embeddings, workspace, builder))
     }
 
     /// Phase 5: Load WASM tools, MCP servers, and create extension manager.
@@ -699,7 +704,7 @@ impl AppBuilder {
         } else {
             self.init_llm().await?
         };
-        let (safety, tools, embeddings, workspace) = self.init_tools(&llm).await?;
+        let (safety, tools, embeddings, workspace, builder) = self.init_tools(&llm).await?;
 
         // Create hook registry early so runtime extension activation can register hooks.
         let hooks = Arc::new(HookRegistry::new());
@@ -819,6 +824,7 @@ impl AppBuilder {
             session: self.session,
             catalog_entries,
             dev_loaded_tool_names,
+            builder,
         })
     }
 }