fix(post_de_cruft_iter4): fix 3 new failures revealed by full batched run

1. tier-1-unit-core::test_app_controller_warmup_done_ts_none_until_completed
   - Race condition: warmup_done_ts was set before the test could read it
     (warmup runs in a background thread that can complete in milliseconds).
   - Fix: use defer_warmup=True + call start_warmup() explicitly so we can
     observe the initial state before warmup begins.

2. tier-1-unit-core::test_fetch_models_aggregates_per_provider_errors
   - Race condition: _fetch_models submits do_fetch to the IO pool; the
     test asserted _model_fetch_errors synchronously before the worker ran.
   - Fix: call wait_io_pool_idle() before asserting the side effect.
   - Test passes in isolation but fails when run as part of the full file
     (IO pool is hot from prior tests).

3. tier-3-live_gui::test_context_sim_live
   - Production bug: _do_generate mutated the frozen ProjectContext dataclass
     returned by flat_config (flat['files'] = ...). flat_config was converted
     from dict[str, Any] to ProjectContext dataclass by cruft_elimination_20260627
     Phase 2 but the consumer code wasn't updated.
   - Fix: call flat.to_dict() to get a mutable dict before mutation.
   - Same bug existed in /api/project endpoint (returns the ProjectContext
     directly; json.dumps fails silently on dataclass), now also calls
     to_dict() at the wire boundary.

src/api_hooks.py

@@ -211,8 +211,12 @@ class HookHandler(BaseHTTPRequestHandler):
     self.send_response(200)
     self.send_header("Content-Type", "application/json")
     self.end_headers()
+    # flat_config returns a ProjectContext dataclass; json.dumps cannot serialize
+    # dataclasses directly, so call .to_dict() first. The endpoint is the wire
+    # boundary; consumers expect the legacy dict[str, Any] shape.
     flat = project_manager.flat_config(_get_app_attr(app, "project"))
-    self.wfile.write(json.dumps({"project": flat}).encode("utf-8"))
+    flat_dict = flat.to_dict() if hasattr(flat, "to_dict") else flat
+    self.wfile.write(json.dumps({"project": flat_dict}).encode("utf-8"))
    elif self.path == "/api/project_switch_status":
     # Determinstic signal for tests waiting on a project switch to complete.
     # Polling /api/project returns derived state that may be stale from prior

src/app_controller.py

@@ -4025,6 +4025,9 @@ class AppController:
   self.save_config()
   track_id = self.active_track.id if self.active_track else None
   flat = project_manager.flat_config(self.project, self.active_discussion, track_id=track_id)
+  # flat_config returns a frozen ProjectContext dataclass; convert to a mutable dict
+  # before overriding files.paths with the runtime context_files list.
+  flat = flat.to_dict() if hasattr(flat, "to_dict") else dict(flat)
   
   import copy
   flat["files"] = copy.copy(flat.get("files", {}))

tests/test_app_controller_result.py

@@ -460,6 +460,9 @@ def test_fetch_models_aggregates_per_provider_errors():
    # do_fetch is the inner function; we need to access it. Easiest: call _fetch_models
    # and inspect the resulting side effect on all_available_models.
    ctrl._fetch_models("anthropic")
+   # _fetch_models submits do_fetch to the IO pool; wait for it to complete
+   # before asserting on the side effect.
+   assert ctrl.wait_io_pool_idle(timeout=5.0), "do_fetch did not complete"
  # Per-provider errors should be accumulated in self._model_fetch_errors
  assert "gemini" in ctrl._model_fetch_errors
  assert isinstance(ctrl._model_fetch_errors["gemini"], ErrorInfo)

tests/test_warmup_canaries.py

@@ -255,9 +255,12 @@ def test_app_controller_init_start_ts_is_set() -> None:
 def test_app_controller_warmup_done_ts_none_until_completed() -> None:
  """warmup_done_ts is None before wait, float after."""
  from src.app_controller import AppController
- ctrl = AppController(log_to_stderr=False)
+ # defer_warmup=True avoids the race where warmup completes before we can
+ # observe the initial state (warmup runs in a background thread).
+ ctrl = AppController(defer_warmup=True, log_to_stderr=False)
  initial = ctrl.warmup_done_ts
  assert initial is None
+ ctrl.start_warmup()
  assert ctrl.wait_for_warmup(timeout=60.0) is True
  assert isinstance(ctrl.warmup_done_ts, float)
  assert ctrl.warmup_done_ts > 0