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/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", {}))