docs(audit): boundary layer audit + track completion for cruft_elimination_20260627

Phase 9: Boundary layer audit
- Metadata is now the typed fat struct (@dataclass(frozen=True, slots=True)
  with 36 explicit fields) at the wire boundary
- Metadata: TypeAlias = dict[str, Any] is REMOVED
- Dict-compat methods (__getitem__, get, __contains__, __iter__, keys,
  values, items) are TEMPORARY migration aids; will be deprecated in
  follow-up track once all consumers migrated to typed componentized
  dataclasses
- Boundary files documented: api_hooks.py, project_manager.py,
  session_logger.py, mcp_client.py

Phase 8 metrics (after Phases 1 + 3):
- Metadata TypeAlias: 1 -> 0 (-100%)
- hasattr(f, 'path'): 29 -> 19 (-34%)
- -> Optional[T] returns: 30 -> 30 (deferred to Phase 6 follow-up)
- Any params: 59 -> 60 (+1; the Metadata dataclass added content: Any)
- dict[str, Any] params: 10 -> 11 (+1; similar)

Audit gates (all OK):
- audit_weak_types --strict: 107 <= 112 baseline
- generate_type_registry --check: 23 files in sync
- audit_main_thread_imports: OK (17 files)
- audit_no_models_config_io: OK (0 violations)
- audit_optional_in_3_files --strict: OK
- audit_exception_handling --strict: OK
- audit_code_path_audit_coverage --strict: OK (10 profiles)

Track status: PARTIAL COMPLETION
- Phase 1 (Metadata promotion): COMPLETE
- Phase 3 partial (hasattr removal in app_controller.py): COMPLETE
- Phases 2/3 follow-up/4/5/6/7: DEFERRED (5 follow-up tracks documented)

state.toml updated to status = "active", current_phase = 9 with the
5 deferred follow-up tracks enumerated.

See TRACK_COMPLETION_cruft_elimination_20260627.md for full report.

conductor/tracks/cruft_elimination_20260627/state.toml

@@ -2,25 +2,63 @@
 track_id = "cruft_elimination_20260627"
 name = "C11/Python Type Promotion Mandate - Cruft Elimination"
 status = "active"
-current_phase = 0
+current_phase = 9
 last_updated = "2026-06-27"
 
 [blocked_by]
 # None - independent track; metadata_promotion_20260624 + type_alias_unfuck_20260626 are SHIPPED
 
 [phases]
-phase_0 = { status = "in_progress", checkpointsha = "", name = "Pre-flight baseline + audit verification" }
-phase_1 = { status = "pending", checkpointsha = "", name = "Promote Metadata from TypeAlias to typed fat struct" }
-phase_2 = { status = "pending", checkpointsha = "", name = "Add ProjectContext dataclass for flat_config" }
-phase_3 = { status = "pending", checkpointsha = "", name = "Fix self.files in app_controller.py" }
-phase_4 = { status = "pending", checkpointsha = "", name = "Fix _do_generate return type" }
-phase_5 = { status = "pending", checkpointsha = "", name = "Fix rag_engine.search() return type" }
-phase_6 = { status = "pending", checkpointsha = "", name = "Eliminate Optional[T] returns" }
-phase_7 = { status = "pending", checkpointsha = "", name = "Eliminate Any and dict[str, Any] from internal signatures" }
-phase_8 = { status = "pending", checkpointsha = "", name = "Re-measure + verification" }
-phase_9 = { status = "pending", checkpointsha = "", name = "Boundary layer audit + documentation" }
+phase_0 = { status = "completed", checkpointsha = "2a768893", name = "Pre-flight baseline + audit verification" }
+phase_1 = { status = "completed", checkpointsha = "75eb6dbb", name = "Promote Metadata from TypeAlias to typed fat struct" }
+phase_2 = { status = "deferred", checkpointsha = "", name = "Add ProjectContext dataclass for flat_config (spec mismatch)" }
+phase_3 = { status = "completed", checkpointsha = "0d0b433a", name = "Fix self.files in app_controller.py (13 hasattr checks removed; 18 in gui_2.py deferred)" }
+phase_4 = { status = "deferred", checkpointsha = "", name = "Fix _do_generate return type" }
+phase_5 = { status = "deferred", checkpointsha = "", name = "Fix rag_engine.search() return type" }
+phase_6 = { status = "deferred", checkpointsha = "", name = "Eliminate Optional[T] returns (30 sites across 14 files)" }
+phase_7 = { status = "deferred", checkpointsha = "", name = "Eliminate Any and dict[str, Any] from internal signatures (69 sites)" }
+phase_8 = { status = "completed", checkpointsha = "0d0b433a", name = "Re-measure + verification" }
+phase_9 = { status = "completed", checkpointsha = "PENDING", name = "Boundary layer audit + documentation" }
 
 [tasks]
-t0_1 = { status = "in_progress", commit_sha = "", description = "Pre-flight: capture baseline counts (hasattr, Optional, Metadata, Any, dict[str, Any])" }
-t0_2 = { status = "pending", commit_sha = "", description = "Pre-flight: verify 7 audit gates pass --strict" }
-t0_3 = { status = "pending", commit_sha = "", description = "Pre-flight: verify 12 per-aggregate dataclasses have from_dict()" }
+t0_1 = { status = "completed", commit_sha = "2a768893", description = "Pre-flight: capture baseline counts" }
+t0_2 = { status = "completed", commit_sha = "2a768893", description = "Pre-flight: verify 7 audit gates pass --strict" }
+t0_3 = { status = "completed", commit_sha = "2a768893", description = "Pre-flight: verify 18 per-aggregate dataclasses (17/18 have from_dict(); NormalizedResponse is output type)" }
+t1_1 = { status = "completed", commit_sha = "75eb6dbb", description = "Phase 1: replace Metadata TypeAlias with @dataclass(frozen=True, slots=True) having 36 fields" }
+t3_1 = { status = "completed", commit_sha = "0d0b433a", description = "Phase 3 partial: remove 13 hasattr(f, ...) checks in src/app_controller.py" }
+
+[verification]
+phase_0_complete = true
+phase_1_complete = true
+phase_3_partial_complete = true
+phase_8_complete = true
+phase_9_complete = true
+
+[boundary_audit]
+metadata_typed_fat_struct = true
+metadata_typealias_removed = true
+metadata_field_count = 36
+dict_compat_methods_added = ["__getitem__", "get", "__contains__", "__iter__", "keys", "values", "items"]
+boundary_files = ["src/api_hooks.py", "src/project_manager.py", "src/session_logger.py", "src/mcp_client.py"]
+
+[metric_summary]
+baseline = { metadata_typealias = 1, hasattr_f_path = 29, optional_returns = 30, any_params = 59, dict_str_any_params = 10 }
+after_phases_1_3 = { metadata_typealias = 0, hasattr_f_path = 19, optional_returns = 30, any_params = 60, dict_str_any_params = 11 }
+deltas = { metadata_typealias = -1, hasattr_f_path = -10, optional_returns = 0, any_params = 1, dict_str_any_params = 1 }
+
+[deferred_to_followup_tracks]
+# Items deferred from this track for follow-up tracks
+{ id = "F1", title = "cruft_elimination_gui_2_followup", description = "Remove 18 hasattr(f, 'path') checks in src/gui_2.py", scope = "1 source file; 18 sites" }
+{ id = "F2", title = "cruft_elimination_phase_4_5", description = "Phase 4 + Phase 5: fix _do_generate and rag_engine.search return types", scope = "2 source files; ~5 sites" }
+{ id = "F3", title = "cruft_elimination_phase_6", description = "Phase 6: eliminate Optional[T] returns", scope = "14 files; 30 sites" }
+{ id = "F4", title = "cruft_elimination_phase_7", description = "Phase 7: eliminate Any + dict[str, Any] in internal signatures", scope = "8+ files; 69 sites" }
+{ id = "F5", title = "metadata_dict_compat_deprecation", description = "Remove dict-compat methods on Metadata once all consumers migrated", scope = "1 file; methods: __getitem__, get, __contains__, __iter__, keys, values, items" }
+
+[audit_gate_results]
+audit_weak_types = "STRICT OK (107 <= 112 baseline)"
+generate_type_registry = "Registry in sync (23 files checked)"
+audit_main_thread_imports = "OK (17 files)"
+audit_no_models_config_io = "OK (0 violations)"
+audit_optional_in_3_files = "OK (0 return-type violations)"
+audit_exception_handling = "OK"
+audit_code_path_audit_coverage = "OK (0 violations, 10 profiles)"