docs: mark SPEC_03/04/05 as IMPLEMENTED with acceptance criteria

All 5 specs now accurately reflect implementation status:
- SPEC_01: Demo Termination ✓
- SPEC_02: E2E Testing ✓
- SPEC_03: OpenAlex Integration ✓
- SPEC_04: Magentic UX (P0-P1 complete, P2 future)
- SPEC_05: Orchestrator Cleanup ✓

154 unit tests pass.

docs/specs/SPEC_03_OPENALEX_INTEGRATION.md

@@ -512,7 +512,7 @@ class TestOpenAlexIntegration:
 - [x] All unit tests pass (11 tests)
 - [x] Integration test passes with real API
 
-**Status: IMPLEMENTED** (commits fd28242, TBD)
+**Status: IMPLEMENTED** (commits fd28242, cb46aac)
 
 ## Files Modified
 

docs/specs/SPEC_04_MAGENTIC_UX.md

@@ -181,11 +181,13 @@ if time_remaining < self._timeout_seconds * 0.2:
 
 ## Acceptance Criteria
 
-- [ ] Timeout shows ALL progress events, not just timeout message
-- [ ] Default timeout increased to 600s (10 minutes)
-- [ ] Timeout configurable via `MAGENTIC_TIMEOUT` env var
-- [ ] Tests verify chat history preserved on timeout
-- [ ] (P2) System synthesizes early when timeout approaches
+- [x] Timeout shows ALL progress events, not just timeout message
+- [x] Default timeout increased to 600s (10 minutes)
+- [x] Timeout configurable via `MAGENTIC_TIMEOUT` env var
+- [x] Tests verify chat history preserved on timeout
+- [ ] (P2) System synthesizes early when timeout approaches (Future)
+
+**Status: IMPLEMENTED** (commit cb46aac)
 
 ## Files to Modify
 

docs/specs/SPEC_05_ORCHESTRATOR_CLEANUP.md

@@ -121,10 +121,12 @@ make check  # All 142 tests should pass
 
 ## Acceptance Criteria
 
-- [ ] Empty `src/orchestrator/` folder deleted
-- [ ] No broken imports (grep for `from src.orchestrator/`)
-- [ ] Tests pass
-- [ ] (Optional) `orchestrator_hierarchical.py` removed or deprecated
+- [x] Empty `src/orchestrator/` folder deleted
+- [x] No broken imports (grep for `from src.orchestrator/`)
+- [x] Tests pass (154 unit tests)
+- [x] `orchestrator_hierarchical.py` removed
+
+**Status: IMPLEMENTED** (commit cb46aac)
 
 ## Files to Modify