fix: wire auto_install_agent_deps into server.py startup (#216)

* fix: wire auto_install_agent_deps into server.py startup; add api/startup.py to ARCHITECTURE.md

* fix(tests): kill stale process on test port before server start in conftest

Stale servers left by QA harness runs (ports 8792/8793 etc.) or prior
test sessions could interfere with conftest starting its own server on
TEST_PORT (8788). If the port was already occupied, _wait_for_server
hit the wrong server and tests got unexpected 404s/500s, failing
non-deterministically — the 'conftest isolation issue' seen this session.

Fix: run fuser -k on TEST_PORT before launching the new server process,
with a 0.5s sleep for port release. The full suite now runs 571/571
reliably regardless of what other servers were previously active.

---------

Co-authored-by: Nathan Esquenazi <nesquena@gmail.com>

ARCHITECTURE.md

@@ -40,6 +40,7 @@ This makes the code easy to modify from a terminal or by an agent.
       models.py            Session model + CRUD, per-session profile tracking (~137 lines)
       profiles.py          Profile state management, hermes_cli wrapper (~246 lines)
       routes.py            All GET + POST route handlers (~1180 lines)
+      startup.py           Startup helpers: auto_install_agent_deps() (~50 lines)
       streaming.py         SSE engine, run_agent, cancel, HERMES_HOME save/restore (~236 lines)
       upload.py            Multipart parser, file upload handler (~78 lines)
       workspace.py         File ops: list_dir, read_file_content, workspace helpers (~77 lines)

server.py

@@ -12,6 +12,7 @@ from api.auth import check_auth
 from api.config import HOST, PORT, STATE_DIR, SESSION_DIR, DEFAULT_WORKSPACE
 from api.helpers import j
 from api.routes import handle_get, handle_post
+from api.startup import auto_install_agent_deps
 
 
 class Handler(BaseHTTPRequestHandler):
@@ -73,9 +74,18 @@ def main() -> None:
     ok, missing, errors = verify_hermes_imports()
     if not ok and _HERMES_FOUND:
         print(f'[!!] Warning: Hermes agent found but missing modules: {missing}', flush=True)
+        for mod, err in errors.items():
+            print(f'     {mod}: {err}', flush=True)
+        print('     Attempting to install missing dependencies from agent requirements.txt...', flush=True)
+        auto_install_agent_deps()
+        ok, missing, errors = verify_hermes_imports()
+        if not ok:
+            print(f'[!!] Still missing after install attempt: {missing}', flush=True)
             for mod, err in errors.items():
                 print(f'     {mod}: {err}', flush=True)
             print('     Agent features may not work correctly.', flush=True)
+        else:
+            print('[ok] Agent dependencies installed successfully.', flush=True)
 
     STATE_DIR.mkdir(parents=True, exist_ok=True)
     SESSION_DIR.mkdir(parents=True, exist_ok=True)

tests/conftest.py

@@ -210,6 +210,18 @@ def test_server():
     Start an isolated test server on TEST_PORT with a clean state directory.
     Paths are discovered dynamically -- no hardcoded absolute path assumptions.
     """
+    # Kill any leftover process on the test port before starting.
+    # Stale servers from QA harness runs or prior test sessions cause
+    # conftest to think the server is already up, producing false failures.
+    try:
+        import subprocess as _sp
+        _sp.run(['fuser', '-k', f'{TEST_PORT}/tcp'],
+                capture_output=True, timeout=5)
+    except Exception:
+        pass
+    import time as _time
+    _time.sleep(0.5)  # brief pause to let the port release
+
     # Clean slate
     if TEST_STATE_DIR.exists():
         shutil.rmtree(TEST_STATE_DIR)