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>

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):
@@ -75,7 +76,16 @@ def main() -> None:
         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('     Agent features may not work correctly.', 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)