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>

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)