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)