fix(ci): restore a green build — FastAPI route introspection and two undocumented MCP tools

[lfnothias]

Summary

CI has been red on main for every run since #24. Two independent causes, neither related to the code in those pull requests. This restores a green build: 2399 unit tests pass, 0 fail.

1. test_web_app_routes.py — 28 failures

assert '/api/health' in routes failed with have: ['/', '/docs', '/favicon.ico', '/openapi.json', '/redoc', '/static'].

The application is not broken. GET /api/health returns 200 under TestClient, and app.openapi() lists every expected path. The test's introspection is what broke.

FastAPI 0.139 changed include_router(): instead of copying an included router's routes onto the app, it appends a single _IncludedRouter wrapper exposing the router as original_router. _route_methods_by_path iterated app.routes and saw ten wrappers whose .path is None, so it reported no /api/* routes at all.

Nothing in the repository pins FastAPI, so this arrived with an upstream release rather than with a commit — which is why the failure appears across unrelated pull requests.

The helper now descends through original_router. It is written to work on both layouts, so it will not break again when the wrapper is added or removed:

included_router = getattr(route, "original_router", None)
if included_router is None:
    yield route
else:
    yield from _flatten_routes(included_router.routes)

2. test_usage_guide.py — 1 failure

AssertionError: undocumented tools: ['ensure_kb', 'ground_paper']

fcbfe7ed registered both tools in _TOOL_NAMES without adding them to build_usage_guide(). The drift guard caught exactly what it exists to catch. Both now have purpose, when_to_use, and key_knobs entries, written from their implementations: ensure_kb idempotently creates a per-paper KB from a DOI, and ground_paper answers a question against that KB, with tier="si" preferring supplementary information.

Verification

Against the CI environment (pip install -e ".[dev]", no rdflib/pyoxigraph/indicium) and CI's own exclusion flags:

• Unit suite: 2399 passed, 5 skipped, 18 deselected — previously 29 failed.
• Integration smoke + config: 75 passed, 65 deselected.
• Ruff reports no new findings; the 19 pre-existing findings in usage_guide.py are unchanged.

No production code changes. Issue #29, which breaks uv sync on fresh clones, is addressed separately in #30.