Stage 3: the caller supplies the bundle and the context budget

[adamjohnwright]

Closes out the retriever rewrite (spec FR-005, FR-006, SC-006). Two module-level facts become arguments.

The bundle

Each create_*_rag had

embeddings_directory: Path = EmbeddingEnvironment.get_dir("reactome"),  # noqa: B008

A default argument is evaluated at import time, so importing a rag module required an installed bundle — which is why these were untestable. And get_dir returns Path | None, so None flowed into a parameter typed Path; four mypy baseline entries existed only to suppress that. All five suppressions are deleted, not re-annotated.

EmbeddingEnvironment.require_dir replaces the lookup at the three call sites that cannot run without a bundle. It also checks the directory exists — which is not tidiness:

get_dir builds a path without touching the disk, and Chroma creates a missing persist_directory rather than complaining. An embeddings/current left pointing at a deleted bundle gave a chatbot that answered every question from an empty collection, confidently, with no error anywhere.

Measured against main:

	missing-bundle failure
before	AttributeError: 'NoneType' object has no attribute 'glob'
after	No embeddings bundle installed for 'uniprot' (installed: reactome). Run ./bin/embeddings_manager install <embedding-id>.

The userguide bundle is deliberately optional; react_to_me.py already resolved it itself and degraded on absence. That path keeps get_dir, and require_dir raises FileNotFoundError specifically so the existing except FileNotFoundError there still means what it meant.

The budget

MAX_DOCUMENTS_PER_COLLECTION becomes DEFAULT_MAX_DOCUMENTS_PER_COLLECTION, the default of a constructor argument. As a module constant, comparing two budgets meant editing the file and restarting — so the answer-quality evaluation meant to settle the number could not be run.

Verification

Against the Release95 reactome bundle:

• the assembled chain answers "What role does TP53 play in apoptosis?" identically through invoke and ainvoke, 40 documents each (constitution Article I)
• budget=3 over 4 collections → 12 documents; budget=10 → 40
• all three profiles construct or refuse correctly: ReactToMe builds, CrossDatabase and PlantReactome refuse with the message above

Each new test was checked to be non-vacuous by perturbing the thing it pins — ignoring the budget argument, reinstating a default, and removing the is_dir check each make exactly the relevant test fail.