Let the last two bin/ scripts run without PYTHONPATH, like the others

[adamjohnwright]

Four of the six bin/ scripts bootstrap their own sys.path and run from anywhere. embeddings_manager and retrieval_baseline did not:

$ ./bin/embeddings_manager ls
ModuleNotFoundError: No module named 'data_generation'

The Dockerfile and CI both set PYTHONPATH (/app/src, ./bin:./src), so these worked there and nowhere else — including in their own documented usage. Same defect fixed for evaluate and probe_model_temperature in cbe20fc; these two were missed.

The cost of leaving it wasn't hypothetical

On 2026-09-14 I hit exactly this on embeddings_manager, worked around it with a PYTHONPATH=src prefix rather than fixing it, and then — because the tool felt awkward — bypassed it entirely and called generate_userguide_embeddings directly.

That skipped the use() call which registers a bundle. So 16 MB of correctly-generated user guide sat on disk, invisible to the app, and it took a wasted deploy and a round trip with Adam to notice.

A tool that doesn't run as documented gets worked around, and the workaround is where the bug was.

After

  answer-sweep               works
  embeddings_manager         works
  evaluate                   works
  mcp-probe                  works
  probe_model_temperature    works
  retrieval_baseline         works

$ .venv/bin/python bin/embeddings_manager ls        # no PYTHONPATH
  * openai/text-embedding-3-large/reactome/Release95
  * openai/text-embedding-3-large/userguide/Release95

ruff, mypy clean; full suite passes.

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