Give each Chroma store its own Settings; a shared one crossed the bundles

[adamjohnwright]

Reactome questions are broken on beta right now. This fixes a live outage.

Asked "What does CDK5 phosphorylate in Alzheimer disease?", the deployed container raises:

PermissionError: [Errno 13] Permission denied:
'/app/embeddings/.../userguide/Release95/sections/9c574827-...'

A reactome question failing inside the user guide bundle — Chroma trying to create a segment folder for a collection that isn't there, in a bundle it should never have opened.

Cause

chroma_settings was one module-level Settings object shared by every store. langchain_chroma mutates what it is handed:

client_settings.persist_directory = (
    persist_directory or client_settings.persist_directory
)

So the last store constructed rewrote the persist directory for every earlier one, and chromadb returned a client keyed on those settings.

With only the reactome bundle installed this was invisible — every store pointed into the same tree, so crossing them changed nothing. Installing the user guide bundle yesterday gave them different trees and turned a latent bug into an outage.

chroma_settings() is now a factory returning a fresh object per store.

Verified in the order that broke beta

User guide first, then reactome, then user guide again:

userguide hits: 6
reactome hits : 40
and again, user guide after reactome: 6

Three tests, all of which fail against the shared constant — including one asserting telemetry stays off, so that isn't lost while fixing the sharing.

I saw this yesterday and dismissed it

The same PermissionError appeared while I was reviewing #216. I wrote it off as "a local artifact of the root-owned bundle" after a check that built the two retrievers and queried each once. That check didn't reproduce the ordering, so it proved nothing — and I reported the system healthy. The bug was in production for a day.

The check that found it was running the three real question types through the deployed container, which is the one I should have run first.

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