Close out spec 003: implemented, #112 and #151 closed with credit - #203
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T025-T027. Both contributed PRs are closed as implemented, each with a comment saying specifically what was taken from it and why the embedding half was not: a query embedded with a different model than built the vectors returns confident nonsense rather than an error, so the model comes from the bundle path and config.yml deliberately cannot name one. Records the two defects writing it found -- pydantic silently ignoring unknown keys, and the same guard being one level too low so a typo in the section name loaded cleanly and did nothing -- and the pattern behind both: the guard was placed on the thing being built rather than on the seam beside it. User Story 3 remains unbuilt on purpose; only chat exists. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
All 27 tasks of spec 003 complete. User Story 3 stays unbuilt -- only chat exists -- but the plan now shows the shape a second surface takes and why one would want to differ: 22.5s per question against 41.2s is a real gap between a search-results panel and a background summarisation. Deliberate this time, rather than discovered later as the context budget was in spec 001. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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All 27 tasks complete. #112 and #151 are closed as implemented, each with a comment saying specifically what was taken from it and why the embedding half was not.
The message both contributors got
A query embedded with a different model than built the stored vectors does not error — it returns confident nonsense. So the embedding model is read from the bundle path, and
config.ymldeliberately cannot name one. @AaryanCode69'sconfig_default.ymlpinnedtext-embedding-3-large; applied to Plant Reactome, which usesbge-m3, that would silently retrieve wrong documents for every question. The same bug we hit from the other direction in July.Credit went where it was due: the nested shape in #201 is @AaryanCode69's, and @bhavyakeerthi3 found the gap and linked it to #108/#148 correctly.
Two defects recorded, and the pattern behind them
embedding_model:insidellm:would have been accepted and silently discarded, arriving through the very door FR-004 was meant to lock.llmm:, still loaded cleanly and did nothing.Both had the same shape: the guard went on the thing being built rather than on the seam beside it. Written down because it will recur.
User Story 3 stays unbuilt
Only chat exists. But the plan now shows what a second surface would add, and why one would want to differ — 22.5s per question against 41.2s is a real gap between a search-results panel and a background summarisation. Deliberate this time, rather than discovered later as the context budget was in spec 001.
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