chore: drop dead ignore rules and fold architecture notes into README - #24
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Removes rules with no producer and no reference anywhere in the tree: graphify-out/ (plus the tracked .graphifyignore, whose three patterns match nothing), **/z_plans, and data/mcp-data-pre-merge/. Also drops **/mlruns.db, which the later *.db rule already shadows at any depth. Adds mlruns/, which is a real gap rather than a stylistic one: hook.py points mlflow's --default-artifact-root at that directory, so the first server start would have left untracked artifacts in the tree. Keeps data/clean/ and data/stix_bundle.json. The first looks dead to a literal grep but is live, cti_pipeline_stage1.py composes the path from a constant. The second has no producer left but guards against re-adding the 46 MB bundle untracked in 5c99bc0.
architecture.md was an unstructured brain dump rather than documentation. Its content now lives in a README Architecture section covering the DSPy/ReAct reasoning stack, the three supporting layers (MCP servers, RAG, MLflow), and how per-plugin server discovery works. PLUGIN_MCP.md loses the range integration test pointer in section 9.1 and the section 12 canonical-extension block. Section numbering stays contiguous at 1 through 11.
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Description
Housekeeping only — no code, no config, no behaviour change. Split out of
chores/artifactsso the cleanup can land independently of theapi_baserefactor on that branch, which is breaking and needs its own review.Three commits:
chore(gitignore)— drop rules matching nothing in the tree (**/z_plans,graphify-out/,data/mcp-data-pre-merge/), delete the now-unused.graphifyignore, and ignore the MLflow artifact rootmlruns/thathook.pycreates next to itself at boot.docs— foldarchitecture.mdinto a proper Architecture section inREADME.md(reasoning stack, plugin discovery) and drop the twoplugins/range/references fromPLUGIN_MCP.mdthat pointed at a plugin no longer vendored here.chores— remove two.gitignorecomments.Diff is 5 files:
.gitignore,.graphifyignore,PLUGIN_MCP.md,README.md,architecture.md. Zero.pyfiles touched.Type of change
How Has This Been Tested?
No code changed, so behaviour is unchanged by construction — but the removals were verified rather than assumed:
z_plans,graphify-out/,data/mcp-data-pre-merge/do not exist in the tree, andgit status --porcelain -uallis empty on this branch — no file becomes newly trackable.mlruns.dbis still ignored. It is covered by the existing*.dbrule; confirmed withgit check-ignore -v mlruns.db→.gitignore:39:*.db. The newmlruns/rule covers the artifact directory alongside it..graphifyignoreis safe to delete.grep -rIl graphifyover the tree returns nothing — no tooling reads it.architecture.mdfold preserves the content, and the new README claims about discovery / RAG / MLflow were checked against the code that implements them.pytest plugins/mcp/tests/test_llm_client.py plugins/mcp/tests/test_model_config.py→28 passed, 13 skipped(the 13 skips are the pre-existingMCP not enabledgate that needs a live CALDERA onlocalhost:8888).Pre-existing and not addressed here:
tests/test_relation_extractor.pyimportscti_relation_extractor, which does not exist (the module iscti_relationships.py), so a fullpytest plugins/mcp/tests/aborts during collection. Present onmaintoo; worth a separate fix.Checklist: