[gouyt13]

Summary

Reduce the repository root from 22 entries to 20 so the GitHub README appears sooner. Move CONTRIBUTING.md into .github/ and relocate the two standalone clustering helpers from python/ to sample/python/clustering_cli/.

Update contribution links, lint paths, the existing example regression, and CI path-classification tests. The helper contents are unchanged; direct callers must use the documented new path. Public APIs, package layout, CMake targets and persistence formats remain unchanged. Agent workflow templates and task records are excluded.

Testing

• 40 Python example tests and 12 CI classification tests passed.
• Both clustering modes produced byte-identical centroid and assignment files before/after relocation on deterministic 128x64 input, 64 clusters, one pinned CPU; --help output also matched.
• Python lint/format, focused Ruff, ShellCheck, strict MkDocs build and diff checks passed.
• Independent review checked documentation, commands, CI descriptions and 86 local links/anchors; no blocking project-documentation findings remain.
• Confirmed the resulting Git tree contains 20 top-level entries.

An initial 4-centroid QG trial was rejected by the unchanged original script because the centroid count must exceed graph degree; the valid 64-centroid trial passed. Live GitHub layout and contribution-entry checks remain pending publication. MkDocs emitted the existing Material advisory about MkDocs 2.0.