fix: deep audit phase D — canonical org URLs, cross-harness code gate, tooling parity#39
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…rcement, tooling parity Phase D of the deep audit (#35). The stale-org sweep: 40 URLs across skills, wiki/core stack pages, README and llms-adjacent docs still pointed at github.com/Jammy2211|rhayes777 for repos that live in the PyAutoLabs org per the sources.yaml/repos.yaml body map — all rewritten (PyAutoLogo untouched; it has not moved). Worst instance: al_setup_environment's editable-clone recipe cloned five repos from the old owners while instructing 'resolve URLs from sources.yaml'; the recipe now matches the registry and notes the redirect. AGENTS.md: the code gate was described as ambient, but the PreToolUse hook only exists on hook-capable harnesses (Claude Code) — Codex/ Gemini/OpenCode/Copilot sessions got no enforcement and no instruction. The invariant now tells non-hook harnesses to self-enforce via audit_skill_apis --code/--file before executing generated PyAuto* code. (Plot-API claim re-verified: MatPlot2D/Output genuinely gone; llms.txt and .gemini wiring checked current.) refresh_api_docs.py --scope gains 'scripts' for parity with the audit's scopes. literature.py and hpc/ reviewed, no changes. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
…p-audit-general # Conflicts: # skills/al_inspect_source_reconstruction.md
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Part of #35 (deep audit, phase D — final phase; do not auto-close). AGENTS.md review + the general tooling phases A–C didn't cover.
What changed
github.com/Jammy2211/rhayes777for repos that are canonicallyPyAutoLabs/persources.yamland the PyAutoMind body map — skills' Further-reading links, wikicore/stack/pages, README. All rewritten;PyAutoLogodeliberately untouched (it has not moved). Worst instance:al_setup_environment's editable-clone recipe cloned all five libraries from the old owners while instructing "resolve URLs fromsources.yaml" — the recipe now matches the registry and notes that old URLs redirect but must not be written anew.autoassistant/audit_skill_apis.py --code "<snippet>"/--file <script.py>on generated PyAuto* code before executing it.refresh_api_docs.py --scopegainsscripts, matching the audit's scopes.Reviewed, no changes needed
AGENTS.md re-verified end-to-end with fresh eyes: the functional plot-API claim is true against the installed stack (
aplt.MatPlot2D/aplt.Outputgone), the--check-versionexit-code documentation matches the tool's constants, session-start ordering and safety invariants are internally consistent post-#34.llms.txtfront door and.gemini/settings.jsonwiring current.literature.pyCLI,hpc/templates + sync,activate.shsound.Validation
PyAutoLogoremains.refresh_api_docs.pyparses; choices verified againstaudit_skill_apis.py --scope.Conflict note
Touches many of the same files as #36/#38 but different lines (URL lines vs recipe/table hunks). Suggested merge order: #36 → #38 → #37 → this; at most trivial rebases.
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