[Jammy2211]

Summary

Complete the human-approved top-level guidance cleanup. The README revision is already on main; this PR carries the remaining policy, citation or legacy-file changes.

Also update or retire the reviewed supporting files:

• .url_check_allowlist.txt
• AGENTS.md
• CODE_OF_CONDUCT.md
• CONTRIBUTING.md
• libraries.txt
• patches/autoarray/0001-PR-A1-Add-autoarray-plot-plots-direct-matplotlib-mod.patch
• patches/autoarray/0002-PR-A2-A3-Switch-all-autoarray-plotters-to-use-direct.patch
• patches/autoarray/0003-PR-A3-replace-mat_plot_2d.plot_array-in-FitImagingPl.patch
• patches/autogalaxy/0001-PR-G1-G2-replace-mat_plot_2d.plot_array-with-_plot_a.patch

API Changes

No scientific API changes.

Test Plan

• Human reviewed and approved the text and removals.
• Applied to current main; git diff --check passes.
• Cross-repository validation: 185 relative Markdown links resolve; root welcome/start scripts parse.
• Science suites were not rerun for this documentation/root-file cleanup. GitHub checks must pass before merge.

Coordination and Heart

Tracked by PyAutoLabs/PyAutoScientist#90 (keep open until all PRs land).
Same-conversation human RED development override: "I approve you to bypass and continue". Current request: "put PRs up for this work and prm". Concurrent task coordination explicitly approved; separate branch.
Exact authoritative RED reasons (2026-11-10T18:35:43.930077+00:00):

• PyAutoGalaxy: CI failure
• PyAutoLens: CI failure
• PyAutoCTI: 1 uncommitted source change(s)

Heart remains RED. No release, required-check bypass or force merge. Current merge authorization lasts only this turn.

[Jammy2211]

Explicit human merge exception in the current conversation: "$prm can we over rule the criteria and then ill try fix the failures". This overrides the local /prm failed-check criterion for this reviewed documentation/root-cleanup PR only. The failing numerical tests were verified on current main and reproduced on retry (Lens 16; Galaxy 11 no-JAX failures). No numerical implementation changed. Heart freeze is clear; GitHub protection is not being overridden. CI remains failed and the human will address the underlying numerical failures separately.