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PyAutoMemory — Agent Guidance

PyAutoMemory is the Memory organ of the PyAuto organism: long-term knowledge — what the science says. Literature wikis, concepts, entities, bibliographies. (The organs and boundaries are defined once in PyAutoBrain/ORGANISM.md.)

The read contract

Memory is pull-only, on demand — no agent queries it automatically. Consult it when the work is scientific or a plan names a domain (lensing, SMBH, CTI/Euclid, inference methods, galaxy evolution); skip it entirely for packaging, tooling, and workflow tasks.

When you do read:

  1. Index first. Start at index.md, then the relevant sub-wiki's own index.md (lensing_wiki/, smbh_wiki/, cti_wiki/, methods_wiki/, galaxies_wiki/).
  2. Then at most 2–3 pages. Read only the concept/entity/source pages the index points you to. Never bulk-load a sub-wiki.
  3. Do not couple to the internal layout — reach pages through the indexes, not hard-coded paths.

What does NOT live here

  • Operational history — what the organism did (prior tasks, decisions, failed approaches) lives in PyAutoMind (complete.md, GitHub issues), not here. Memory = what the science says; Mind = what the organism did.
  • Workflow state, health, execution — Mind / Heart / Build respectively.

This repo is personal

PyAutoMemory contains personal research material. Never reference or copy PyAutoMemory content into public or user-facing repos (libraries, workspaces, tutorials, assistants).

Never rewrite history

NEVER perform these operations on any repo with a remote:

  • git init in a directory already tracked by git
  • rm -rf .git && git init
  • Commit with subject "Initial commit", "Fresh start", "Start fresh", "Reset for AI workflow", or any equivalent message on a branch with a remote
  • git push --force to main (or any branch tracked as origin/HEAD)
  • git filter-repo / git filter-branch on shared branches
  • git rebase -i rewriting commits already pushed to a shared branch

If the working tree needs a clean state, the only correct sequence is:

git fetch origin
git reset --hard origin/main
git clean -fd

This applies equally to humans, local Claude Code, cloud Claude agents, Codex, and any other agent. The "Initial commit — fresh start for AI workflow" pattern that appeared independently on origin and local for three workspace repos is exactly what this rule prevents — it costs ~40 commits of redundant local work every time it happens.