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AGENTS.md

This file is for AI coding agents (Claude Code, Codex, Cursor, etc.) discovering this repository.

What this repo is

PyAutoMind is the Mind of the PyAuto organism and the starting point of the PyAuto workflow. It holds the organism's ideas, intent, goals, priorities and workflow state. Every task that ends up as a PR in PyAutoConf, PyAutoFit, PyAutoArray, PyAutoGalaxy, PyAutoLens, or any of the *_workspace* repos begins as a markdown file here.

PyAutoMind is the organism's Mind (intent and direction). The organs and their boundaries are defined once in PyAutoBrain/ORGANISM.md; see README.md for this repo's full picture.

For the full workflow narrative, conventions, and registry schemas, read README.md. The summary below is just enough to operate.

Layout (operational)

  • Prompts — <work-type>/<target>/<name>.md (free-form markdown, one task per file). The first folder is the kind of work; the second is the target repo or domain. Work-types: feature/, bug/, refactor/, docs/, test/, release/, maintenance/, research/, experiment/ (plus triage/ for prompts whose classification is still unclear). PyAutoBrain routes by the first folder — see README.md "Prompt taxonomy" and ROUTING.md. Lifecycle/meta folders are not work-types and keep their own names: issued/ (routed prompts), z_features/ (multi-task epic trackers), z_vault/ (deferred prompts — the former shelved/ merged here), and autoprompt/ (prompts about this repo's own infrastructure).
  • Registry — root-level markdown files, each with one job: active.md (in-flight tasks), planned.md (scoped, not started), complete.md (shipped), parked.md (started but not in flight), queue.md (ordered input for register_and_iterate --queue), ideas.md (raw inbox swept by $intake, /intake in Claude). Mutate these only via the skills in skills/ so commit messages stay consistent. parked.md holds tasks that were started or scoped but are not currently in flight (e.g. work parked in a stash, orphan worktrees); move back to active.md (or planned.md if re-scoping) when resuming.
  • Body map — repos.yaml is the single source of repo identity (GitHub home, category, one-line role) for every repo in the workspace. The routing table in the workspace-root AGENTS.md and the owner map in PyAutoBrain/skills/WORKFLOW.md are generated from it, and the repo lists in Heart/Build/admin scripts are drift-checked against it: python3 scripts/repos_sync.py --write.
  • Skills — skills/<name>/ are agent skills and command bodies tightly coupled to the registry. Claude and Codex discovery is installed by PyAutoBrain; they source scripts/prompt_sync.sh for commit/push.
  • Scripts — scripts/status.sh (inventory), scripts/prompt_sync.sh (commit/push helpers).

Hard rules

  1. Never rewrite history on any branch with a remote. No git init over an existing repo, no git push --force to main. The 2026-04-27 drift incident that motivated autoprompt/03_history_rewrite_guard.md is the reason.
  2. Pull before edit. git fetch && git status first, every time. If behind origin/main, git pull --ff-only before touching anything. See autoprompt/04_source_of_truth_rule.md.
  3. One prompt = one task = one PR. If a prompt outlines multiple loosely-related changes, split into separate prompt files before issuing.
  4. tmp/ is scratch. Never commit anything under it.

When you are asked to add a new prompt

Write the file under <work-type>/<target>/<name>.md — pick the work-type from the list above (use triage/ if genuinely unsure) and the target repo/domain as the second folder, e.g. feature/autolens/potential_corrections.md or bug/autoarray/mask_edge_case.md. Don't touch active.md or issued/ directly — those are managed by $start-dev and $create-issue (/start_dev and /create_issue in Claude).

To skip the manual filing, run $intake (/intake in Claude), the PyAutoBrain Intake/Conception Agent. It classifies a raw idea into the right <work-type>/<target>/ folder, writes the light header (incl. the optional Difficulty:/Autonomy:/Priority: keys — see README "Prompt file format"), and files the prompt for you. It files a prompt only; $start-dev (/start_dev in Claude) remains the separate next step.

When you are asked to start work on an existing prompt

Use $start-dev <work-type>/<target>/<name>.md (/start_dev in Claude). Older <target>/<name>.md paths from before the taxonomy migration still work. It routes to $start-library or $start-workspace (/start_library or /start_workspace in Claude) based on the repos referenced in the prompt body; routing keys off @RepoName references in the content, not the folder.

When in doubt

Read README.md. It is current as of the last commit on this branch.

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.