Relocate cross-organ skill installer into bin/

README.md

@@ -96,4 +96,10 @@ bin/pyauto-brain vitals      # (faculty) one tick + the unified dashboard card (
 PyAutoBrain runs from its checkout (no pip install), resolving the sibling
 `pyauto-heart` and `autobuild` binaries from PATH or `~/Code/PyAutoLabs/`.
 
+`bin/` also hosts the cross-organ Claude skill **installer** (`install.sh`) and
+line-count **guard** (`check_skill_line_counts.sh`) — organism-wide infrastructure
+that used to live in `admin_jammy/skills/`. Run `bash PyAutoBrain/bin/install.sh`
+to (re-)symlink every organ's skills/commands into `~/.claude/`. See
+[`bin/README.md`](bin/README.md).
+
 See [`AGENTS.md`](AGENTS.md) for the full description.

bin/README.md

@@ -0,0 +1,59 @@
+# PyAutoBrain/bin/
+
+Executable tooling for the PyAuto organism.
+
+- **`pyauto-brain`** — the PyAutoBrain CLI (reasoning-layer entry point).
+- **`install.sh`** — the cross-organ Claude skill/command **installer**.
+- **`check_skill_line_counts.sh`** — the skill line-count **guard** (primary
+  skill `.md` files must stay < 200 lines).
+
+The installer and guard used to live in `admin_jammy/skills/`. They moved here
+because they are organism-wide infrastructure, not admin_jammy's own tooling —
+admin_jammy hosts no skills and is slated to leave `PyAutoLabs/`.
+
+## install.sh
+
+Auto-discovers (no hardcoded skill list) by scanning each organ repo's
+`skills/` dir for `*/` subdirs, then symlinks each into `~/.claude/`:
+
+- **`PyAutoMind/skills/`** — registry-coupled skills (`create_issue`).
+- **`PyAutoBrain/skills/`** — development-workflow skills (`start_dev`,
+  `start_dev_for_user`, `plan_branches`, `start_library`, `start_workspace`,
+  `ship_library`, `ship_workspace`, `register_and_iterate`, `repo_cleanup`,
+  `update_issue`).
+- **`PyAutoHeart/skills/`** — status / readiness / validation skills
+  (`pyauto-status`, `pyauto-status-full`, `worktree_status`, `smoke_test`,
+  `dep_audit`, `verify_install`, `review_release`, `audit_docs`, `cli_noise_clean`).
+- **`PyAutoBuild/skills/`** — release-execution skills **only** (`pre_build`).
+  Build owns no dev-workflow skills; `ship_*` (Brain) only *call* its release step.
+- **`autolens_profiling/skills/`** — science-profiling skills (`profile_likelihood`).
+- **`admin_jammy/skills/`** — vestigial: hosts no skills; scanned only so an old
+  checkout still resolves, auto-skipped once admin_jammy leaves.
+
+Discovery rule per root:
+
+- A directory with `SKILL.md` → **skill**, symlinked to `~/.claude/skills/<name>/`.
+- A directory with `<dirname>.md` (and no `SKILL.md`) → **command**, symlinked to
+  `~/.claude/commands/<name>.md`.
+
+Roots that aren't checked out are skipped. It is idempotent — existing symlinks
+are replaced, non-symlink files are left alone, and broken symlinks pointing into
+a PyAuto root are pruned. Re-run it after pulling updates.
+
+## Bootstrap on a new machine
+
+```bash
+cd ~/Code/PyAutoLabs
+git clone git@github.com:PyAutoLabs/PyAutoBrain.git
+git clone git@github.com:PyAutoLabs/PyAutoMind.git
+git clone git@github.com:PyAutoLabs/PyAutoHeart.git
+bash PyAutoBrain/bin/install.sh
+```
+
+## Execution environments
+
+There is **no special "mobile" or "phone" mode**. Skills run the same logic in
+any environment and only differ in where they read state from: a `local-dev`
+checkout uses local git + task worktrees; a `web-github` / `ci-only` session uses
+the clones present in the working directory (and the GitHub API for branch
+state). The full environment model is in `PyAutoBrain/skills/WORKFLOW.md`.

bin/check_skill_line_counts.sh

@@ -0,0 +1,59 @@
+#!/usr/bin/env bash
+# Report any *primary* skill .md file over the line limit (default 200).
+#
+# Claude skill guidance keeps primary skill files short; long background,
+# templates and examples belong in supporting docs (`reference.md`, shared
+# `WORKFLOW.md`), which are exempt here. A "primary" file is a skill's `SKILL.md`
+# or its command body `<dirname>.md`.
+#
+# Scans the same discovery roots as install.sh. Exit 0 = all within limit,
+# exit 1 = at least one primary file is over the limit.
+#
+# Usage:
+#   bash PyAutoBrain/bin/check_skill_line_counts.sh [limit]
+
+set -euo pipefail
+
+LIMIT="${1:-200}"
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+PYAUTO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
+
+ROOTS=(
+  "$PYAUTO_ROOT/admin_jammy/skills"         # vestigial (hosts no skills)
+  "$PYAUTO_ROOT/PyAutoMind/skills"
+  "$PYAUTO_ROOT/PyAutoBrain/skills"
+  "$PYAUTO_ROOT/PyAutoHeart/skills"
+  "$PYAUTO_ROOT/PyAutoBuild/skills"
+  "$PYAUTO_ROOT/autolens_profiling/skills"
+)
+
+over=0
+checked=0
+
+for root in "${ROOTS[@]}"; do
+  [ -d "$root" ] || continue
+  for dir in "$root"/*/; do
+    [ -d "$dir" ] || continue
+    name="$(basename "$dir")"
+    # Primary files: SKILL.md (dispatcher/frontmatter) and the command/body
+    # <dirname>.md. Supporting docs (reference.md, examples, etc.) are exempt.
+    for primary in "$dir/SKILL.md" "$dir/$name.md"; do
+      [ -f "$primary" ] || continue
+      checked=$((checked + 1))
+      lines=$(wc -l < "$primary")
+      if [ "$lines" -gt "$LIMIT" ]; then
+        echo "OVER  ${lines}  ${primary#$PYAUTO_ROOT/}"
+        over=$((over + 1))
+      fi
+    done
+  done
+done
+
+echo ""
+if [ "$over" -eq 0 ]; then
+  echo "OK: all $checked primary skill files are within $LIMIT lines."
+  exit 0
+else
+  echo "FAIL: $over primary skill file(s) exceed $LIMIT lines — factor detail into reference.md."
+  exit 1
+fi

bin/install.sh

@@ -0,0 +1,152 @@
+#!/usr/bin/env bash
+# Bootstrap Claude Code skills/commands into ~/.claude/ from every PyAuto
+# organism repo that hosts skills.
+#
+# This installer lives in PyAutoBrain (the reasoning/orchestration organ). It
+# scans every organ repo's skills/ dir and symlinks their skills+commands into
+# ~/.claude/. Roots that aren't checked out are simply skipped.
+#
+# Discovery roots (scanned in order):
+#   - admin_jammy/skills/   — vestigial: admin_jammy hosts no skills and is
+#                             slated to leave PyAutoLabs/; kept only so an old
+#                             checkout still resolves, auto-skipped once gone
+#   - PyAutoMind/skills/    — registry-coupled skills (create_issue, handoff)
+#   - PyAutoBrain/skills/   — development-workflow skills (start_*/ship_*/plan_branches/…)
+#   - PyAutoHeart/skills/   — status / readiness / diagnostic skills
+#   - PyAutoBuild/skills/   — release-execution skills ONLY (pre_build)
+#   - autolens_profiling/skills/ — science-profiling skills (profile_likelihood)
+#
+# (PyAutoBuild's root is for its own release/packaging-execution skills only — it
+#  owns NO dev-workflow skills; the ship_* skills merely call its release step.)
+#
+# Auto-discovers skills in each root:
+#   - A directory with SKILL.md → installed as ~/.claude/skills/<name>/
+#   - A directory with <name>.md (and no SKILL.md) → installed as a flat
+#     command at ~/.claude/commands/<name>.md
+#
+# Safe to re-run — existing symlinks are replaced, non-symlink files are skipped.
+#
+# Usage:
+#   bash PyAutoBrain/bin/install.sh
+
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+PYAUTO_ROOT="$(cd "$SCRIPT_DIR/../.." && pwd)"
+ADMIN_SKILLS_DIR="$PYAUTO_ROOT/admin_jammy/skills"
+MIND_SKILLS_DIR="$PYAUTO_ROOT/PyAutoMind/skills"
+BRAIN_SKILLS_DIR="$PYAUTO_ROOT/PyAutoBrain/skills"
+HEART_SKILLS_DIR="$PYAUTO_ROOT/PyAutoHeart/skills"
+BUILD_SKILLS_DIR="$PYAUTO_ROOT/PyAutoBuild/skills"
+PROFILING_SKILLS_DIR="$PYAUTO_ROOT/autolens_profiling/skills"
+
+# ---------- Execution-environment note ----------
+#
+# Skill discovery is identical in every execution environment (local-dev,
+# web-github, ci-only). When a root repo is not checked out, it is simply
+# skipped — the skills from the roots that ARE present still install.
+
+if [ -d "$PYAUTO_ROOT/PyAutoFit" ] || [ -d "$HOME/Code/PyAutoLabs/PyAutoFit" ]; then
+  echo "Environment: local-dev (PyAuto repos detected)"
+else
+  echo "Environment: web-github / ci-only (clone roots on demand)"
+fi
+echo ""
+
+mkdir -p "$HOME/.claude/skills" "$HOME/.claude/commands"
+
+# ---------- Prune stale symlinks ----------
+#
+# Self-healing: when a skill is removed or re-homed, its old ~/.claude symlink
+# would otherwise dangle. Remove only BROKEN symlinks whose target points into a
+# PyAuto root — never touch real files or symlinks that resolve, and never touch
+# links pointing outside the managed roots (e.g. user-added skills).
+
+prune_stale_symlinks() {
+  local dir="$1"
+  [ -d "$dir" ] || return 0
+  for link in "$dir"/*; do
+    [ -L "$link" ] || continue
+    [ -e "$link" ] && continue                      # resolves fine — keep
+    local tgt; tgt="$(readlink "$link")"
+    case "$tgt" in
+      "$PYAUTO_ROOT"/*|"$HOME/Code/PyAutoLabs"/*)
+        echo "  PRUNE $(basename "$link") (stale → $tgt)"; rm -f "$link" ;;
+    esac
+  done
+}
+
+prune_stale_symlinks "$HOME/.claude/skills"
+prune_stale_symlinks "$HOME/.claude/commands"
+
+# ---------- Install one source dir's skills/commands ----------
+
+install_from_dir() {
+  local source_dir="$1"
+  local label="$2"
+
+  if [ ! -d "$source_dir" ]; then
+    echo "${label}: (source dir not present, skipping)"
+    return
+  fi
+
+  echo "$label"
+  local installed_count=0
+
+  for entry in "$source_dir"/*/; do
+    [ -d "$entry" ] || continue
+    local name
+    name=$(basename "$entry")
+
+    # Skip the install.sh dir itself, or any non-skill dirs
+    [ "$name" = "skills" ] && continue
+
+    if [ -f "$entry/SKILL.md" ]; then
+      # Skill — symlink the directory
+      local dst="$HOME/.claude/skills/$name"
+      _link_symlink "$entry" "$dst" "skill"
+      installed_count=$((installed_count + 1))
+    elif [ -f "$entry/$name.md" ]; then
+      # Command — symlink the flat .md file
+      local dst="$HOME/.claude/commands/$name.md"
+      _link_symlink "$entry/$name.md" "$dst" "command"
+      installed_count=$((installed_count + 1))
+    else
+      echo "  SKIP $name (no SKILL.md or $name.md found)"
+    fi
+  done
+
+  echo "  ($installed_count installed from $label)"
+  echo ""
+}
+
+_link_symlink() {
+  local src="$1"
+  local dst="$2"
+  local kind="$3"
+  local name
+  name=$(basename "$dst")
+
+  if [ -L "$dst" ]; then
+    rm "$dst"
+  elif [ -e "$dst" ]; then
+    echo "  SKIP $name ($kind — non-symlink exists at $dst)"
+    return
+  fi
+
+  ln -s "$src" "$dst"
+  echo "  LINK $name ($kind)"
+}
+
+# ---------- Run installs ----------
+
+install_from_dir "$ADMIN_SKILLS_DIR" "admin_jammy/skills/ — vestigial (hosts no skills)"
+install_from_dir "$MIND_SKILLS_DIR"  "PyAutoMind/skills/ — registry-coupled skills (Mind)"
+install_from_dir "$BRAIN_SKILLS_DIR" "PyAutoBrain/skills/ — development-workflow skills (Brain)"
+install_from_dir "$HEART_SKILLS_DIR" "PyAutoHeart/skills/ — status / readiness skills (Heart)"
+install_from_dir "$BUILD_SKILLS_DIR" "PyAutoBuild/skills/ — release-execution skills (Hands)"
+install_from_dir "$PROFILING_SKILLS_DIR" "autolens_profiling/skills/ — science-profiling skills"
+
+# ---------- Summary ----------
+
+echo "Done. Restart Claude Code to pick up changes."