feat: add Codex skill discovery from shared instructions

README.md

@@ -63,6 +63,22 @@ bin/pyauto-brain vitals                    # read the Heart's readiness verdict
 bash bin/install.sh                        # symlink every organ's skills into ~/.claude
 ```
 
+Project discovery is generated separately from the registered repository body
+map. For example, after adding an assistant skill:
+
+```bash
+bash bin/install.sh --write-project-discovery autolens_assistant
+bash bin/install.sh --check-project-discovery autolens_assistant
+```
+
+Without repository arguments these commands cover registered checkouts with
+canonical `skills/` content. Flat assistant skills keep their Claude names and
+get namespaced Codex adapters; workspace skills use neutral
+`skills/<name>/SKILL.md` bodies. Codex discovery descriptions are bounded summaries;
+the linked canonical file retains the full instructions. Commit the generated
+adapters with the skill. Regeneration checks name collisions across the installed
+repository inventory and refuses conflicting user-owned destinations.
+
 The eight organs the Brain coordinates — Brain (reasoning), Mind (intent),
 Cortex (learning what is true), Memory (knowledge), Heart (health), Hands
 (release), Nerves (configuration), Gut (shedding) — are defined once in

agents/conductors/clone/_clone.py

@@ -97,6 +97,8 @@
     ".claude/hooks/*", ".claude/settings.json", ".codex/hooks.json", ".gemini/*",
     ".claude/skills/_*", ".claude/skills/start-new-project*",
     ".claude/skills/contribute-upstream*",
+    ".claude/commands/_*", ".claude/commands/start-new-project*",
+    ".claude/commands/contribute-upstream*",
 ]
 
 # Domain content a newborn regenerates/stubs rather than copies blind, shared
@@ -105,6 +107,8 @@
 # in a domain assistant, but the near-empty framework scaffold (generic) in the
 # domain-agnostic base — so each profile places it, not this shared set.
 _SHARED_DOMAIN = [
+    # Generated names/targets belong to the parent; regenerate for the newborn.
+    ".codex/skills/*",
     "dataset/*",
     "README.md",                  # science framing + the example prompts
     "hpc/*",
@@ -133,6 +137,8 @@
         ),
         "generic": _SHARED_GENERIC,
         "domain": [
+            ".claude/commands/al_*.md",
+            ".claude/commands/euclid_*.md", ".claude/commands/init-slam.md",
             "skills/al_*.md",             # every al_* skill body
             ".claude/skills/al_*.md",     # ... and their harness mirrors
             "skills/init-slam.md", ".claude/skills/init-slam.md",  # SLAM = lensing
@@ -166,6 +172,7 @@
             *_SHARED_GENERIC,
             "skills/af_*.md",             # generic inference skills
             ".claude/skills/af_*.md",     # ... and their harness mirrors
+            ".claude/commands/af_*.md",
             "wiki/core/*",                # statistics/inference reference
             "wiki/literature/*",          # the near-empty literature scaffold
         ],

bin/install.sh

@@ -7,7 +7,7 @@
 # Claude-only command files remain available as slash commands. Roots that
 # aren't checked out are simply skipped.
 #
-# Discovery roots (scanned in order):
+# User-level install 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
@@ -276,100 +276,22 @@ workspace_policy() {
 
 # ---------- Committed per-tool discovery (web/cloud) ----------
 #
-# The user-level ~/.claude / ~/.codex symlinks (below) are NOT loaded in cloud/
-# web sessions — only committed repo files travel. So each skill-hosting repo
-# also COMMITS a project-level discovery tree — .claude/commands, .claude/skills
-# and .codex/skills — as relative symlinks into that repo's own skills/, so the
-# slash commands and skills register on web with no user-level install. Per-repo:
-# each repo mirrors its OWN skills/ (no cross-repo duplication); a Brain-loaded
-# web session gets Brain's verbs, and every other repo's commands register when it
-# is checked out. The AGENTS.md command surface (above) still advertises the full
-# verb set + hosting organ. Generated + drift-checked — do not hand-edit these
-# dirs. Symlinks (single source = skills/), matching the user-level install.
-DISCOVERY_REPOS=(PyAutoBrain PyAutoMind PyAutoHeart PyAutoHands autolens_profiling)
-DISCOVERY_DIRS=(.claude/commands .claude/skills .codex/skills)
-
-# Emit the (link<TAB>target) pairs a repo's committed discovery should contain,
-# derived from its skills/. Link is relative to the repo root; target relative to
-# the link's own directory. Mirrors the user-level install rules: a SKILL.md dir
-# becomes a Claude + Codex skill (Codex uses the frontmatter `name:` when valid);
-# a <name>.md becomes a Claude slash command.
-_discovery_manifest() {
-  local repo_dir="$1" skills_dir="$1/skills" entry name sk
-  [ -d "$skills_dir" ] || return 0
-  for entry in "$skills_dir"/*/; do
-    [ -d "$entry" ] || continue
-    name=$(basename "$entry")
-    if [ -f "$entry/SKILL.md" ]; then
-      printf '.claude/skills/%s\t../../skills/%s\n' "$name" "$name"
-      sk=$(sed -n 's/^name:[[:space:]]*//p' "$entry/SKILL.md" | head -1)
-      if [ -n "$sk" ] && [[ "$sk" != *[!a-z0-9-]* ]]; then
-        printf '.codex/skills/%s\t../../skills/%s\n' "$sk" "$name"
-      fi
-    fi
-    if [ -f "$entry/$name.md" ]; then
-      printf '.claude/commands/%s.md\t../../skills/%s/%s.md\n' "$name" "$name" "$name"
-    fi
-  done | sort
-}
-
-# All currently-present managed symlinks in a repo, as (link<TAB>target), sorted.
-_discovery_actual() {
-  local repo_dir="$1" d link
-  for d in "${DISCOVERY_DIRS[@]}"; do
-    [ -d "$repo_dir/$d" ] || continue
-    for link in "$repo_dir/$d"/*; do
-      [ -L "$link" ] || continue
-      printf '%s\t%s\n' "${link#"$repo_dir"/}" "$(readlink "$link")"
-    done
-  done | sort
-}
-
+# Project discovery is generated from every registered repository in the Mind
+# body map. Claude links remain relative to canonical skills/; Codex adapters
+# expose flat assistant and workspace skills under stable namespaced names.
+# This committed tree is available in cloud/web sessions without user-level setup.
+# The Python generator uses the registered body map and preserves user-owned files.
 write_project_discovery() {
-  local repo repo_dir link target d
-  for repo in "${DISCOVERY_REPOS[@]}"; do
-    repo_dir="$(pyauto_repo_path "$repo" "$PYAUTO_ROOT")"
-    if [ ! -d "$repo_dir/skills" ]; then echo "skipped (no skills/): $repo_dir"; continue; fi
-    # Drop our managed symlinks (only symlinks — never real files) so a removed
-    # or renamed skill does not leave a stale committed link.
-    for d in "${DISCOVERY_DIRS[@]}"; do
-      [ -d "$repo_dir/$d" ] && find "$repo_dir/$d" -maxdepth 1 -type l -delete 2>/dev/null || true
-    done
-    while IFS=$'\t' read -r link target; do
-      [ -n "$link" ] || continue
-      mkdir -p "$repo_dir/$(dirname "$link")"
-      ln -sf "$target" "$repo_dir/$link"
-    done < <(_discovery_manifest "$repo_dir")
-    echo "wrote discovery: $repo (.claude/{commands,skills}, .codex/skills)"
-  done
+  python3 "$SCRIPT_DIR/project_discovery.py" write --root "$PYAUTO_ROOT" "$@"
 }
-
-# Optional trailing repo names narrow the check to those repos (the pytest leg
-# checks PyAutoBrain alone, so a local run is not reddened by a sibling's drift).
 check_project_discovery() {
-  local repo repo_dir want got drift=0
-  local repos=("${DISCOVERY_REPOS[@]}")
-  [ "$#" -gt 0 ] && repos=("$@")
-  for repo in "${repos[@]}"; do
-    repo_dir="$(pyauto_repo_path "$repo" "$PYAUTO_ROOT")"
-    [ -d "$repo_dir/skills" ] || continue
-    want="$(_discovery_manifest "$repo_dir")"
-    got="$(_discovery_actual "$repo_dir")"
-    if [ "$want" = "$got" ]; then
-      echo "OK: $repo"
-    else
-      echo "DRIFT: $repo — run: bash PyAutoBrain/bin/install.sh --write-project-discovery"
-      diff <(printf '%s\n' "$want") <(printf '%s\n' "$got") | sed 's/^/    /'
-      drift=1
-    fi
-  done
-  return "$drift"
+  python3 "$SCRIPT_DIR/project_discovery.py" check --root "$PYAUTO_ROOT" "$@"
 }
 
 case "${1:-}" in
   --write-agents-surface) write_agents_surface; exit 0 ;;
   --check-agents-surface) check_agents_surface; exit $? ;;
-  --write-project-discovery) write_project_discovery; exit 0 ;;
+  --write-project-discovery) shift; write_project_discovery "$@"; exit $? ;;
   --check-project-discovery) shift; check_project_discovery "$@"; exit $? ;;
   --write-workspace-policy) workspace_policy write; exit $? ;;
   --check-workspace-policy) workspace_policy check; exit $? ;;