agent-bios 0.9.7 → 0.9.8

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "agent-bios",
-  "version": "0.9.7",
+  "version": "0.9.8",
   "releaseDate": "2026-07-26",
   "description": "A thin, low-level instruction layer for LLM CLI agents: one set of principles and behavior whichever model you run. Deploys into $HOME by copy via an explicit `agent-bios install`.",
   "bin": {
@@ -23,6 +23,7 @@
     "shell/agent-launch.zsh",
     "scripts/agent-launch.py",
     "scripts/pkgid.py",
+    "scripts/register-hooks.py",
     "scripts/assemble.py",
     "scripts/check-domains.py",
     "scripts/canary.sh",

package/scripts/assemble.py

@@ -152,16 +152,31 @@ def copy_filtered(src_dir, names, dest, rewrite=None, dry=False):
         (dest / n).write_text(body, encoding="utf-8")
 
 
-def merge_settings(claude_dir, hook_names, template_path, dry=False):
-    """Path-marker merge: central-owned hook entries reference central/hooks/."""
-    marker = "/central/hooks/"
+def merge_settings(claude_dir, hook_names, template_path, dry=False, owned_names=None):
+    """Merge our hook registrations into the user's settings, owning by NAME.
+
+    `hook_names` is what to register now (the selection); `owned_names` is every
+    hook the manifest declares, which is what we may remove. Ownership is the
+    manifest name rather than a path marker because the same hook has lived at
+    two paths — `<claude>/hooks/` on the old full-install layout and
+    `central/hooks/` now — and a path-marker drop would leave the old entry
+    behind, registering the hook twice after the move. Dropping every declared
+    name and re-adding only the selected ones also makes deselection work.
+
+    Entries we do not own are never touched: `<claude>/hooks/` is shared with
+    other tools' hooks and state.
+    """
+    owned = set(owned_names if owned_names is not None else hook_names)
     spath = claude_dir / "settings.json"
     settings = json.loads(spath.read_text(encoding="utf-8")) if spath.exists() else {}
     template = json.loads(template_path.read_text(encoding="utf-8")) if template_path.exists() else {}
     hooks = settings.setdefault("hooks", {})
-    for event, entries in list(hooks.items()):  # drop stale central-owned
-        hooks[event] = [en for en in entries
-                        if not any(marker in h.get("command", "") for h in en.get("hooks", []))]
+
+    def ours(en):
+        return any(n in h.get("command", "") for h in en.get("hooks", []) for n in owned)
+
+    for event, entries in list(hooks.items()):  # drop every entry we own
+        hooks[event] = [en for en in entries if not ours(en)]
     for event, entries in template.get("hooks", {}).items():  # re-add per selection
         for en in entries:
             cmds = [h.get("command", "") for h in en.get("hooks", [])]
@@ -299,7 +314,8 @@ def main():
                   rewrite=(f"{CLAUDE_VAR}/guides/", f"{CLAUDE_VAR}/central/guides/"), dry=dry)
     copy_filtered(REPO / "claude" / "hooks", hooks, central / "hooks", dry=dry)
     copy_filtered(REPO / "claude" / "agents", agents, central / "agents", dry=dry)
-    merge_settings(claude_dir, hooks, REPO / "claude" / "settings.template.json", dry=dry)
+    merge_settings(claude_dir, hooks, REPO / "claude" / "settings.template.json", dry=dry,
+                   owned_names=manifest.get("hooks", {}))   # deselected hooks must drop too
     entry_state = seed_entry(claude_dir, monolith, dry=dry)
 
     merge_codex(codex_dir, codex_bundle, dry=dry)

package/scripts/install.sh

@@ -111,6 +111,15 @@ deploy_glob() {
 # marker region, settings merge); the entry CLAUDE.md and AGENTS.md are NOT
 # manifested — the entry is user-owned after seeding, AGENTS.md holds a
 # personal region — so uninstall never deletes them.
+# Full mode never runs the assembler, so nothing registered the hooks it
+# deployed — the files landed and never fired. Reuse the assembler's own merge
+# so both install paths register identically, under one ownership rule.
+register_hooks_full() {
+  [ "$DRY_RUN" = 1 ] && { info "[dry-run] register central hooks"; return 0; }
+  python3 "$REPO/scripts/register-hooks.py" "$REPO" "$CLAUDE_DIR" \
+    || log "note: hook registration failed; the deployed hooks will not fire"
+}
+
 packaged_mode() { [ "${DOMAINS_SET:-0}" = 1 ] || [ -f "$STATE_DIR/selection.json" ]; }
 
 assemble_packaged() {
@@ -450,7 +459,10 @@ cmd_install() {
     deploy_file "$REPO/claude/CLAUDE.md" "$CLAUDE_DIR/CLAUDE.md"
     deploy_glob "$REPO/claude/guides" "*.md" "$CLAUDE_DIR/guides"
     deploy_glob "$REPO/claude/agents" "*.md" "$CLAUDE_DIR/agents"
-    deploy_glob "$REPO/claude/hooks" "*.py" "$CLAUDE_DIR/hooks" "+x"
+    # Our hooks go under central/: <claude>/hooks is shared with other tools
+    # files, caches, and state, and we must not own a directory we share.
+    deploy_glob "$REPO/claude/hooks" "*.py" "$CLAUDE_DIR/central/hooks" "+x"
+    register_hooks_full
     deploy_file "$REPO/codex/AGENTS.md" "$CODEX_DIR/AGENTS.md"
     deploy_glob "$REPO/codex/guides" "*.md" "$CODEX_DIR/guides"
   fi
@@ -540,7 +552,7 @@ cmd_verify() {
     verify_match "$REPO/codex/AGENTS.md"         "$CODEX_DIR/AGENTS.md"         || fail=1
     for gp in "$REPO"/claude/guides/*.md; do verify_present "$CLAUDE_DIR/guides/$(basename "$gp")" || fail=1; done
     for gp in "$REPO"/claude/agents/*.md; do verify_present "$CLAUDE_DIR/agents/$(basename "$gp")" || fail=1; done
-    for gp in "$REPO"/claude/hooks/*.py;  do verify_present "$CLAUDE_DIR/hooks/$(basename "$gp")"  || fail=1; done
+    for gp in "$REPO"/claude/hooks/*.py;  do verify_present "$CLAUDE_DIR/central/hooks/$(basename "$gp")"  || fail=1; done
     for gp in "$REPO"/codex/guides/*.md;  do verify_present "$CODEX_DIR/guides/$(basename "$gp")"  || fail=1; done
   fi
   verify_match "$REPO/scripts/agent-launch.py" "$BIN_DIR/agent-launch"        || fail=1

package/scripts/register-hooks.py

@@ -0,0 +1,44 @@
+#!/usr/bin/env python3
+"""Register the manifest's hooks in a deployed settings.json (full-install path).
+
+The packaged path gets this for free: assemble.py composes the corpus and calls
+merge_settings on the way out. A full install never runs the assembler, so the
+hook files were deployed and nothing ever registered them — they sat on disk and
+never fired. This runs the assembler's own merge so both paths register
+identically, under the same name-based ownership rule.
+
+Usage: register-hooks.py <repo> <claude-dir>
+Exit 0 on success; non-zero (with a message) if the merge could not run, which
+the installer reports as a note rather than failing the whole install.
+"""
+import importlib.util
+import json
+import pathlib
+import sys
+
+
+def load_assemble(repo):
+    """Import assemble.py by path — scripts/ is a flat toolbox, not a package."""
+    spec = importlib.util.spec_from_file_location("assemble", repo / "scripts" / "assemble.py")
+    mod = importlib.util.module_from_spec(spec)
+    spec.loader.exec_module(mod)
+    return mod
+
+
+def main():
+    if len(sys.argv) != 3:
+        sys.exit("usage: register-hooks.py <repo> <claude-dir>")
+    repo, claude_dir = pathlib.Path(sys.argv[1]), pathlib.Path(sys.argv[2])
+    manifest = json.loads((repo / "config" / "domains.json").read_text(encoding="utf-8"))
+    names = sorted(manifest.get("hooks", {}))
+    if not names:
+        sys.exit("register-hooks: manifest declares no hooks — refusing to rewrite settings")
+    mod = load_assemble(repo)
+    mod.merge_settings(claude_dir, names,
+                       repo / "claude" / "settings.template.json",
+                       owned_names=names)
+    print(f"  hooks registered ({len(names)})")
+
+
+if __name__ == "__main__":
+    main()