agent-bios 0.2.0 → 0.4.0

package/scripts/install.sh

@@ -102,6 +102,29 @@ deploy_glob() {
   done
 }
 
+# ---- packaged (domain-selected) corpus deploy ----------------------------
+# Active when --domains is passed or a prior selection exists in STATE_DIR.
+# assemble.py owns the corpus surfaces (central tree, entry seeding, codex
+# 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.
+packaged_mode() { [ "${DOMAINS_SET:-0}" = 1 ] || [ -f "$STATE_DIR/selection.json" ]; }
+
+assemble_packaged() {
+  local args=(--claude-dir "$CLAUDE_DIR" --codex-dir "$CODEX_DIR" --state-dir "$STATE_DIR") rc=0
+  [ "${DOMAINS_SET:-0}" = 1 ] && args+=(--domains "$DOMAINS_ARG")
+  [ "$DRY_RUN" = 1 ] && args+=(--dry-run)
+  python3 "$REPO/scripts/assemble.py" "${args[@]}" || rc=$?
+  if [ "$rc" = 2 ]; then
+    log "packaged: entry file needs user action (import line missing); central content will not load until it is added"
+  elif [ "$rc" != 0 ]; then
+    return 1
+  fi
+  if [ "$DRY_RUN" != 1 ]; then
+    find "$CLAUDE_DIR/central" "$CODEX_DIR/guides" -type f 2>/dev/null >> "$MANIFEST"
+  fi
+}
+
 add_zsh_hook() {
   if [ -f "$ZSHRC" ] && grep -qF "$HOOK_MARK" "$ZSHRC"; then
     info "zsh hook present  $ZSHRC"
@@ -126,6 +149,152 @@ migrate_state() {
   mv "$LEGACY_STATE_DIR" "$STATE_DIR" && info "migrated state  $LEGACY_STATE_DIR -> $STATE_DIR"
 }
 
+# ---- codex live-config additions -----------------------------------------
+# The live ~/.codex/config.toml is user/runtime-owned; agent-bios never
+# deploys or overwrites it. codex/config-additions.toml declares the only
+# content agent-bios manages there — one marked [agents.*] block plus a tagged
+# features.multi_agent line — and this helper merges (install), checks
+# (verify), or removes (uninstall) exactly that content, backed up and
+# tomllib-validated before any write. Modes: merge | check | remove.
+codex_config_additions() {
+  AB_MODE="$1" AB_CODEX_DIR="$CODEX_DIR" AB_FRAGMENT="$REPO/codex/config-additions.toml" \
+  AB_BACKUP="${BACKUP_DIR:-}" AB_DRY="$DRY_RUN" python3 - <<'PY'
+import os, pathlib, sys, tomllib
+
+mode = os.environ["AB_MODE"]
+codex_dir = pathlib.Path(os.environ["AB_CODEX_DIR"])
+fragment_path = pathlib.Path(os.environ["AB_FRAGMENT"])
+backup_root = os.environ.get("AB_BACKUP", "")
+dry = os.environ.get("AB_DRY") == "1"
+target = codex_dir / "config.toml"
+BEGIN = "# >>> agent-bios additions >>>"
+END = "# <<< agent-bios additions <<<"
+TAG = "# agent-bios"
+
+def info(msg): print(f"  {msg}")
+def fail(msg): print(msg); sys.exit(1)
+
+frag_text = fragment_path.read_text().replace("${CODEX_HOME}", str(codex_dir))
+want_agents = tomllib.loads(frag_text)["agents"]
+live_text = target.read_text() if target.is_file() else ""
+try:
+    live = tomllib.loads(live_text) if live_text else {}
+except Exception as exc:
+    fail(f"live codex config does not parse; not touching it: {target} ({exc})")
+
+def state_ok():
+    if live.get("features", {}).get("multi_agent") is not True:
+        return False
+    return all(
+        live.get("agents", {}).get(name, {}).get(key) == spec[key]
+        for name, spec in want_agents.items()
+        for key in ("description", "config_file")
+    )
+
+if mode == "check":
+    problems = []
+    if live.get("features", {}).get("multi_agent") is not True:
+        problems.append("features.multi_agent is not true")
+    for name, spec in want_agents.items():
+        if live.get("agents", {}).get(name, {}).get("config_file") != spec["config_file"]:
+            problems.append(f"agents.{name}.config_file drifted or missing")
+        elif not pathlib.Path(spec["config_file"]).is_file():
+            problems.append(f"agents.{name} template missing: {spec['config_file']}")
+    if problems:
+        fail(f"codex config additions: {'; '.join(problems)} ({target})")
+    info("codex config additions OK")
+    sys.exit(0)
+
+def strip_managed(text):
+    out, skipping = [], False
+    for line in text.splitlines(keepends=True):
+        s = line.strip()
+        if s == BEGIN: skipping = True; continue
+        if s == END: skipping = False; continue
+        if skipping or s.endswith(TAG): continue
+        out.append(line)
+    return "".join(out)
+
+if mode == "remove":
+    if not target.is_file():
+        sys.exit(0)
+    stripped = strip_managed(live_text)
+    if stripped == live_text:
+        info(f"no agent-bios additions in {target}")
+        sys.exit(0)
+    try:
+        tomllib.loads(stripped)
+    except Exception as exc:
+        fail(f"refusing removal; result would not parse: {exc}")
+    if dry:
+        info(f"[dry-run] remove agent-bios additions from {target}")
+        sys.exit(0)
+    backup = target.with_name(target.name + ".bak-agent-bios-uninstall")
+    backup.write_text(live_text)
+    target.write_text(stripped)
+    info(f"removed additions  {target} (backup: {backup.name})")
+    sys.exit(0)
+
+# mode == merge
+if state_ok():
+    info(f"unchanged  {target} (additions present)")
+    sys.exit(0)
+
+# A drifted [agents.<tier>] outside our markers would become a duplicate
+# table if we appended ours; that conflict needs the user, not a clobber.
+base = strip_managed(live_text)
+base_data = tomllib.loads(base) if base.strip() else {}
+clash = [name for name in want_agents if name in base_data.get("agents", {})]
+if clash:
+    fail(
+        f"unmanaged [agents.{'/'.join(clash)}] with drifted content in {target}; "
+        "align or remove them, then rerun install"
+    )
+
+block_lines = [BEGIN]
+if "features" not in base_data:
+    block_lines += ["[features]", f"multi_agent = true  {TAG}"]
+for name, spec in want_agents.items():
+    block_lines += [
+        f"[agents.{name}]",
+        f'description = "{spec["description"]}"',
+        f'config_file = "{spec["config_file"]}"',
+    ]
+block_lines.append(END)
+block = "\n".join(block_lines) + "\n"
+
+new_text = base
+if "features" in base_data:
+    if base_data["features"].get("multi_agent") is None:
+        lines = new_text.splitlines(keepends=True)
+        for i, line in enumerate(lines):
+            if line.strip() == "[features]":
+                lines.insert(i + 1, f"multi_agent = true  {TAG}\n")
+                break
+        new_text = "".join(lines)
+    elif base_data["features"].get("multi_agent") is not True:
+        info(f"note: features.multi_agent explicitly set in {target}; leaving it")
+if new_text and not new_text.endswith("\n"):
+    new_text += "\n"
+new_text += ("\n" if new_text else "") + block
+
+try:
+    tomllib.loads(new_text)
+except Exception as exc:
+    fail(f"merge result would not parse; live config untouched ({exc})")
+if dry:
+    info(f"[dry-run] merge agent-bios additions into {target}")
+    sys.exit(0)
+if live_text and backup_root:
+    bpath = pathlib.Path(backup_root + str(target))
+    bpath.parent.mkdir(parents=True, exist_ok=True)
+    bpath.write_text(live_text)
+target.parent.mkdir(parents=True, exist_ok=True)
+target.write_text(new_text)
+info(f"merged additions  {target}")
+PY
+}
+
 # ---- optional dependencies -----------------------------------------------
 # Capabilities are optional: a missing one only degrades the review routes that
 # need it. config/agent-launch.toml is the single source for both the command
@@ -253,11 +422,19 @@ cmd_install() {
     : > "$MANIFEST"
   fi
   log "Deploying agent-bios from $REPO"
-  deploy_file "$REPO/claude/CLAUDE.md" "$CLAUDE_DIR/CLAUDE.md"
-  deploy_glob "$REPO/claude/guides" "*.md" "$CLAUDE_DIR/guides"
-  deploy_file "$REPO/codex/AGENTS.md" "$CODEX_DIR/AGENTS.md"
-  deploy_glob "$REPO/codex/guides" "*.md" "$CODEX_DIR/guides"
+  if packaged_mode; then
+    log "packaged mode: assembling selected domains (state: $STATE_DIR/selection.json)"
+    assemble_packaged || exit 1
+  else
+    deploy_file "$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" "$CLAUDE_DIR/hooks" "+x"
+    deploy_file "$REPO/codex/AGENTS.md" "$CODEX_DIR/AGENTS.md"
+    deploy_glob "$REPO/codex/guides" "*.md" "$CODEX_DIR/guides"
+  fi
   deploy_glob "$REPO/codex/agents" "*.toml" "$CODEX_DIR/agents"
+  codex_config_additions merge || exit 1
   deploy_file "$REPO/scripts/codex-run.sh"  "$CODEX_DIR/bin/codex-run"  "+x"
   deploy_file "$REPO/scripts/codex-helm.sh" "$CODEX_DIR/bin/codex-helm" "+x"
   migrate_user_presets || exit 1   # must precede the deploy below, which overwrites profiles.toml
@@ -275,12 +452,19 @@ cmd_install() {
       || log "warning: venv provisioning failed (numbered-prompt fallback applies)"
   fi
   add_zsh_hook
+  if python3 "$REPO/scripts/session-distill/corpus-state.py" project --repo "$REPO" >/dev/null 2>&1; then
+    info "corpus-status projected"
+  else
+    log "note: corpus-status projection unavailable (versions.json/ledger missing?)"
+  fi
   log ""
   log "Verifying deployment..."
   if cmd_verify; then
     log ""
     log "Done. Open a new shell (or: source \"$ZSHRC\") to activate the zero-arg launcher."
-    [ -n "$BACKUP_DIR" ] && [ -d "$BACKUP_DIR" ] && log "Replaced files were backed up under $BACKUP_DIR"
+    # An untouched backup dir means nothing was replaced; that healthy state
+    # must not become a nonzero exit under set -e.
+    { [ -n "$BACKUP_DIR" ] && [ -d "$BACKUP_DIR" ] && log "Replaced files were backed up under $BACKUP_DIR"; } || true
   else
     log "VERIFY FAILED after install — see messages above"
     exit 1
@@ -292,13 +476,32 @@ verify_present() { if [ -f "$1" ]; then return 0; else log "missing  $1"; return
 
 cmd_verify() {
   local fail=0 gp
-  verify_match "$REPO/claude/CLAUDE.md"        "$CLAUDE_DIR/CLAUDE.md"        || fail=1
-  verify_match "$REPO/codex/AGENTS.md"         "$CODEX_DIR/AGENTS.md"         || fail=1
+  if packaged_mode; then
+    # Packaged: corpus surfaces are selection-derived, not repo-identical.
+    # The entry file is user-owned — READ-check the import line, never rewrite.
+    python3 "$REPO/scripts/check-domains.py" >/dev/null 2>&1 && info "domains gate OK" || { log "domains gate FAILED"; fail=1; }
+    verify_present "$CLAUDE_DIR/central/bundle.md" || fail=1
+    if grep -qF '@central/bundle.md' "$CLAUDE_DIR/CLAUDE.md" 2>/dev/null; then
+      info "entry import line present"
+    else
+      log "entry $CLAUDE_DIR/CLAUDE.md lacks '@central/bundle.md' — central corpus is NOT loading"; fail=1
+    fi
+    if grep -qF 'agent-bios:central:start' "$CODEX_DIR/AGENTS.md" 2>/dev/null; then
+      info "codex central region present"
+    else
+      log "codex AGENTS.md central region missing"; fail=1
+    fi
+  else
+    verify_match "$REPO/claude/CLAUDE.md"        "$CLAUDE_DIR/CLAUDE.md"        || fail=1
+    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 "$REPO"/codex/guides/*.md;  do verify_present "$CODEX_DIR/guides/$(basename "$gp")"  || fail=1; done
+  fi
   verify_match "$REPO/scripts/agent-launch.py" "$BIN_DIR/agent-launch"        || fail=1
   verify_match "$REPO/config/agent-launch.toml" "$LAUNCH_DIR/profiles.toml"   || fail=1
   verify_match "$REPO/shell/agent-launch.zsh"  "$LAUNCH_DIR/shell.zsh"        || fail=1
-  for gp in "$REPO"/claude/guides/*.md; do verify_present "$CLAUDE_DIR/guides/$(basename "$gp")" || fail=1; done
-  for gp in "$REPO"/codex/guides/*.md;  do verify_present "$CODEX_DIR/guides/$(basename "$gp")"  || fail=1; done
   python3 - "$CODEX_DIR/agents" <<'PY' && info "agent TOMLs OK" || fail=1
 import sys, pathlib, tomllib
 root = pathlib.Path(sys.argv[1])
@@ -308,6 +511,7 @@ assert not missing, f"missing agent TOMLs in {root}: {sorted(missing)}"
 for p in sorted(root.glob("*.toml")):
     tomllib.loads(p.read_text())
 PY
+  codex_config_additions check || fail=1
   if command -v codex >/dev/null 2>&1 && [ -x "$CODEX_DIR/bin/codex-helm" ]; then
     if "$CODEX_DIR/bin/codex-helm" --dry-run --mode review "probe" >/dev/null 2>&1; then
       info "codex-helm dry-run OK"
@@ -340,6 +544,7 @@ PY
 
 cmd_uninstall() {
   migrate_state
+  codex_config_additions remove || log "warning: could not remove codex config additions"
   if [ -f "$MANIFEST" ]; then
     local f
     while IFS= read -r f; do
@@ -357,7 +562,7 @@ cmd_uninstall() {
     done
   fi
   local d
-  for d in "$CLAUDE_DIR/guides" "$CODEX_DIR/guides" "$CODEX_DIR/agents" "$CODEX_DIR/bin" "$LAUNCH_DIR"; do
+  for d in "$CLAUDE_DIR/guides" "$CLAUDE_DIR/agents" "$CODEX_DIR/guides" "$CODEX_DIR/agents" "$CODEX_DIR/bin" "$LAUNCH_DIR"; do
     [ -d "$d" ] && rmdir "$d" 2>/dev/null && info "removed empty  $d" || true
   done
   remove_zsh_hook
@@ -366,6 +571,49 @@ cmd_uninstall() {
   log "Kept: managed venv + backups under $STATE_DIR (rm -rf \"$STATE_DIR\" to purge)."
 }
 
+cmd_onboard() {
+  log "agent-bios onboarding — pick your domain packages (core + infra always install)"
+  local names=() line i=1 choice sel="" n picks
+  while IFS= read -r line; do names+=("$line"); done \
+    < <(python3 -c "import json;print('\n'.join(sorted(json.load(open('$REPO/config/domains.json'))['domains'])))")
+  [ "${#names[@]}" -ge 1 ] || { log "no domains found in config/domains.json"; exit 1; }
+  if [ "$DOMAINS_SET" = 1 ]; then
+    # Non-interactive path, per this installer's input contract (stdin is
+    # detached at the top of the script): selection arrives as domain names.
+    [ "$DOMAINS_ARG" = none ] && DOMAINS_ARG=""
+    sel="$DOMAINS_ARG"
+  elif ( : </dev/tty ) 2>/dev/null; then
+    for line in "${names[@]}"; do info "$i) $line"; i=$((i+1)); done
+    printf 'Select by number, comma-separated (empty = core+infra only): '
+    read -r choice </dev/tty || choice=""
+    if [ -n "$choice" ]; then
+      # bash 3.2 + set -u: expanding an EMPTY array errors, so split only
+      # when there is input; empty input means core+infra only.
+      IFS=',' read -ra picks <<<"$choice"
+      for n in "${picks[@]}"; do
+        n="${n// /}"; [ -n "$n" ] || continue
+        case "$n" in (*[!0-9]*) log "invalid selection: $n"; exit 2 ;; esac
+        [ "$n" -ge 1 ] && [ "$n" -le "${#names[@]}" ] || { log "selection out of range: $n"; exit 2; }
+        sel="$sel${sel:+,}${names[$((n-1))]}"
+      done
+    fi
+  else
+    log "onboard needs a terminal or an explicit selection — run:"
+    log "  agent-bios onboard --domains a,b   (or --domains none for core+infra only)"
+    exit 2
+  fi
+  DOMAINS_ARG="$sel"; DOMAINS_SET=1
+  log "selection: ${sel:-<core+infra only>}"
+  cmd_install
+  log ""
+  log "Activation canary (proves the bundle loads in a live session)..."
+  if [ "$DRY_RUN" = 1 ]; then info "[dry-run] skip canary probe"; return; fi
+  bash "$REPO/scripts/canary.sh" || {
+    log "ONBOARDING INCOMPLETE: the bundle is installed but not loading — fix the cause above and re-run: agent-bios verify"
+    exit 1
+  }
+}
+
 cmd_status() {
   local version p
   if [ -d "$REPO/.git" ]; then
@@ -401,6 +649,7 @@ usage() {
 agent-bios — deploy the Claude/Codex instruction SSOT into $HOME (by copy).
 
   agent-bios install     deploy into this environment (backs up + verifies)
+  agent-bios onboard     interactive domain selection + packaged install + activation canary
   agent-bios verify      check the deployed state matches the source
   agent-bios status      show what is installed and where
   agent-bios update      git pull + reinstall (clone), or print the npm update line
@@ -408,6 +657,13 @@ agent-bios — deploy the Claude/Codex instruction SSOT into $HOME (by copy).
   agent-bios help
 
 Flags: --dry-run       print actions without changing anything
+       --domains a,b  packaged mode (install/onboard): assemble ONLY the named
+                      domain packages (plus core+infra) instead of the full
+                      corpus; with onboard, 'none' means core+infra only. The
+                      selection persists in the state dir, so later
+                      installs/updates stay packaged until the selection file
+                      is removed. Default (no flag, no saved selection) keeps
+                      today's full-corpus deploy.
        --with a,b     also install the named optional dependencies (install only).
                       Without it, install offers each missing one when the terminal
                       is interactive, and otherwise just prints its install line.
@@ -421,11 +677,15 @@ EOF
 CMD="${1:-help}"
 if [ $# -gt 0 ]; then shift; fi
 WITH=""
+DOMAINS_ARG=""
+DOMAINS_SET=0
 while [ $# -gt 0 ]; do
   case "$1" in
     --dry-run) DRY_RUN=1 ;;
     --with) shift; WITH="${1:-}"; [ -n "$WITH" ] || { log "--with needs a comma-separated capability list"; exit 2; } ;;
     --with=*) WITH="${1#--with=}"; [ -n "$WITH" ] || { log "--with needs a comma-separated capability list"; exit 2; } ;;
+    --domains) shift; DOMAINS_ARG="${1:-}"; DOMAINS_SET=1; [ -n "$DOMAINS_ARG" ] || { log "--domains needs a comma-separated domain list (use onboard for core-only)"; exit 2; } ;;
+    --domains=*) DOMAINS_ARG="${1#--domains=}"; DOMAINS_SET=1; [ -n "$DOMAINS_ARG" ] || { log "--domains needs a comma-separated domain list (use onboard for core-only)"; exit 2; } ;;
     *) log "unknown flag: $1"; exit 2 ;;
   esac
   shift
@@ -433,6 +693,7 @@ done
 
 case "$CMD" in
   install)   cmd_install ;;
+  onboard)   cmd_onboard ;;
   update)    cmd_update ;;
   uninstall) cmd_uninstall ;;
   verify)    if cmd_verify; then log "VERIFY OK"; else log "VERIFY FAILED"; exit 1; fi ;;