diff --git a/references/agents-registry.md b/references/agents-registry.md
old mode 100644
new mode 100755
index 460e031..6b1696c
--- a/references/agents-registry.md
+++ b/references/agents-registry.md
@@ -18,6 +18,8 @@ The registry is designed to grow: custom agents (see Issue #12) are added as new
 | librarian | Vault Health & Quality Assurance | Detect/merge duplicates, fix broken links, audit frontmatter, growth analytics. Full Bash access. | Maintenance, audit, cleanup, health check, duplicate detection | Health reports, fixed links, merged duplicates, consistency reports | active |
 | transcriber | Audio & Meeting Intelligence | Process transcriptions into structured notes, extract action items, speaker detection | Audio recordings, transcriptions, meeting notes, lecture/podcast processing | Structured meeting/lecture notes in `00-Inbox/` with action items, decisions, topics | active |
 | postman | Email & Calendar Intelligence | Read/archive/delete email (Gmail via `gws`, Hey.com via `hey`), search emails, read/create/update calendar events, draft and send replies. Uses Google Workspace CLI (`gws`) and/or Hey CLI (`hey`) via Bash, with MCP as read-only fallback. | Email triage, calendar queries, deadline tracking, meeting prep, VIP filtering | Email summaries saved as notes in `00-Inbox/`, calendar events created, deadline reports | active |
+<!-- MBIFC:CUSTOM_AGENTS_START -->
+<!-- MBIFC:CUSTOM_AGENTS_END -->
 
 ---
 
diff --git a/references/agents.md b/references/agents.md
old mode 100644
new mode 100755
index 5d7a138..30b473e
--- a/references/agents.md
+++ b/references/agents.md
@@ -155,6 +155,9 @@ Custom agents are created by the Architect and live in `.claude/agents/` alongsi
 
 For the definitive list of all agents (core + custom) with capabilities, inputs, outputs, and status, see `.claude/references/agents-registry.md`.
 
+<!-- MBIFC:CUSTOM_AGENTS_START -->
+<!-- MBIFC:CUSTOM_AGENTS_END -->
+
 ### How Custom Agents Coordinate
 
 Custom agents participate in the same orchestration protocol as core agents:
diff --git a/scripts/launchme.sh b/scripts/launchme.sh
index 9bf60cb..64ab4c5 100755
--- a/scripts/launchme.sh
+++ b/scripts/launchme.sh
@@ -7,44 +7,25 @@
 #   cd /path/to/your-vault/My-Brain-Is-Full-Crew
 #   bash scripts/launchme.sh
 #
-# It copies agents and references into your vault's .claude/ directory.
+# It copies agents, skills, references, hooks, and settings into the vault's
+# .claude/ directory.
 # =============================================================================
 
 set -eo pipefail
 
-# ── Colors ──────────────────────────────────────────────────────────────────
-if [[ -t 1 ]]; then
-  GREEN='\033[0;32m'; CYAN='\033[0;36m'; YELLOW='\033[1;33m'
-  RED='\033[0;31m'; BOLD='\033[1m'; DIM='\033[2m'; NC='\033[0m'
-else
-  GREEN=''; CYAN=''; YELLOW=''; RED=''; BOLD=''; DIM=''; NC=''
-fi
-
-info()    { echo -e "   ${CYAN}>${NC} $*"; }
-success() { echo -e "   ${GREEN}✓${NC} $*"; }
-warn()    { echo -e "   ${YELLOW}!${NC} $*"; }
-die()     { echo -e "\n   ${RED}Error: $*${NC}\n" >&2; exit 1; }
-
-# ── Find paths ──────────────────────────────────────────────────────────────
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-REPO_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"
-VAULT_DIR="$(cd "$REPO_DIR/.." && pwd)"
+# shellcheck source=scripts/lib.sh
+source "$SCRIPT_DIR/lib.sh"
 
-# Sanity checks
-[[ -d "$REPO_DIR/agents" ]] || die "Can't find agents/ in $REPO_DIR — are you running this from the repo?"
-[[ -d "$REPO_DIR/references" ]] || die "Can't find references/ in $REPO_DIR"
+resolve_paths "${BASH_SOURCE[0]}"
 
-# ── Banner ──────────────────────────────────────────────────────────────────
-echo ""
-echo -e "${BOLD}╔══════════════════════════════════════════╗${NC}"
-echo -e "${BOLD}║  My Brain Is Full - Crew :: Setup        ║${NC}"
-echo -e "${BOLD}╚══════════════════════════════════════════╝${NC}"
-echo ""
+# ── Banner ────────────────────────────────────────────────────────────────────
+print_banner "Setup        "
 echo -e "   Repo:   ${BOLD}${REPO_DIR}${NC}"
 echo -e "   Vault:  ${BOLD}${VAULT_DIR}${NC}"
 echo ""
 
-# ── Confirm vault location ─────────────────────────────────────────────────
+# ── Confirm vault location ────────────────────────────────────────────────────
 echo -e "${BOLD}Is this your Obsidian vault folder?${NC}"
 echo -e "   ${DIM}${VAULT_DIR}${NC}"
 echo ""
@@ -55,107 +36,65 @@ if ! read -r -p "   > " CONFIRM 2>/dev/null; then CONFIRM=""; fi
 if [[ "$CONFIRM" =~ ^[Nn]$ ]]; then
   echo ""
   echo -e "${BOLD}Enter the full path to your Obsidian vault:${NC}"
-  if ! read -r -p "   > " VAULT_DIR 2>/dev/null; then die "Cannot read input — are you running in a non-interactive shell?"; fi
+  if ! read -r -p "   > " VAULT_DIR 2>/dev/null; then
+    die "Cannot read input — are you running in a non-interactive shell?"
+  fi
   VAULT_DIR="${VAULT_DIR/#\~/$HOME}"
   [[ -d "$VAULT_DIR" ]] || die "Directory not found: $VAULT_DIR"
 fi
 
-# ── Check for existing installation ───────────────────────────────────────
-echo ""
+# ── Check for existing installation ──────────────────────────────────────────
 EXISTING=0
-if [[ -d "$VAULT_DIR/.claude" ]]; then EXISTING=1; fi
-if [[ -f "$VAULT_DIR/CLAUDE.md" ]]; then EXISTING=1; fi
+[[ -d "$VAULT_DIR/.claude" ]] && EXISTING=1
+[[ -f "$VAULT_DIR/CLAUDE.md" ]] && EXISTING=1
 
 if [[ $EXISTING -eq 1 ]]; then
   warn "An existing installation was detected:"
   [[ -d "$VAULT_DIR/.claude" ]] && warn "  .claude/ directory exists"
   [[ -f "$VAULT_DIR/CLAUDE.md" ]] && warn "  CLAUDE.md exists"
   echo ""
-  echo -e "   ${BOLD}The installer needs to overwrite these files.${NC}"
-  echo -e "   ${DIM}Custom agents in .claude/agents/ will NOT be deleted.${NC}"
+  echo -e "   ${BOLD}The installer will overwrite core files. Custom agents are never deleted.${NC}"
   echo -e "   ${DIM}Your vault notes are never touched.${NC}"
   echo ""
-  echo -e "   ${BOLD}c)${NC} Continue (overwrite core files, keep custom agents)"
+  echo -e "   ${BOLD}c)${NC} Continue"
   echo -e "   ${BOLD}q)${NC} Quit"
-  if ! read -r -p "   > " OVERWRITE_ANSWER 2>/dev/null; then OVERWRITE_ANSWER=""; fi
-  if [[ ! "$OVERWRITE_ANSWER" =~ ^[Cc]$ ]]; then
-    echo ""
-    info "Installation cancelled."
-    echo ""
-    exit 0
+  if ! read -r -p "   > " ANSWER 2>/dev/null; then ANSWER=""; fi
+  if [[ ! "$ANSWER" =~ ^[Cc]$ ]]; then
+    echo ""; info "Installation cancelled."; echo ""; exit 0
   fi
 fi
 
-# ── Deprecate stale core agents on reinstall ─────────────────────────────
 echo ""
-mkdir -p "$VAULT_DIR/.claude/agents"
-OLD_MANIFEST="$VAULT_DIR/.claude/agents/.core-manifest"
-if [[ $EXISTING -eq 1 && -f "$OLD_MANIFEST" ]]; then
-  while IFS= read -r old_name; do
-    [[ -z "$old_name" ]] && continue
-    [[ -f "$REPO_DIR/agents/$old_name" ]] && continue
-    vault_file="$VAULT_DIR/.claude/agents/$old_name"
-    [[ -f "$vault_file" ]] || continue
-    deprecated_name="${old_name%.md}-DEPRECATED.md"
-    mkdir -p "$VAULT_DIR/.claude/deprecated"
-    [[ -f "$VAULT_DIR/.claude/deprecated/$deprecated_name" ]] && continue
-    mv "$vault_file" "$VAULT_DIR/.claude/deprecated/$deprecated_name"
-    { echo "########"; echo "DEPRECATED DO NOT USE"; echo "########"; echo ""; cat "$VAULT_DIR/.claude/deprecated/$deprecated_name"; } > "$VAULT_DIR/.claude/deprecated/$deprecated_name.tmp"
-    mv "$VAULT_DIR/.claude/deprecated/$deprecated_name.tmp" "$VAULT_DIR/.claude/deprecated/$deprecated_name"
-    warn "Deprecated stale agent: $old_name -> deprecated/$deprecated_name"
-  done < "$OLD_MANIFEST"
+
+# ── Migrate legacy manifests (if any) ────────────────────────────────────────
+manifest_migrate
+
+# ── Deprecate agents/refs removed from repo (reinstall only) ─────────────────
+DEP_COUNT=0
+if [[ $EXISTING -eq 1 ]]; then
+  DEP_COUNT=$(deprecate_removed "agents"     "$REPO_DIR/agents"     "$VAULT_DIR/.claude/agents")
+  DEP_COUNT=$((DEP_COUNT + $(deprecate_removed "references" "$REPO_DIR/references" "$VAULT_DIR/.claude/references")))
 fi
 
-# ── Copy agents ─────────────────────────────────────────────────────────────
-info "Creating .claude/agents/ in vault..."
-
-AGENT_COUNT=0
-: > "$VAULT_DIR/.claude/agents/.core-manifest"
-for agent in "$REPO_DIR/agents/"*.md; do
-  cp "$agent" "$VAULT_DIR/.claude/agents/"
-  basename "$agent" >> "$VAULT_DIR/.claude/agents/.core-manifest"
-  AGENT_COUNT=$((AGENT_COUNT + 1))
-done
-success "Copied $AGENT_COUNT agents"
-
-# ── Create Meta/states/ for agent post-its ──────────────────────────────────
+# ── Ensure vault support dirs ─────────────────────────────────────────────────
 mkdir -p "$VAULT_DIR/Meta/states"
-info "Created Meta/states/ (agent post-it directory)"
 
-# ── Copy references ─────────────────────────────────────────────────────────
-info "Creating .claude/references/ in vault..."
-mkdir -p "$VAULT_DIR/.claude/references"
-# User-mutable references (modified by Architect when creating custom agents)
-USER_MUTABLE_REFS="agents-registry.md agents.md"
+# ── Install components ────────────────────────────────────────────────────────
+info "Installing agents..."
+AGENT_COUNT=$(install_agents "$REPO_DIR/agents" "$VAULT_DIR/.claude/agents")
+success "Agents: $AGENT_COUNT installed/updated"
 
-: > "$VAULT_DIR/.claude/references/.core-manifest"
-for ref in "$REPO_DIR/references/"*.md; do
-  ref_name="$(basename "$ref")"
-  # On reinstall, preserve user-mutable reference files
-  if [[ $EXISTING -eq 1 && -f "$VAULT_DIR/.claude/references/$ref_name" ]]; then
-    if [[ " $USER_MUTABLE_REFS " == *" $ref_name "* ]]; then
-      warn "Preserving existing $ref_name (run updateme.sh to merge upstream changes)"
-      echo "$ref_name" >> "$VAULT_DIR/.claude/references/.core-manifest"
-      continue
-    fi
-  fi
-  cp "$ref" "$VAULT_DIR/.claude/references/"
-  echo "$ref_name" >> "$VAULT_DIR/.claude/references/.core-manifest"
-done
-success "Copied references"
+info "Installing references..."
+REF_COUNT=$(install_refs "$REPO_DIR/references" "$VAULT_DIR/.claude/references")
+success "References: $REF_COUNT installed/updated"
 
-# ── Copy skills ──────────────────────────────────────────────────────────────
-SKILL_COUNT=0
-if [[ -d "$REPO_DIR/skills" ]]; then
-  for skill_dir in "$REPO_DIR/skills/"*/; do
-    [[ -f "$skill_dir/SKILL.md" ]] || continue
-    skill_name="$(basename "$skill_dir")"
-    mkdir -p "$VAULT_DIR/.claude/skills/$skill_name"
-    cp "$skill_dir"SKILL.md "$VAULT_DIR/.claude/skills/$skill_name/"
-    SKILL_COUNT=$((SKILL_COUNT + 1))
-  done
-  success "Copied $SKILL_COUNT skills"
-fi
+info "Installing skills..."
+SKILL_COUNT=$(install_skills "$REPO_DIR/skills" "$VAULT_DIR/.claude/skills")
+success "Skills: $SKILL_COUNT installed/updated"
+
+info "Installing hooks..."
+HOOK_COUNT=$(install_hooks "$REPO_DIR/hooks" "$VAULT_DIR/.claude/hooks")
+success "Hooks: $HOOK_COUNT installed/updated"
 
 # ── Deprecate stale orchestra scripts on reinstall ──────────────────────────
 OLD_ORCH_MANIFEST="$VAULT_DIR/Meta/scripts/.core-manifest"
@@ -193,31 +132,11 @@ if [[ -f "$REPO_DIR/CLAUDE.md" ]]; then
   success "Copied CLAUDE.md"
 fi
 
-# ── Copy hooks ───────────────────────────────────────────────────────────────
-HOOK_COUNT=0
-if [[ -d "$REPO_DIR/hooks" ]]; then
-  mkdir -p "$VAULT_DIR/.claude/hooks"
-  for hook in "$REPO_DIR/hooks/"*.sh; do
-    [[ -f "$hook" ]] || continue
-    cp "$hook" "$VAULT_DIR/.claude/hooks/"
-    chmod +x "$VAULT_DIR/.claude/hooks/$(basename "$hook")"
-    HOOK_COUNT=$((HOOK_COUNT + 1))
-  done
-  success "Copied $HOOK_COUNT hooks"
-fi
 
-# ── Copy settings.json ───────────────────────────────────────────────────────
-if [[ -f "$REPO_DIR/settings.json" ]]; then
-  if [[ -f "$VAULT_DIR/.claude/settings.json" ]]; then
-    warn ".claude/settings.json already exists — skipping (won't overwrite)"
-  else
-    mkdir -p "$VAULT_DIR/.claude"
-    cp "$REPO_DIR/settings.json" "$VAULT_DIR/.claude/settings.json"
-    success "Copied settings.json (hooks configuration)"
-  fi
-fi
+install_settings "$REPO_DIR/settings.json" "$VAULT_DIR/.claude"
+install_claude_md "$REPO_DIR/CLAUDE.md" "$VAULT_DIR"
 
-# ── MCP servers (Gmail + Calendar) ──────────────────────────────────────────
+# ── MCP servers (Gmail + Calendar) ───────────────────────────────────────────
 echo ""
 echo -e "${BOLD}Do you use Gmail, Hey.com, or Google Calendar?${NC}"
 echo -e "   ${DIM}The Postman agent can read your inbox and calendar.${NC}"
@@ -240,24 +159,26 @@ else
   info "Skipped MCP setup"
 fi
 
-# ── Done ────────────────────────────────────────────────────────────────────
+# ── Done ──────────────────────────────────────────────────────────────────────
 echo ""
 echo -e "${GREEN}${BOLD}   Setup complete!${NC}"
 echo ""
-echo -e "   Your vault is ready. Here's what was installed:"
-echo ""
 echo -e "   ${VAULT_DIR}/"
 echo -e "   ├── .claude/"
-echo -e "   │   ├── agents/          ${DIM}← ${AGENT_COUNT} crew agents${NC}"
-echo -e "   │   ├── skills/          ${DIM}← ${SKILL_COUNT:-0} crew skills (Desktop/Cowork)${NC}"
-echo -e "   │   ├── hooks/           ${DIM}← ${HOOK_COUNT:-0} hooks${NC}"
+echo -e "   │   ├── agents/          ${DIM}← agents${NC}"
+echo -e "   │   ├── skills/          ${DIM}← skills${NC}"
+echo -e "   │   ├── hooks/           ${DIM}← hooks${NC}"
 echo -e "   │   ├── settings.json    ${DIM}← hooks configuration${NC}"
 echo -e "   │   └── references/      ${DIM}← shared docs${NC}"
 echo -e "   ├── Meta/"
 echo -e "   │   └── scripts/         ${DIM}← ${ORCH_COUNT:-0} orchestra scripts${NC}"
 echo -e "   ├── CLAUDE.md            ${DIM}← project instructions${NC}"
 if [[ "$MCP_ANSWER" =~ ^[Yy]$ ]]; then
-echo -e "   └── .mcp.json            ${DIM}← Gmail + Calendar${NC}"
+  echo -e "   └── .mcp.json            ${DIM}← Gmail + Calendar${NC}"
+fi
+if [[ $DEP_COUNT -gt 0 ]]; then
+  echo ""
+  warn "$DEP_COUNT file(s) were deprecated (moved to .claude/deprecated/)"
 fi
 echo ""
 echo -e "   ${BOLD}Next steps:${NC}"
diff --git a/scripts/lib.sh b/scripts/lib.sh
new file mode 100755
index 0000000..5f504aa
--- /dev/null
+++ b/scripts/lib.sh
@@ -0,0 +1,419 @@
+#!/usr/bin/env bash
+# =============================================================================
+# My Brain Is Full - Crew :: Shared library
+# Sourced by launchme.sh and updateme.sh — do NOT execute directly.
+# =============================================================================
+
+# ── Colors ────────────────────────────────────────────────────────────────────
+if [[ -t 1 ]]; then
+  GREEN='\033[0;32m'; CYAN='\033[0;36m'; YELLOW='\033[1;33m'
+  RED='\033[0;31m'; BOLD='\033[1m'; DIM='\033[2m'; NC='\033[0m'
+else
+  GREEN=''; CYAN=''; YELLOW=''; RED=''; BOLD=''; DIM=''; NC=''
+fi
+
+# ── Logging ───────────────────────────────────────────────────────────────────
+# Everything is on stderr to keep stdout clean for machine-readable output in updateme.sh.
+info()    { echo -e "   ${CYAN}>${NC} $*" >&2; }
+success() { echo -e "   ${GREEN}✓${NC} $*" >&2; }
+warn()    { echo -e "   ${YELLOW}!${NC} $*" >&2; }
+die()     { echo -e "\n   ${RED}Error: $*${NC}\n" >&2; exit 1; }
+
+# ── Path resolution ───────────────────────────────────────────────────────────
+# Sets SCRIPT_DIR, REPO_DIR, VAULT_DIR globals.
+# Usage: resolve_paths "${BASH_SOURCE[0]}"
+resolve_paths() {
+  SCRIPT_DIR="$(cd "$(dirname "$1")" && pwd)"
+  REPO_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"
+  VAULT_DIR="$(cd "$REPO_DIR/.." && pwd)"
+  [[ -d "$REPO_DIR/agents"     ]] || die "Can't find agents/ in $REPO_DIR — are you running this from the repo?"
+  [[ -d "$REPO_DIR/references" ]] || die "Can't find references/ in $REPO_DIR"
+}
+
+# ── Change tracking ───────────────────────────────────────────────────────────
+# Set by copy_if_changed and merge_marked_file after every call.
+_LAST_CHANGED=0
+
+# Controls per-file logging in install_* functions.
+# Set VERBOSE_COPY=1 in the caller for per-file change output (used by updateme.sh).
+VERBOSE_COPY=0
+
+# ── copy_if_changed <src> <dst> ───────────────────────────────────────────────
+# Copies src to dst only when they differ or dst doesn't exist.
+# Sets _LAST_CHANGED=1 if a copy was made, 0 otherwise.
+copy_if_changed() {
+  local src="$1" dst="$2"
+  _LAST_CHANGED=0
+  if ! diff -q "$src" "$dst" >/dev/null 2>&1; then
+    mkdir -p "$(dirname "$dst")"
+    cp "$src" "$dst"
+    _LAST_CHANGED=1
+  fi
+}
+
+# ── _insert_after_start_marker <dst> <content> ───────────────────────────────
+# Inserts <content> immediately after the MBIFC:CUSTOM_AGENTS_START line in dst.
+# dst must already exist and contain the marker.
+_insert_after_start_marker() {
+  local dst="$1" content="$2"
+  [[ -z "$content" ]] && return 0
+
+  local start_line
+  start_line=$(grep -n '<!-- MBIFC:CUSTOM_AGENTS_START -->' "$dst" | head -1 | cut -d: -f1)
+  [[ -z "$start_line" ]] && return 0
+
+  local saved_file tmpfile
+  saved_file="$(mktemp)"
+  tmpfile="$(mktemp)"
+  # printf '%s\n' ensures a trailing newline so the next file line starts cleanly.
+  # bash $() strips trailing newlines, so content never has one already.
+  printf '%s\n' "$content" > "$saved_file"
+
+  {
+    head -n "$start_line" "$dst"
+    cat "$saved_file"
+    tail -n +"$((start_line + 1))" "$dst"
+  } > "$tmpfile"
+
+  mv "$tmpfile" "$dst"
+  rm -f "$saved_file"
+}
+
+# ── merge_marked_file <src> <dst> ─────────────────────────────────────────────
+# Copies src to dst, preserving content between <!-- MBIFC:CUSTOM_AGENTS_START -->
+# and <!-- MBIFC:CUSTOM_AGENTS_END --> markers from the existing dst.
+#
+# Handles three cases:
+#   1. dst doesn't exist              → plain copy
+#   2. Both src and dst have markers  → marker-based merge (primary path)
+#   3. src has markers, dst doesn't   → migration: extracts legacy custom rows
+#                                       from pre-marker installations
+#
+# Sets _LAST_CHANGED=1 if dst was written.
+merge_marked_file() {
+  local src="$1" dst="$2"
+  _LAST_CHANGED=0
+
+  # Case 1: dst doesn't exist yet
+  if [[ ! -f "$dst" ]]; then
+    mkdir -p "$(dirname "$dst")"
+    cp "$src" "$dst"
+    _LAST_CHANGED=1
+    return 0
+  fi
+
+  local src_has_markers=0 dst_has_markers=0
+  grep -q '<!-- MBIFC:CUSTOM_AGENTS_START -->' "$src" 2>/dev/null && src_has_markers=1
+  grep -q '<!-- MBIFC:CUSTOM_AGENTS_START -->' "$dst" 2>/dev/null && dst_has_markers=1
+
+  # src has no markers → standard copy-if-changed
+  if [[ $src_has_markers -eq 0 ]]; then
+    copy_if_changed "$src" "$dst"
+    return 0
+  fi
+
+  # Case 3: src has markers, dst doesn't → migration from old format
+  if [[ $dst_has_markers -eq 0 ]]; then
+    local custom_rows=""
+    local CORE_NAMES="architect scribe sorter seeker connector librarian transcriber postman"
+    while IFS= read -r row; do
+      local aname
+      aname=$(printf '%s' "$row" | awk -F'|' '{gsub(/^[[:space:]]+|[[:space:]]+$/, "", $2); print $2}')
+      if [[ -n "$aname" ]] && ! echo " $CORE_NAMES " | grep -qw " $aname "; then
+        custom_rows="${custom_rows}${row}"$'\n'
+      fi
+    done < <(grep "^|" "$dst" 2>/dev/null \
+               | grep -v "^|[[:space:]]*Name[[:space:]]*|" \
+               | grep -v "^|[-:[:space:]]*|")
+
+    cp "$src" "$dst"
+    _LAST_CHANGED=1
+
+    if [[ -n "$custom_rows" ]]; then
+      _insert_after_start_marker "$dst" "$custom_rows"
+      warn "Migrated legacy custom agents in $(basename "$dst") to MBIFC marker format"
+    fi
+    return 0
+  fi
+
+  # Case 2: both have markers → extract saved content, build merged result,
+  # only update dst if the result actually differs (ensures idempotency).
+  local saved_content
+  saved_content=$(awk \
+    '/<!-- MBIFC:CUSTOM_AGENTS_START -->/{f=1; next}
+     /<!-- MBIFC:CUSTOM_AGENTS_END -->/{f=0}
+     f{print}' \
+    "$dst")
+
+  local merged; merged="$(mktemp)"
+  cp "$src" "$merged"
+  [[ -n "$saved_content" ]] && _insert_after_start_marker "$merged" "$saved_content"
+
+  if ! diff -q "$merged" "$dst" >/dev/null 2>&1; then
+    cp "$merged" "$dst"
+    _LAST_CHANGED=1
+    [[ $VERBOSE_COPY -eq 1 && -n "$saved_content" ]] && info "Merged: $(basename "$src") (custom content preserved)"
+  fi
+  rm -f "$merged"
+}
+
+# ── Manifest helpers ──────────────────────────────────────────────────────────
+# Single unified manifest at $VAULT_DIR/.claude/.mbifc-manifest
+# Format: INI-style with [section] headers, one entry per line.
+
+manifest_read() {
+  local section="$1"
+  local file="$VAULT_DIR/.claude/.mbifc-manifest"
+  [[ -f "$file" ]] || return 0
+  awk -v sec="[$section]" '
+    $0 == sec         { found=1; next }
+    found && /^\[[a-zA-Z0-9_-]+\]$/ { exit }
+    found && NF > 0   { print }
+  ' "$file"
+}
+
+manifest_write() {
+  local section="$1"; shift
+  local entries=("$@")
+  local file="$VAULT_DIR/.claude/.mbifc-manifest"
+  mkdir -p "$(dirname "$file")"
+  local tmpfile; tmpfile="$(mktemp)"
+  local in_section=0 section_written=0
+
+  if [[ -f "$file" ]]; then
+    while IFS= read -r line || [[ -n "$line" ]]; do
+      if [[ "$line" == "[$section]" ]]; then
+        in_section=1; continue
+      fi
+      if [[ "$line" =~ ^\[[a-zA-Z0-9_-]+\]$ ]] && [[ $in_section -eq 1 ]]; then
+        in_section=0
+        # Write the replacement section, then the next section header
+        { printf '[%s]\n' "$section"
+          for e in "${entries[@]}"; do [[ -n "$e" ]] && printf '%s\n' "$e"; done
+          printf '\n'
+        } >> "$tmpfile"
+        section_written=1
+      fi
+      [[ $in_section -eq 0 ]] && printf '%s\n' "$line" >> "$tmpfile"
+    done < "$file"
+  fi
+
+  # Section wasn't encountered, or was at end of file with no following section
+  if [[ $section_written -eq 0 ]]; then
+    { printf '[%s]\n' "$section"
+      for e in "${entries[@]}"; do [[ -n "$e" ]] && printf '%s\n' "$e"; done
+      printf '\n'
+    } >> "$tmpfile"
+  fi
+
+  mv "$tmpfile" "$file"
+}
+
+manifest_remove() {
+  local section="$1" name="$2"
+  local file="$VAULT_DIR/.claude/.mbifc-manifest"
+  [[ -f "$file" ]] || return 0
+  local tmpfile; tmpfile="$(mktemp)"
+  local in_section=0
+  while IFS= read -r line || [[ -n "$line" ]]; do
+    if [[ "$line" == "[$section]" ]]; then in_section=1; printf '%s\n' "$line" >> "$tmpfile"; continue; fi
+    if [[ "$line" =~ ^\[[a-zA-Z0-9_-]+\]$ ]]; then in_section=0; fi
+    if [[ $in_section -eq 1 && "$line" == "$name" ]]; then continue; fi
+    printf '%s\n' "$line" >> "$tmpfile"
+  done < "$file"
+  mv "$tmpfile" "$file"
+}
+
+# Converts legacy per-directory .core-manifest files to the unified format.
+# Runs only when legacy files are present; idempotent thereafter.
+manifest_migrate() {
+  local agents_mf="$VAULT_DIR/.claude/agents/.core-manifest"
+  local refs_mf="$VAULT_DIR/.claude/references/.core-manifest"
+  [[ -f "$agents_mf" ]] || [[ -f "$refs_mf" ]] || return 0
+
+  warn "Migrating legacy manifests to unified .mbifc-manifest..."
+
+  if [[ -f "$agents_mf" ]]; then
+    local entries=()
+    while IFS= read -r line || [[ -n "$line" ]]; do [[ -n "$line" ]] && entries+=("$line"); done < "$agents_mf"
+    manifest_write "agents" "${entries[@]}"
+    rm "$agents_mf"
+  fi
+
+  if [[ -f "$refs_mf" ]]; then
+    local entries=()
+    while IFS= read -r line || [[ -n "$line" ]]; do [[ -n "$line" ]] && entries+=("$line"); done < "$refs_mf"
+    manifest_write "references" "${entries[@]}"
+    rm "$refs_mf"
+  fi
+
+  success "Manifest migrated to .claude/.mbifc-manifest"
+}
+
+# ── Deprecation ───────────────────────────────────────────────────────────────
+
+# deprecate_removed <section> <src_dir> <dst_dir>
+# Moves files listed in the manifest for <section> that no longer exist in
+# <src_dir> to $VAULT_DIR/.claude/deprecated/, prepending a DEPRECATED header.
+# Prints the count of deprecated files to stdout.
+deprecate_removed() {
+  local section="$1" src_dir="$2" dst_dir="$3"
+  local count=0
+
+  while IFS= read -r name; do
+    [[ -z "$name" ]] && continue
+    [[ -f "$src_dir/$name" ]] && continue        # still in repo — keep it
+    local vault_file="$dst_dir/$name"
+    [[ -f "$vault_file" ]] || continue            # not present — skip
+    [[ "$name" == *"-DEPRECATED"* ]] && continue  # already deprecated
+
+    local dep_name="${name%.md}-DEPRECATED.md"
+    local dep_dir="$VAULT_DIR/.claude/deprecated"
+    mkdir -p "$dep_dir"
+    [[ -f "$dep_dir/$dep_name" ]] && continue     # already done in a prior run
+
+    mv "$vault_file" "$dep_dir/$dep_name"
+    { printf '########\nDEPRECATED DO NOT USE\n########\n\n'
+      cat "$dep_dir/$dep_name"
+    } > "$dep_dir/$dep_name.tmp"
+    mv "$dep_dir/$dep_name.tmp" "$dep_dir/$dep_name"
+
+    manifest_remove "$section" "$name"
+    warn "Deprecated: $name → .claude/deprecated/$dep_name"
+    count=$((count + 1))
+  done < <(manifest_read "$section")
+
+  printf '%d' "$count"
+}
+
+# ── Component installers ──────────────────────────────────────────────────────
+# Each function installs one component type and prints the changed-file count
+# to stdout. All respect VERBOSE_COPY for per-file logging.
+#
+# USER_MUTABLE_REFS: space-separated list of reference filenames that may
+# contain user-added content between MBIFC markers. These use merge_marked_file
+# instead of copy_if_changed.
+USER_MUTABLE_REFS="agents-registry.md agents.md"
+
+install_agents() {
+  local src_dir="$1" dst_dir="$2"
+  local count=0 manifest=()
+  mkdir -p "$dst_dir"
+  for src in "$src_dir/"*.md; do
+    [[ -f "$src" ]] || continue
+    local name; name="$(basename "$src")"
+    manifest+=("$name")
+    copy_if_changed "$src" "$dst_dir/$name"
+    if [[ $_LAST_CHANGED -eq 1 ]]; then
+      [[ $VERBOSE_COPY -eq 1 ]] && info "Updated agent: $name"
+      count=$((count + 1))
+    fi
+  done
+  manifest_write "agents" "${manifest[@]}"
+  printf '%d' "$count"
+}
+
+install_refs() {
+  local src_dir="$1" dst_dir="$2"
+  local count=0 manifest=()
+  mkdir -p "$dst_dir"
+  for src in "$src_dir/"*.md; do
+    [[ -f "$src" ]] || continue
+    local name; name="$(basename "$src")"
+    local dst="$dst_dir/$name"
+    manifest+=("$name")
+    if [[ " $USER_MUTABLE_REFS " == *" $name "* ]]; then
+      merge_marked_file "$src" "$dst"
+    else
+      copy_if_changed "$src" "$dst"
+    fi
+    if [[ $_LAST_CHANGED -eq 1 ]]; then
+      [[ $VERBOSE_COPY -eq 1 ]] && info "Updated reference: $name"
+      count=$((count + 1))
+    fi
+  done
+  manifest_write "references" "${manifest[@]}"
+  printf '%d' "$count"
+}
+
+install_skills() {
+  local src_dir="$1" dst_dir="$2"
+  local count=0 manifest=()
+  [[ -d "$src_dir" ]] || { printf '0'; return 0; }
+  for skill_src in "$src_dir/"*/; do
+    [[ -f "${skill_src}SKILL.md" ]] || continue
+    local name; name="$(basename "$skill_src")"
+    manifest+=("$name")
+    mkdir -p "$dst_dir/$name"
+    copy_if_changed "${skill_src}SKILL.md" "$dst_dir/$name/SKILL.md"
+    if [[ $_LAST_CHANGED -eq 1 ]]; then
+      [[ $VERBOSE_COPY -eq 1 ]] && info "Updated skill: $name"
+      count=$((count + 1))
+    fi
+  done
+  manifest_write "skills" "${manifest[@]}"
+  printf '%d' "$count"
+}
+
+install_hooks() {
+  local src_dir="$1" dst_dir="$2"
+  local count=0 manifest=()
+  [[ -d "$src_dir" ]] || { printf '0'; return 0; }
+  mkdir -p "$dst_dir"
+  for src in "$src_dir/"*.sh; do
+    [[ -f "$src" ]] || continue
+    local name; name="$(basename "$src")"
+    local dst="$dst_dir/$name"
+    manifest+=("$name")
+    copy_if_changed "$src" "$dst"
+    if [[ $_LAST_CHANGED -eq 1 ]]; then
+      chmod +x "$dst"
+      [[ $VERBOSE_COPY -eq 1 ]] && info "Updated hook: $name"
+      count=$((count + 1))
+    fi
+  done
+  manifest_write "hooks" "${manifest[@]}"
+  printf '%d' "$count"
+}
+
+# install_settings <src_json> <dst_dir>
+# Always syncs settings.json from src to dst when they differ.
+# Creates a .bak of the previous version so users can recover custom entries.
+# Sets _LAST_CHANGED.
+install_settings() {
+  local src="$1" dst_dir="$2"
+  local dst="$dst_dir/settings.json"
+  _LAST_CHANGED=0
+  [[ -f "$src" ]] || return 0
+  mkdir -p "$dst_dir"
+  if [[ ! -f "$dst" ]]; then
+    cp "$src" "$dst"
+    _LAST_CHANGED=1
+  elif ! diff -q "$src" "$dst" >/dev/null 2>&1; then
+    cp "$dst" "${dst}.bak"
+    cp "$src" "$dst"
+    _LAST_CHANGED=1
+    [[ $VERBOSE_COPY -eq 1 ]] && info "Updated settings.json (previous version saved as settings.json.bak)"
+    [[ $VERBOSE_COPY -eq 1 ]] && info "For custom hooks, use settings.local.json instead"
+  fi
+}
+
+# install_claude_md <src> <vault_dir>
+# Sets _LAST_CHANGED.
+install_claude_md() {
+  local src="$1" vault_dir="$2"
+  [[ -f "$src" ]] || return 0
+  copy_if_changed "$src" "$vault_dir/CLAUDE.md"
+  [[ $_LAST_CHANGED -eq 1 && $VERBOSE_COPY -eq 1 ]] && info "Updated CLAUDE.md"
+}
+
+# ── UI helpers ────────────────────────────────────────────────────────────────
+
+print_banner() {
+  local title="$1"
+  echo ""
+  echo -e "${BOLD}╔══════════════════════════════════════════╗${NC}"
+  echo -e "${BOLD}║  My Brain Is Full - Crew :: ${title}${NC}"
+  echo -e "${BOLD}╚══════════════════════════════════════════╝${NC}"
+  echo ""
+}
diff --git a/scripts/updateme.sh b/scripts/updateme.sh
index edb902e..49b8426 100755
--- a/scripts/updateme.sh
+++ b/scripts/updateme.sh
@@ -2,8 +2,7 @@
 # =============================================================================
 # My Brain Is Full - Crew :: Updater
 # =============================================================================
-# After pulling new changes from the repo, run this to update the agents
-# in your vault:
+# After pulling new changes from the repo, run this to update the crew:
 #
 #   cd /path/to/your-vault/My-Brain-Is-Full-Crew
 #   git pull
@@ -13,316 +12,67 @@
 
 set -eo pipefail
 
-# ── Colors ──────────────────────────────────────────────────────────────────
-if [[ -t 1 ]]; then
-  GREEN='\033[0;32m'; CYAN='\033[0;36m'; YELLOW='\033[1;33m'
-  RED='\033[0;31m'; BOLD='\033[1m'; DIM='\033[2m'; NC='\033[0m'
-else
-  GREEN=''; CYAN=''; YELLOW=''; RED=''; BOLD=''; DIM=''; NC=''
-fi
-
-info()    { echo -e "   ${CYAN}>${NC} $*"; }
-success() { echo -e "   ${GREEN}✓${NC} $*"; }
-warn()    { echo -e "   ${YELLOW}!${NC} $*"; }
-die()     { echo -e "\n   ${RED}Error: $*${NC}\n" >&2; exit 1; }
-
-# ── Find paths ──────────────────────────────────────────────────────────────
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-REPO_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"
-VAULT_DIR="$(cd "$REPO_DIR/.." && pwd)"
+# shellcheck source=scripts/lib.sh
+source "$SCRIPT_DIR/lib.sh"
 
-[[ -d "$REPO_DIR/agents" ]] || die "Can't find agents/ — are you running this from the repo?"
+resolve_paths "${BASH_SOURCE[0]}"
 
-# ── Check vault has been set up ─────────────────────────────────────────────
-if [[ ! -d "$VAULT_DIR/.claude/agents" ]]; then
-  die "No .claude/agents/ found in $VAULT_DIR — run launchme.sh first"
-fi
+# ── Banner ────────────────────────────────────────────────────────────────────
+print_banner "Update       "
 
-# ── Banner ──────────────────────────────────────────────────────────────────
-echo ""
-echo -e "${BOLD}╔══════════════════════════════════════════╗${NC}"
-echo -e "${BOLD}║  My Brain Is Full - Crew :: Update       ║${NC}"
-echo -e "${BOLD}╚══════════════════════════════════════════╝${NC}"
-echo ""
+# ── Check vault has been set up ───────────────────────────────────────────────
+[[ -d "$VAULT_DIR/.claude/agents" ]] \
+  || die "No .claude/agents/ found in $VAULT_DIR — run launchme.sh first"
 
-# ── Confirm overwrite ────────────────────────────────────────────────────
-echo -e "${BOLD}This will overwrite core agent files, references, and CLAUDE.md.${NC}"
-echo -e "   ${DIM}Custom agent files in .claude/agents/ will not be deleted or overwritten.${NC}"
-echo -e "   ${DIM}Custom agent entries in registry/directory will be preserved during update.${NC}"
+# ── Confirm ───────────────────────────────────────────────────────────────────
+echo -e "${BOLD}This will update core agents, skills, references, hooks, and CLAUDE.md.${NC}"
+echo -e "   ${DIM}Custom agents in .claude/agents/ are never overwritten or deleted.${NC}"
+echo -e "   ${DIM}Custom content between MBIFC markers in references is preserved.${NC}"
 echo -e "   ${DIM}Your vault notes are never touched.${NC}"
 echo ""
 echo -e "   ${BOLD}c)${NC} Continue"
 echo -e "   ${BOLD}q)${NC} Quit"
-if ! read -r -p "   > " UPDATE_ANSWER 2>/dev/null; then UPDATE_ANSWER=""; fi
-if [[ ! "$UPDATE_ANSWER" =~ ^[Cc]$ ]]; then
-  echo ""
-  info "Update cancelled."
-  echo ""
-  exit 0
+if ! read -r -p "   > " ANSWER 2>/dev/null; then ANSWER=""; fi
+if [[ ! "$ANSWER" =~ ^[Cc]$ ]]; then
+  echo ""; info "Update cancelled."; echo ""; exit 0
 fi
 echo ""
 
-# ── Deprecate removed core agents ─────────────────────────────────────────
-# Read the OLD manifest first (before rewriting it) so we know which files
-# were previously installed as core. Agents removed from the repo will still
-# be in the old manifest and can be correctly deprecated.
-MANIFEST="$VAULT_DIR/.claude/agents/.core-manifest"
-DEPRECATED_COUNT=0
-for vault_agent in "$VAULT_DIR/.claude/agents/"*.md; do
-  [[ -f "$vault_agent" ]] || continue
-  name="$(basename "$vault_agent")"
-  # Skip if it still exists in repo
-  [[ -f "$REPO_DIR/agents/$name" ]] && continue
-  # Skip if already deprecated
-  [[ "$name" == *"-DEPRECATED"* ]] && continue
-  # Require manifest to distinguish core from custom agents
-  if [[ ! -f "$MANIFEST" ]]; then
-    continue
-  fi
-  # Skip custom agents: only deprecate if listed in the manifest
-  if ! grep -qxF "$name" "$MANIFEST"; then
-    continue
-  fi
-  deprecated_name="${name%.md}-DEPRECATED.md"
-  mkdir -p "$VAULT_DIR/.claude/deprecated"
-  # Skip if already deprecated in a previous run
-  [[ -f "$VAULT_DIR/.claude/deprecated/$deprecated_name" ]] && continue
-  mv "$vault_agent" "$VAULT_DIR/.claude/deprecated/$deprecated_name"
-  # Prepend deprecation header
-  { echo "########"; echo "DEPRECATED DO NOT USE"; echo "########"; echo ""; cat "$VAULT_DIR/.claude/deprecated/$deprecated_name"; } > "$VAULT_DIR/.claude/deprecated/$deprecated_name.tmp"
-  mv "$VAULT_DIR/.claude/deprecated/$deprecated_name.tmp" "$VAULT_DIR/.claude/deprecated/$deprecated_name"
-  warn "Deprecated agent: $name -> deprecated/$deprecated_name"
-  DEPRECATED_COUNT=$((DEPRECATED_COUNT + 1))
-  # Remove deprecated agent from manifest
-  if [[ -f "$MANIFEST" ]]; then
-    grep -vxF "$name" "$MANIFEST" > "$MANIFEST.tmp" || true
-    mv "$MANIFEST.tmp" "$MANIFEST"
-  fi
-done
+# ── Migrate legacy manifests (if any) ────────────────────────────────────────
+manifest_migrate
 
-# ── Update agents and rewrite manifest ────────────────────────────────────
-AGENT_COUNT=0
-: > "$VAULT_DIR/.claude/agents/.core-manifest"
-for agent in "$REPO_DIR/agents/"*.md; do
-  name="$(basename "$agent")"
-  basename "$agent" >> "$VAULT_DIR/.claude/agents/.core-manifest"
-  if [[ -f "$VAULT_DIR/.claude/agents/$name" ]]; then
-    if ! diff -q "$agent" "$VAULT_DIR/.claude/agents/$name" >/dev/null 2>&1; then
-      cp "$agent" "$VAULT_DIR/.claude/agents/"
-      info "Updated $name"
-      AGENT_COUNT=$((AGENT_COUNT + 1))
-    fi
-  else
-    cp "$agent" "$VAULT_DIR/.claude/agents/"
-    info "Added $name (new agent)"
-    AGENT_COUNT=$((AGENT_COUNT + 1))
-  fi
-done
+# ── Deprecate agents/refs removed from repo ──────────────────────────────────
+DEP_COUNT=$(deprecate_removed "agents"     "$REPO_DIR/agents"     "$VAULT_DIR/.claude/agents")
+DEP_COUNT=$((DEP_COUNT + $(deprecate_removed "references" "$REPO_DIR/references" "$VAULT_DIR/.claude/references")))
 
-# ── Deprecate removed references ──────────────────────────────────────────
-# Read the old manifest before rewriting, same logic as agents.
-REF_MANIFEST="$VAULT_DIR/.claude/references/.core-manifest"
-for vault_ref in "$VAULT_DIR/.claude/references/"*.md; do
-  [[ -f "$vault_ref" ]] || continue
-  name="$(basename "$vault_ref")"
-  [[ -f "$REPO_DIR/references/$name" ]] && continue
-  [[ "$name" == *"-DEPRECATED"* ]] && continue
-  # Require manifest to distinguish core from user-created references
-  if [[ ! -f "$REF_MANIFEST" ]]; then
-    continue
-  fi
-  # Skip user-created references: only deprecate if listed in the manifest
-  if ! grep -qxF "$name" "$REF_MANIFEST"; then
-    continue
-  fi
-  deprecated_name="${name%.md}-DEPRECATED.md"
-  mkdir -p "$VAULT_DIR/.claude/deprecated"
-  [[ -f "$VAULT_DIR/.claude/deprecated/$deprecated_name" ]] && continue
-  mv "$vault_ref" "$VAULT_DIR/.claude/deprecated/$deprecated_name"
-  { echo "########"; echo "DEPRECATED DO NOT USE"; echo "########"; echo ""; cat "$VAULT_DIR/.claude/deprecated/$deprecated_name"; } > "$VAULT_DIR/.claude/deprecated/$deprecated_name.tmp"
-  mv "$VAULT_DIR/.claude/deprecated/$deprecated_name.tmp" "$VAULT_DIR/.claude/deprecated/$deprecated_name"
-  warn "Deprecated reference: $name -> deprecated/$deprecated_name"
-  DEPRECATED_COUNT=$((DEPRECATED_COUNT + 1))
-done
-
-# ── Update references and rewrite manifest ────────────────────────────────
-# Files the Architect modifies with user content (custom agent rows/sections).
-# These need special merge logic to preserve the "## Custom Agents" section.
-USER_MUTABLE_REFS="agents-registry.md agents.md"
-
-# ── Ensure Meta/states/ exists (agent post-its) ─────────────────────────────
+# ── Ensure vault support dirs ─────────────────────────────────────────────────
 mkdir -p "$VAULT_DIR/Meta/states"
 
-REF_COUNT=0
-mkdir -p "$VAULT_DIR/.claude/references"
-: > "$VAULT_DIR/.claude/references/.core-manifest"
-for ref in "$REPO_DIR/references/"*.md; do
-  name="$(basename "$ref")"
-  basename "$ref" >> "$VAULT_DIR/.claude/references/.core-manifest"
-  vault_copy="$VAULT_DIR/.claude/references/$name"
+# ── Update components (per-file logging enabled) ─────────────────────────────
+VERBOSE_COPY=1
 
-  # For user-mutable files: preserve custom agent content
-  if [[ " $USER_MUTABLE_REFS " == *" $name "* ]] && [[ -f "$vault_copy" ]]; then
-    # Extract user's custom section (from "## Custom Agents" to end of file)
-    custom_section=""
-    if grep -qn "^## Custom Agents" "$vault_copy"; then
-      custom_line=$(grep -n "^## Custom Agents" "$vault_copy" | head -1 | cut -d: -f1)
-      custom_section=$(tail -n +"$custom_line" "$vault_copy")
-    fi
+AGENT_COUNT=$(install_agents "$REPO_DIR/agents"     "$VAULT_DIR/.claude/agents")
+REF_COUNT=$(install_refs     "$REPO_DIR/references" "$VAULT_DIR/.claude/references")
+SKILL_COUNT=$(install_skills "$REPO_DIR/skills"     "$VAULT_DIR/.claude/skills")
+HOOK_COUNT=$(install_hooks   "$REPO_DIR/hooks"      "$VAULT_DIR/.claude/hooks")
 
-    # For agents-registry.md: also extract custom rows from the Registry table
-    # Custom rows are table lines whose agent name is NOT a core agent
-    custom_table_rows=""
-    if [[ "$name" == "agents-registry.md" ]]; then
-      CORE_NAMES="architect scribe sorter seeker connector librarian transcriber postman"
-      while IFS= read -r row; do
-        # Extract agent name from first column: | name | ...
-        agent_name=$(echo "$row" | awk -F'|' '{gsub(/^[ \t]+|[ \t]+$/, "", $2); print $2}')
-        if [[ -n "$agent_name" ]] && ! echo "$CORE_NAMES" | grep -qw "$agent_name"; then
-          custom_table_rows="${custom_table_rows}${row}"$'\n'
-        fi
-      done < <(grep "^|" "$vault_copy" | grep -v "^|[[:space:]]*Name[[:space:]]*|" | grep -v "^|[-[:space:]]*|")
-    fi
+install_settings  "$REPO_DIR/settings.json" "$VAULT_DIR/.claude"
+SETTINGS_CHANGED=$_LAST_CHANGED
 
-    # Copy the new repo version
-    if ! diff -q "$ref" "$vault_copy" >/dev/null 2>&1; then
-      cp "$ref" "$vault_copy"
+install_claude_md "$REPO_DIR/CLAUDE.md" "$VAULT_DIR"
+CLAUDE_MD_CHANGED=$_LAST_CHANGED
 
-      # Re-insert custom table rows into the registry table (after the last table row)
-      if [[ -n "$custom_table_rows" ]]; then
-        # Find the last table row (any line starting with |) — avoids hard-coding a specific agent name
-        last_table_line=$(grep -n "^|" "$vault_copy" | tail -1 | cut -d: -f1)
-        if [[ -n "$last_table_line" ]]; then
-          { head -n "$last_table_line" "$vault_copy"; printf "%s" "$custom_table_rows"; tail -n +"$((last_table_line + 1))" "$vault_copy"; } > "$vault_copy.tmp"
-          mv "$vault_copy.tmp" "$vault_copy"
-        fi
-      fi
-
-      # Re-append preserved custom section (replace the repo's empty custom section)
-      if [[ -n "$custom_section" ]]; then
-        repo_custom_line=$(grep -n "^## Custom Agents" "$vault_copy" | head -1 | cut -d: -f1)
-        if [[ -n "$repo_custom_line" ]]; then
-          head -n "$((repo_custom_line - 1))" "$vault_copy" > "$vault_copy.tmp"
-          printf '%s\n' "$custom_section" >> "$vault_copy.tmp"
-          mv "$vault_copy.tmp" "$vault_copy"
-        fi
-      fi
-      info "Updated reference: $name (preserved custom content)"
-      REF_COUNT=$((REF_COUNT + 1))
-    fi
-    continue
-  fi
-
-  if [[ ! -f "$vault_copy" ]] || ! diff -q "$ref" "$vault_copy" >/dev/null 2>&1; then
-    cp "$ref" "$vault_copy"
-    info "Updated reference: $name"
-    REF_COUNT=$((REF_COUNT + 1))
-  fi
-done
-
-# ── Update skills ────────────────────────────────────────────────────────────
-SKILL_COUNT=0
-if [[ -d "$REPO_DIR/skills" ]]; then
-  for skill_dir in "$REPO_DIR/skills/"*/; do
-    [[ -f "$skill_dir/SKILL.md" ]] || continue
-    skill_name="$(basename "$skill_dir")"
-    src="$skill_dir/SKILL.md"
-    dst="$VAULT_DIR/.claude/skills/$skill_name/SKILL.md"
-    if [[ ! -f "$dst" ]] || ! diff -q "$src" "$dst" >/dev/null 2>&1; then
-      mkdir -p "$VAULT_DIR/.claude/skills/$skill_name"
-      cp "$src" "$dst"
-      info "Updated skill: $skill_name"
-      SKILL_COUNT=$((SKILL_COUNT + 1))
-    fi
-  done
-fi
-
-# ── Update hooks ──────────────────────────────────────────────────────────
-HOOK_COUNT=0
-if [[ -d "$REPO_DIR/hooks" ]]; then
-  mkdir -p "$VAULT_DIR/.claude/hooks"
-  for hook in "$REPO_DIR/hooks/"*.sh; do
-    [[ -f "$hook" ]] || continue
-    name="$(basename "$hook")"
-    dst="$VAULT_DIR/.claude/hooks/$name"
-    if [[ ! -f "$dst" ]] || ! diff -q "$hook" "$dst" >/dev/null 2>&1; then
-      cp "$hook" "$dst"
-      chmod +x "$dst"
-      info "Updated hook: $name"
-      HOOK_COUNT=$((HOOK_COUNT + 1))
-    fi
-  done
-fi
-
-# ── Update settings.json ──────────────────────────────────────────────────
-SETTINGS_UPDATED=""
-if [[ -f "$REPO_DIR/settings.json" ]]; then
-  dst="$VAULT_DIR/.claude/settings.json"
-  if [[ ! -f "$dst" ]] || ! diff -q "$REPO_DIR/settings.json" "$dst" >/dev/null 2>&1; then
-    mkdir -p "$VAULT_DIR/.claude"
-    cp "$REPO_DIR/settings.json" "$dst"
-    info "Updated settings.json"
-    SETTINGS_UPDATED="1"
-  fi
-fi
-
-# ── Remove stale orchestra scripts ────────────────────────────────────────
-ORCH_MANIFEST="$VAULT_DIR/Meta/scripts/.core-manifest"
-REMOVED_SCRIPTS=0
-if [[ -d "$REPO_DIR/orchestra" && -f "$ORCH_MANIFEST" ]]; then
-  while IFS= read -r old_script; do
-    [[ -z "$old_script" ]] && continue
-    [[ -f "$REPO_DIR/orchestra/$old_script" ]] && continue
-    vault_script="$VAULT_DIR/Meta/scripts/$old_script"
-    [[ -f "$vault_script" ]] || continue
-    rm "$vault_script"
-    warn "Removed stale script: $old_script"
-    REMOVED_SCRIPTS=$((REMOVED_SCRIPTS + 1))
-  done < "$ORCH_MANIFEST"
-fi
-
-# ── Update orchestra scripts ──────────────────────────────────────────────
-ORCH_COUNT=0
-if [[ -d "$REPO_DIR/orchestra" ]]; then
-  mkdir -p "$VAULT_DIR/Meta/scripts"
-  : > "$VAULT_DIR/Meta/scripts/.core-manifest"
-  for script in "$REPO_DIR/orchestra/"*; do
-    [[ -f "$script" ]] || continue
-    bname="$(basename "$script")"
-    [[ "$bname" == "README.md" ]] && continue
-    echo "$bname" >> "$VAULT_DIR/Meta/scripts/.core-manifest"
-    dst="$VAULT_DIR/Meta/scripts/$bname"
-    if [[ ! -f "$dst" ]] || ! diff -q "$script" "$dst" >/dev/null 2>&1; then
-      cp "$script" "$dst"
-      chmod +x "$dst"
-      info "Updated script: $bname"
-      ORCH_COUNT=$((ORCH_COUNT + 1))
-    fi
-  done
-fi
-
-# ── Update CLAUDE.md ──────────────────────────────────────────────────────
-CLAUDE_MD_UPDATED=""
-if [[ -f "$REPO_DIR/CLAUDE.md" ]]; then
-  if [[ ! -f "$VAULT_DIR/CLAUDE.md" ]] || ! diff -q "$REPO_DIR/CLAUDE.md" "$VAULT_DIR/CLAUDE.md" >/dev/null 2>&1; then
-    cp "$REPO_DIR/CLAUDE.md" "$VAULT_DIR/CLAUDE.md"
-    info "Updated CLAUDE.md"
-    CLAUDE_MD_UPDATED="1"
-  fi
-fi
-
-# ── Summary ─────────────────────────────────────────────────────────────────
+# ── Summary ───────────────────────────────────────────────────────────────────
 echo ""
-if [[ $AGENT_COUNT -eq 0 && $REF_COUNT -eq 0 && $SKILL_COUNT -eq 0 && $HOOK_COUNT -eq 0 && $ORCH_COUNT -eq 0 && $DEPRECATED_COUNT -eq 0 && $REMOVED_SCRIPTS -eq 0 && -z "$CLAUDE_MD_UPDATED" && -z "$SETTINGS_UPDATED" ]]; then
+TOTAL=$((AGENT_COUNT + REF_COUNT + SKILL_COUNT + HOOK_COUNT + SETTINGS_CHANGED + CLAUDE_MD_CHANGED))
+if [[ $TOTAL -eq 0 && $DEP_COUNT -eq 0 ]]; then
   success "Everything is already up to date!"
 else
-  success "Updated $AGENT_COUNT agent(s), $SKILL_COUNT skill(s), $REF_COUNT reference(s), $HOOK_COUNT hook(s), $ORCH_COUNT script(s)"
-  if [[ $DEPRECATED_COUNT -gt 0 ]]; then
-    warn "Deprecated $DEPRECATED_COUNT file(s) no longer in the project"
-  fi
-  if [[ $REMOVED_SCRIPTS -gt 0 ]]; then
-    warn "Removed $REMOVED_SCRIPTS stale script(s) from Meta/scripts/"
-  fi
+  success "Updated $AGENT_COUNT agent(s), $SKILL_COUNT skill(s), $REF_COUNT reference(s), $HOOK_COUNT hook(s)"
+  [[ $SETTINGS_CHANGED -eq 1 ]] && info "settings.json updated (backup saved as settings.json.bak)"
+  [[ $CLAUDE_MD_CHANGED -eq 1 ]] && info "CLAUDE.md updated"
+  [[ $DEP_COUNT -gt 0 ]] && warn "$DEP_COUNT file(s) deprecated (moved to .claude/deprecated/)"
 fi
 echo ""
 echo -e "   ${DIM}Restart Claude Code to pick up the changes.${NC}"
diff --git a/skills/create-agent/SKILL.md b/skills/create-agent/SKILL.md
old mode 100644
new mode 100755
index 999689e..c604de0
--- a/skills/create-agent/SKILL.md
+++ b/skills/create-agent/SKILL.md
@@ -174,8 +174,8 @@ Before writing the agent .md file, verify you have checked off ALL of these. If
    - Write a detailed Core Responsibilities section (this is what makes the agent good or bad)
    - Include concrete examples and templates for any notes the agent creates
 4. **Save the file** to `.claude/agents/{name}.md`
-5. **Update the registry**: add a new row to `.claude/references/agents-registry.md`
-6. **Update the directory**: add a new section under "Custom Agents" in `.claude/references/agents.md`
+5. **Update the registry**: add a new row to `.claude/references/agents-registry.md` — insert it between the `<!-- MBIFC:CUSTOM_AGENTS_START -->` and `<!-- MBIFC:CUSTOM_AGENTS_END -->` markers in the Registry table (after the postman row)
+6. **Update the directory**: add a new section under "Custom Agents" in `.claude/references/agents.md` — insert it between the `<!-- MBIFC:CUSTOM_AGENTS_START -->` and `<!-- MBIFC:CUSTOM_AGENTS_END -->` markers in that file
 7. **Log the creation** in `Meta/agent-log.md`
 8. **Report to the user**: "Your new agent `{name}` is now active. You can try it by saying one of your trigger phrases."
 
diff --git a/skills/manage-agent/SKILL.md b/skills/manage-agent/SKILL.md
old mode 100644
new mode 100755
index 83177fd..7c52572
--- a/skills/manage-agent/SKILL.md
+++ b/skills/manage-agent/SKILL.md
@@ -67,7 +67,7 @@ When the user says "edit my agent", "update agent X", "modify agent X", or equiv
 
 4. **Apply changes.** Modify the agent file at `.claude/agents/{name}.md` with the requested changes.
 
-5. **Update the registry.** If the change affects the agent's description, triggers, or capabilities, update the corresponding row in `.claude/references/agents-registry.md`.
+5. **Update the registry.** If the change affects the agent's description, triggers, or capabilities, update the corresponding row in `.claude/references/agents-registry.md`. Custom agent rows live between the `<!-- MBIFC:CUSTOM_AGENTS_START -->` and `<!-- MBIFC:CUSTOM_AGENTS_END -->` markers — edit only within that block.
 
 6. **Update agents.md.** If the change affects the agent's role description, update `.claude/references/agents.md`.