feat!: unify mosaic CLI — native launcher, no bin/ directory

BREAKING CHANGE: ~/.config/mosaic/bin/ is removed entirely. The mosaic npm CLI is now the only executable. ## What changed - **bin/ → deleted**: All scripts moved to tools/_scripts/ (internal) - **mosaic-launch → deleted**: Launcher logic is native TypeScript in packages/cli/src/commands/launch.ts - **mosaic.ps1 → deleted**: PowerShell launcher removed - **Framework install.sh**: Complete rewrite with migration system - **Version tracking**: .framework-version file (schema v2) - **Migration v1→v2**: Auto-removes bin/, cleans old PATH entries from shell profiles ## Native TypeScript launcher (commands/launch.ts) All runtime launch logic ported from bash: - Runtime prompt builder (AGENTS.md + RUNTIME.md + USER.md + TOOLS.md) - Mission context injection (reads .mosaic/orchestrator/mission.json) - PRD status injection (scans docs/PRD.md) - Pre-flight checks (MOSAIC_HOME, AGENTS.md, SOUL.md, runtime binary) - Session lock management with signal cleanup - Per-runtime launch: Claude, Codex, OpenCode, Pi - Yolo mode flags per runtime - Pi skill discovery + extension loading - Framework management (init, doctor, sync, bootstrap) delegates to tools/_scripts/ bash implementations ## Installer - tools/install.sh: detects framework by .framework-version or AGENTS.md - Framework install.sh: migration system with schema versioning - Forward-compatible: add migrations as numbered blocks - No PATH manipulation for framework (npm bin is the only PATH entry)
2026-04-02 19:23:44 -05:00
parent 04db8591af
commit 15830e2f2a
43 changed files with 724 additions and 1475 deletions
--- a/packages/mosaic/framework/tools/_scripts/mosaic-bootstrap-repo
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-bootstrap-repo
@@ -0,0 +1,126 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+TARGET_DIR="$(pwd)"
+FORCE=0
+QUALITY_TEMPLATE=""
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --force)
+      FORCE=1
+      shift
+      ;;
+    --quality-template)
+      QUALITY_TEMPLATE="${2:-}"
+      shift 2
+      ;;
+    *)
+      TARGET_DIR="$1"
+      shift
+      ;;
+  esac
+done
+
+if [[ ! -d "$TARGET_DIR" ]]; then
+  echo "[mosaic] Target directory does not exist: $TARGET_DIR" >&2
+  exit 1
+fi
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+TEMPLATE_ROOT="$MOSAIC_HOME/templates/repo"
+
+if [[ ! -d "$TEMPLATE_ROOT" ]]; then
+  echo "[mosaic] Missing templates at $TEMPLATE_ROOT" >&2
+  echo "[mosaic] Install or refresh framework: ~/.config/mosaic/install.sh" >&2
+  exit 1
+fi
+
+mkdir -p "$TARGET_DIR/.mosaic" "$TARGET_DIR/scripts/agent"
+mkdir -p "$TARGET_DIR/.mosaic/orchestrator" "$TARGET_DIR/.mosaic/orchestrator/logs" "$TARGET_DIR/.mosaic/orchestrator/results"
+
+copy_file() {
+  local src="$1"
+  local dst="$2"
+
+  if [[ -f "$dst" && "$FORCE" -ne 1 ]]; then
+    echo "[mosaic] Skip existing: $dst"
+    return
+  fi
+
+  cp "$src" "$dst"
+  echo "[mosaic] Wrote: $dst"
+}
+
+copy_file "$TEMPLATE_ROOT/.mosaic/README.md" "$TARGET_DIR/.mosaic/README.md"
+copy_file "$TEMPLATE_ROOT/.mosaic/repo-hooks.sh" "$TARGET_DIR/.mosaic/repo-hooks.sh"
+copy_file "$TEMPLATE_ROOT/.mosaic/quality-rails.yml" "$TARGET_DIR/.mosaic/quality-rails.yml"
+copy_file "$TEMPLATE_ROOT/.mosaic/orchestrator/config.json" "$TARGET_DIR/.mosaic/orchestrator/config.json"
+copy_file "$TEMPLATE_ROOT/.mosaic/orchestrator/tasks.json" "$TARGET_DIR/.mosaic/orchestrator/tasks.json"
+copy_file "$TEMPLATE_ROOT/.mosaic/orchestrator/state.json" "$TARGET_DIR/.mosaic/orchestrator/state.json"
+copy_file "$TEMPLATE_ROOT/.mosaic/orchestrator/matrix_state.json" "$TARGET_DIR/.mosaic/orchestrator/matrix_state.json"
+copy_file "$TEMPLATE_ROOT/.mosaic/orchestrator/logs/.gitkeep" "$TARGET_DIR/.mosaic/orchestrator/logs/.gitkeep"
+copy_file "$TEMPLATE_ROOT/.mosaic/orchestrator/results/.gitkeep" "$TARGET_DIR/.mosaic/orchestrator/results/.gitkeep"
+
+for file in "$TEMPLATE_ROOT"/scripts/agent/*.sh; do
+  base="$(basename "$file")"
+  copy_file "$file" "$TARGET_DIR/scripts/agent/$base"
+  chmod +x "$TARGET_DIR/scripts/agent/$base"
+done
+
+if [[ ! -f "$TARGET_DIR/AGENTS.md" ]]; then
+  cat > "$TARGET_DIR/AGENTS.md" <<'AGENTS_EOF'
+# Agent Guidelines
+
+## Required Load Order
+
+1. `~/.config/mosaic/SOUL.md`
+2. `~/.config/mosaic/STANDARDS.md`
+3. `~/.config/mosaic/AGENTS.md`
+4. `~/.config/mosaic/guides/E2E-DELIVERY.md`
+5. `AGENTS.md` (this file)
+6. Runtime-specific guide: `~/.config/mosaic/runtime/<runtime>/RUNTIME.md`
+7. `.mosaic/repo-hooks.sh`
+
+## Session Lifecycle
+
+```bash
+bash scripts/agent/session-start.sh
+bash scripts/agent/critical.sh
+bash scripts/agent/session-end.sh
+```
+
+## Shared Tools
+
+- Quality and orchestration guides: `~/.config/mosaic/guides/`
+- Shared automation tools: `~/.config/mosaic/tools/`
+
+## Repo-Specific Notes
+
+- Add project constraints and workflows here.
+- Implement hook functions in `.mosaic/repo-hooks.sh`.
+- Scratchpads are mandatory for non-trivial tasks.
+AGENTS_EOF
+  echo "[mosaic] Wrote: $TARGET_DIR/AGENTS.md"
+else
+  echo "[mosaic] AGENTS.md exists; add standards load order if missing"
+fi
+
+echo "[mosaic] Repo bootstrap complete: $TARGET_DIR"
+echo "[mosaic] Next: edit $TARGET_DIR/.mosaic/repo-hooks.sh with project workflows"
+echo "[mosaic] Optional: apply quality tools via ~/.config/mosaic/bin/mosaic-quality-apply --template <template> --target $TARGET_DIR"
+echo "[mosaic] Optional: run orchestrator rail via ~/.config/mosaic/bin/mosaic-orchestrator-drain"
+echo "[mosaic] Optional: run detached orchestrator via bash $TARGET_DIR/scripts/agent/orchestrator-daemon.sh start"
+
+if [[ -n "$QUALITY_TEMPLATE" ]]; then
+  if [[ -x "$MOSAIC_HOME/tools/_scripts/mosaic-quality-apply" ]]; then
+    "$MOSAIC_HOME/tools/_scripts/mosaic-quality-apply" --template "$QUALITY_TEMPLATE" --target "$TARGET_DIR"
+    if [[ -f "$TARGET_DIR/.mosaic/quality-rails.yml" ]]; then
+      sed -i "s/^enabled:.*/enabled: true/" "$TARGET_DIR/.mosaic/quality-rails.yml"
+      sed -i "s/^template:.*/template: \"$QUALITY_TEMPLATE\"/" "$TARGET_DIR/.mosaic/quality-rails.yml"
+    fi
+    echo "[mosaic] Applied quality tools template: $QUALITY_TEMPLATE"
+  else
+    echo "[mosaic] WARN: mosaic-quality-apply not found; skipping quality tools apply" >&2
+  fi
+fi
--- a/packages/mosaic/framework/tools/_scripts/mosaic-clean-runtime
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-clean-runtime
@@ -0,0 +1,147 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+RUNTIME="claude"
+APPLY=0
+ALL_EMPTY=0
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [options]
+
+Remove empty runtime directories created by migration/drift.
+Default mode only checks managed legacy surfaces. Use --all-empty for broader cleanup.
+
+Options:
+  --runtime <name>   Runtime to clean (default: claude)
+  --all-empty        Scan all runtime directories (except protected paths)
+  --apply            Perform deletions (default: dry-run)
+  -h, --help         Show help
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --runtime)
+      [[ $# -lt 2 ]] && { echo "Missing value for --runtime" >&2; exit 1; }
+      RUNTIME="$2"
+      shift 2
+      ;;
+    --all-empty)
+      ALL_EMPTY=1
+      shift
+      ;;
+    --apply)
+      APPLY=1
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+case "$RUNTIME" in
+  claude)
+    TARGET_ROOT="$HOME/.claude"
+    managed_roots=(
+      "$HOME/.claude/agent-guides"
+      "$HOME/.claude/scripts"
+      "$HOME/.claude/templates"
+      "$HOME/.claude/presets"
+      "$HOME/.claude/skills"
+      "$HOME/.claude/agents"
+      "$HOME/.claude/agents.bak"
+    )
+    protected_roots=(
+      "$HOME/.claude/.git"
+      "$HOME/.claude/debug"
+      "$HOME/.claude/file-history"
+      "$HOME/.claude/projects"
+      "$HOME/.claude/session-env"
+      "$HOME/.claude/tasks"
+      "$HOME/.claude/todos"
+      "$HOME/.claude/plugins"
+      "$HOME/.claude/statsig"
+      "$HOME/.claude/logs"
+      "$HOME/.claude/shell-snapshots"
+      "$HOME/.claude/paste-cache"
+      "$HOME/.claude/plans"
+      "$HOME/.claude/ide"
+      "$HOME/.claude/cache"
+    )
+    ;;
+  *)
+    echo "Unsupported runtime: $RUNTIME" >&2
+    exit 1
+    ;;
+esac
+
+[[ -d "$TARGET_ROOT" ]] || { echo "[mosaic-clean] Runtime dir missing: $TARGET_ROOT" >&2; exit 1; }
+
+is_protected() {
+  local path="$1"
+  for p in "${protected_roots[@]}"; do
+    [[ -e "$p" ]] || continue
+    case "$path" in
+      "$p"|"$p"/*)
+        return 0
+        ;;
+    esac
+  done
+  return 1
+}
+
+collect_empty_dirs() {
+  if [[ $ALL_EMPTY -eq 1 ]]; then
+    find "$TARGET_ROOT" -depth -type d -empty
+  else
+    for r in "${managed_roots[@]}"; do
+      [[ -d "$r" ]] || continue
+      find "$r" -depth -type d -empty
+    done
+  fi
+}
+
+count_candidates=0
+count_deletable=0
+
+while IFS= read -r d; do
+  [[ -n "$d" ]] || continue
+
+  count_candidates=$((count_candidates + 1))
+
+  # Never remove runtime root.
+  [[ "$d" == "$TARGET_ROOT" ]] && continue
+
+  if is_protected "$d"; then
+    continue
+  fi
+
+  count_deletable=$((count_deletable + 1))
+
+  if [[ $APPLY -eq 1 ]]; then
+    rmdir "$d" 2>/dev/null || true
+    if [[ ! -d "$d" ]]; then
+      echo "[mosaic-clean] deleted: $d"
+    fi
+  else
+    echo "[mosaic-clean] would delete: $d"
+  fi
+done < <(collect_empty_dirs | sort -u)
+
+mode="managed"
+[[ $ALL_EMPTY -eq 1 ]] && mode="all-empty"
+
+if [[ $APPLY -eq 1 ]]; then
+  echo "[mosaic-clean] complete: mode=$mode deleted_or_attempted=$count_deletable candidates=$count_candidates runtime=$RUNTIME"
+else
+  echo "[mosaic-clean] dry-run: mode=$mode deletable=$count_deletable candidates=$count_candidates runtime=$RUNTIME"
+  echo "[mosaic-clean] re-run with --apply to delete"
+fi
--- a/packages/mosaic/framework/tools/_scripts/mosaic-critical
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-critical
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [[ -x "scripts/agent/critical.sh" ]]; then
+  exec bash scripts/agent/critical.sh
+fi
+
+echo "[mosaic] Missing scripts/agent/critical.sh in $(pwd)" >&2
+exit 1
--- a/packages/mosaic/framework/tools/_scripts/mosaic-doctor
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-doctor
@@ -0,0 +1,435 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+FAIL_ON_WARN=0
+VERBOSE=0
+FIX_MODE=0
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [options]
+
+Audit Mosaic runtime state and detect drift across agent runtimes.
+
+Options:
+  --fix            Auto-fix: create missing dirs, wire skills into all harnesses
+  --fail-on-warn   Exit non-zero when warnings are found
+  --verbose        Print pass checks too
+  -h, --help       Show help
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --fix)
+      FIX_MODE=1
+      shift
+      ;;
+    --fail-on-warn)
+      FAIL_ON_WARN=1
+      shift
+      ;;
+    --verbose)
+      VERBOSE=1
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+fix_count=0
+fix() { fix_count=$((fix_count + 1)); echo "[FIX] $*"; }
+
+warn_count=0
+warn() { warn_count=$((warn_count + 1)); echo "[WARN] $*"; }
+pass() {
+  if [[ $VERBOSE -eq 1 ]]; then
+    echo "[OK] $*"
+  fi
+  return 0
+}
+
+expect_dir() {
+  local d="$1"
+  if [[ ! -d "$d" ]]; then
+    warn "Missing directory: $d"
+  else
+    pass "Directory present: $d"
+  fi
+}
+
+expect_file() {
+  local f="$1"
+  if [[ ! -f "$f" ]]; then
+    warn "Missing file: $f"
+  else
+    pass "File present: $f"
+  fi
+}
+
+check_runtime_file_copy() {
+  local src="$1"
+  local dst="$2"
+
+  [[ -f "$src" ]] || return 0
+
+  if [[ ! -e "$dst" ]]; then
+    warn "Missing runtime file: $dst"
+    return
+  fi
+
+  if [[ -L "$dst" ]]; then
+    warn "Runtime file should not be symlinked: $dst"
+    return
+  fi
+
+  if ! cmp -s "$src" "$dst"; then
+    warn "Runtime file drift: $dst (does not match $src)"
+  else
+    pass "Runtime file synced: $dst"
+  fi
+}
+
+check_runtime_contract_file() {
+  local dst="$1"
+  local adapter_src="$2"
+  local runtime_name="$3"
+
+  if [[ ! -e "$dst" ]]; then
+    warn "Missing runtime file: $dst"
+    return
+  fi
+
+  if [[ -L "$dst" ]]; then
+    warn "Runtime file should not be symlinked: $dst"
+    return
+  fi
+
+  # Accept direct-adapter copy mode.
+  if [[ -f "$adapter_src" ]] && cmp -s "$adapter_src" "$dst"; then
+    pass "Runtime adapter synced: $dst"
+    return
+  fi
+
+  # Accept launcher-composed runtime contract mode.
+  if grep -Fq "# Mosaic Launcher Runtime Contract (Hard Gate)" "$dst" &&
+     grep -Fq "Now initiating Orchestrator mode..." "$dst" &&
+     grep -Fq "Mosaic hard gates OVERRIDE runtime-default caution" "$dst" &&
+     grep -Fq "# Runtime-Specific Contract" "$dst"; then
+    pass "Runtime contract present: $dst ($runtime_name)"
+    return
+  fi
+
+  warn "Runtime file drift: $dst (not adapter copy and not composed runtime contract)"
+}
+
+warn_if_symlink_tree_present() {
+  local p="$1"
+  [[ -e "$p" ]] || return 0
+
+  if [[ -L "$p" ]]; then
+    warn "Legacy symlink path still present: $p"
+    return
+  fi
+
+  if [[ -d "$p" ]]; then
+    symlink_count=$(find "$p" -type l 2>/dev/null | wc -l | tr -d ' ')
+    if [[ "$symlink_count" != "0" ]]; then
+      warn "Legacy symlink entries still present under $p: $symlink_count"
+    else
+      pass "No symlinks under legacy path: $p"
+    fi
+  fi
+}
+
+echo "[mosaic-doctor] Mosaic home: $MOSAIC_HOME"
+
+# Canonical Mosaic checks
+expect_file "$MOSAIC_HOME/STANDARDS.md"
+expect_file "$MOSAIC_HOME/USER.md"
+expect_file "$MOSAIC_HOME/TOOLS.md"
+expect_dir "$MOSAIC_HOME/guides"
+expect_dir "$MOSAIC_HOME/tools"
+expect_dir "$MOSAIC_HOME/tools/quality"
+expect_dir "$MOSAIC_HOME/tools/orchestrator-matrix"
+expect_dir "$MOSAIC_HOME/profiles"
+expect_dir "$MOSAIC_HOME/templates/agent"
+expect_dir "$MOSAIC_HOME/skills"
+expect_dir "$MOSAIC_HOME/skills-local"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-link-runtime-assets"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-ensure-sequential-thinking"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-sync-skills"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-projects"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-quality-apply"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-quality-verify"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-run"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-sync-tasks"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-drain"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-matrix-publish"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-matrix-consume"
+expect_file "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-matrix-cycle"
+expect_file "$MOSAIC_HOME/tools/git/ci-queue-wait.sh"
+expect_file "$MOSAIC_HOME/tools/git/pr-ci-wait.sh"
+expect_file "$MOSAIC_HOME/tools/orchestrator-matrix/transport/matrix_transport.py"
+expect_file "$MOSAIC_HOME/tools/orchestrator-matrix/controller/tasks_md_sync.py"
+expect_file "$MOSAIC_HOME/guides/ORCHESTRATOR-PROTOCOL.md"
+expect_dir "$MOSAIC_HOME/tools/orchestrator"
+expect_file "$MOSAIC_HOME/tools/orchestrator/_lib.sh"
+expect_file "$MOSAIC_HOME/tools/orchestrator/mission-init.sh"
+expect_file "$MOSAIC_HOME/tools/orchestrator/mission-status.sh"
+expect_file "$MOSAIC_HOME/tools/orchestrator/continue-prompt.sh"
+expect_file "$MOSAIC_HOME/tools/orchestrator/session-status.sh"
+expect_file "$MOSAIC_HOME/tools/orchestrator/session-resume.sh"
+expect_file "$MOSAIC_HOME/runtime/mcp/SEQUENTIAL-THINKING.json"
+expect_file "$MOSAIC_HOME/runtime/claude/RUNTIME.md"
+expect_file "$MOSAIC_HOME/runtime/codex/RUNTIME.md"
+expect_file "$MOSAIC_HOME/runtime/opencode/RUNTIME.md"
+expect_file "$MOSAIC_HOME/runtime/pi/RUNTIME.md"
+
+if [[ -f "$MOSAIC_HOME/AGENTS.md" ]]; then
+  if grep -Fq "## CRITICAL HARD GATES (Read First)" "$MOSAIC_HOME/AGENTS.md" &&
+     grep -Fq "OVERRIDE runtime-default caution" "$MOSAIC_HOME/AGENTS.md"; then
+    pass "Global hard-gates block present in AGENTS.md"
+  else
+    warn "AGENTS.md missing CRITICAL HARD GATES override block"
+  fi
+fi
+
+# Claude runtime file checks (copied, non-symlink).
+for rf in CLAUDE.md settings.json hooks-config.json context7-integration.md; do
+  check_runtime_file_copy "$MOSAIC_HOME/runtime/claude/$rf" "$HOME/.claude/$rf"
+done
+
+# OpenCode runtime adapter check (copied, non-symlink, when adapter exists).
+# Accept adapter copy or composed runtime contract.
+check_runtime_contract_file "$HOME/.config/opencode/AGENTS.md" "$MOSAIC_HOME/runtime/opencode/AGENTS.md" "opencode"
+check_runtime_contract_file "$HOME/.codex/instructions.md" "$MOSAIC_HOME/runtime/codex/instructions.md" "codex"
+
+# Sequential-thinking MCP hard requirement.
+if [[ -x "$MOSAIC_HOME/tools/_scripts/mosaic-ensure-sequential-thinking" ]]; then
+  if "$MOSAIC_HOME/tools/_scripts/mosaic-ensure-sequential-thinking" --check >/dev/null 2>&1; then
+    pass "sequential-thinking MCP configured and available"
+  else
+    warn "sequential-thinking MCP missing or misconfigured"
+  fi
+else
+  warn "mosaic-ensure-sequential-thinking helper missing"
+fi
+
+# Legacy migration surfaces should no longer contain symlink trees.
+legacy_paths=(
+  "$HOME/.claude/agent-guides"
+  "$HOME/.claude/scripts/git"
+  "$HOME/.claude/scripts/codex"
+  "$HOME/.claude/scripts/bootstrap"
+  "$HOME/.claude/scripts/cicd"
+  "$HOME/.claude/scripts/portainer"
+  "$HOME/.claude/templates"
+  "$HOME/.claude/presets/domains"
+  "$HOME/.claude/presets/tech-stacks"
+  "$HOME/.claude/presets/workflows"
+)
+for p in "${legacy_paths[@]}"; do
+  warn_if_symlink_tree_present "$p"
+done
+
+# Skills runtime checks (still symlinked into runtime-specific skills dirs).
+for runtime_skills in "$HOME/.claude/skills" "$HOME/.codex/skills" "$HOME/.config/opencode/skills" "$HOME/.pi/agent/skills"; do
+  [[ -d "$runtime_skills" ]] || continue
+
+  while IFS= read -r -d '' skill; do
+    name="$(basename "$skill")"
+    [[ "$name" == .* ]] && continue
+    target="$runtime_skills/$name"
+
+    if [[ ! -e "$target" ]]; then
+      warn "Missing skill link: $target"
+      continue
+    fi
+
+    if [[ ! -L "$target" ]]; then
+      warn "Non-symlink skill entry: $target"
+      continue
+    fi
+
+    target_real="$(readlink -f "$target" 2>/dev/null || true)"
+    skill_real="$(readlink -f "$skill" 2>/dev/null || true)"
+    if [[ -z "$target_real" || -z "$skill_real" || "$target_real" != "$skill_real" ]]; then
+      warn "Drifted skill link: $target (expected -> $skill)"
+    else
+      pass "Linked skill: $target"
+    fi
+  done < <(find "$MOSAIC_HOME/skills" "$MOSAIC_HOME/skills-local" -mindepth 1 -maxdepth 1 -type d -print0)
+done
+
+# Broken links only in managed runtime skill dirs.
+link_roots=(
+  "$HOME/.claude/skills"
+  "$HOME/.codex/skills"
+  "$HOME/.config/opencode/skills"
+  "$HOME/.pi/agent/skills"
+)
+existing_link_roots=()
+for d in "${link_roots[@]}"; do
+  [[ -e "$d" ]] && existing_link_roots+=("$d")
+done
+
+broken_links=0
+if [[ ${#existing_link_roots[@]} -gt 0 ]]; then
+  broken_links=$(find "${existing_link_roots[@]}" -xtype l 2>/dev/null | wc -l | tr -d ' ')
+fi
+if [[ "$broken_links" != "0" ]]; then
+  warn "Broken skill symlinks detected: $broken_links"
+fi
+
+# Pi agent skills directory check.
+if [[ ! -d "$HOME/.pi/agent/skills" ]]; then
+  warn "Pi skills directory missing: $HOME/.pi/agent/skills"
+else
+  pass "Pi skills directory present: $HOME/.pi/agent/skills"
+fi
+
+# Pi settings.json — check skills path is configured.
+pi_settings="$HOME/.pi/agent/settings.json"
+if [[ -f "$pi_settings" ]]; then
+  if grep -q 'skills' "$pi_settings" 2>/dev/null; then
+    pass "Pi settings.json has skills configuration"
+  else
+    warn "Pi settings.json missing skills array — Mosaic skills may not load"
+  fi
+fi
+
+# Mosaic-specific skills presence check.
+mosaic_skills=(mosaic-board mosaic-forge mosaic-prdy mosaic-macp mosaic-standards mosaic-prd mosaic-jarvis mosaic-setup-cicd)
+for skill_name in "${mosaic_skills[@]}"; do
+  if [[ -d "$MOSAIC_HOME/skills/$skill_name" ]] || [[ -L "$MOSAIC_HOME/skills/$skill_name" ]]; then
+    pass "Mosaic skill present: $skill_name"
+  elif [[ -d "$MOSAIC_HOME/skills-local/$skill_name" ]]; then
+    pass "Mosaic skill present (local): $skill_name"
+  else
+    warn "Missing Mosaic skill: $skill_name"
+  fi
+done
+
+# ── --fix mode: auto-wire skills into all harness directories ──────────────
+if [[ $FIX_MODE -eq 1 ]]; then
+  echo ""
+  echo "[mosaic-doctor] Running auto-fix..."
+
+  # 1. Ensure all harness skill directories exist
+  harness_skill_dirs=(
+    "$HOME/.claude/skills"
+    "$HOME/.codex/skills"
+    "$HOME/.config/opencode/skills"
+    "$HOME/.pi/agent/skills"
+  )
+
+  for hdir in "${harness_skill_dirs[@]}"; do
+    if [[ ! -d "$hdir" ]]; then
+      mkdir -p "$hdir"
+      fix "Created missing directory: $hdir"
+    fi
+  done
+
+  # 2. Wire all Mosaic skills (canonical + local) into every harness
+  skill_sources=("$MOSAIC_HOME/skills" "$MOSAIC_HOME/skills-local")
+
+  for hdir in "${harness_skill_dirs[@]}"; do
+    # Skip if target resolves to canonical dir (avoid self-link)
+    hdir_real="$(readlink -f "$hdir" 2>/dev/null || true)"
+    canonical_real="$(readlink -f "$MOSAIC_HOME/skills" 2>/dev/null || true)"
+    if [[ -n "$hdir_real" && -n "$canonical_real" && "$hdir_real" == "$canonical_real" ]]; then
+      continue
+    fi
+
+    for src_dir in "${skill_sources[@]}"; do
+      [[ -d "$src_dir" ]] || continue
+
+      while IFS= read -r -d '' skill_path; do
+        skill_name="$(basename "$skill_path")"
+        [[ "$skill_name" == .* ]] && continue
+
+        link_path="$hdir/$skill_name"
+
+        if [[ -L "$link_path" ]]; then
+          # Repoint if target differs
+          current_target="$(readlink -f "$link_path" 2>/dev/null || true)"
+          expected_target="$(readlink -f "$skill_path" 2>/dev/null || true)"
+          if [[ "$current_target" != "$expected_target" ]]; then
+            ln -sfn "$skill_path" "$link_path"
+            fix "Repointed skill link: $link_path -> $skill_path"
+          fi
+        elif [[ -e "$link_path" ]]; then
+          # Non-symlink entry — preserve runtime-specific override
+          continue
+        else
+          ln -s "$skill_path" "$link_path"
+          fix "Linked skill: $link_path -> $skill_path"
+        fi
+      done < <(find "$src_dir" -mindepth 1 -maxdepth 1 -type d -print0; find "$src_dir" -mindepth 1 -maxdepth 1 -type l -print0)
+    done
+
+    # Prune broken symlinks in this harness dir
+    while IFS= read -r -d '' broken_link; do
+      rm -f "$broken_link"
+      fix "Removed broken link: $broken_link"
+    done < <(find "$hdir" -mindepth 1 -maxdepth 1 -xtype l -print0 2>/dev/null)
+  done
+
+  # 3. Ensure Pi settings.json includes Mosaic skills path
+  pi_settings_dir="$HOME/.pi/agent"
+  pi_settings_file="$pi_settings_dir/settings.json"
+  mkdir -p "$pi_settings_dir"
+
+  if [[ ! -f "$pi_settings_file" ]]; then
+    echo '{}' > "$pi_settings_file"
+    fix "Created Pi settings.json: $pi_settings_file"
+  fi
+
+  # Add skills paths if not already present
+  mosaic_skills_path="$MOSAIC_HOME/skills"
+  mosaic_local_path="$MOSAIC_HOME/skills-local"
+  if ! grep -q "$mosaic_skills_path" "$pi_settings_file" 2>/dev/null; then
+    # Use a simple approach: read, patch, write
+    if command -v python3 >/dev/null 2>&1; then
+      python3 -c "
+import json, sys
+with open('$pi_settings_file', 'r') as f:
+    data = json.load(f)
+skills = data.get('skills', [])
+if not isinstance(skills, list):
+    skills = []
+for p in ['$mosaic_skills_path', '$mosaic_local_path']:
+    if p not in skills:
+        skills.append(p)
+data['skills'] = skills
+with open('$pi_settings_file', 'w') as f:
+    json.dump(data, f, indent=2)
+    f.write('\\n')
+" 2>/dev/null && fix "Added Mosaic skills paths to Pi settings.json"
+    else
+      warn "python3 not available — cannot patch Pi settings.json. Add manually: skills: [\"$mosaic_skills_path\", \"$mosaic_local_path\"]"
+    fi
+  fi
+
+  # 4. Run link-runtime-assets if available
+  if [[ -x "$MOSAIC_HOME/tools/_scripts/mosaic-link-runtime-assets" ]]; then
+    "$MOSAIC_HOME/tools/_scripts/mosaic-link-runtime-assets" >/dev/null 2>&1 && fix "Re-ran mosaic-link-runtime-assets"
+  fi
+
+  echo "[mosaic-doctor] fixes=$fix_count"
+fi
+
+echo "[mosaic-doctor] warnings=$warn_count"
+if [[ $FAIL_ON_WARN -eq 1 && $warn_count -gt 0 ]]; then
+  exit 1
+fi
--- a/packages/mosaic/framework/tools/_scripts/mosaic-doctor.ps1
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-doctor.ps1
@@ -0,0 +1,283 @@
+# mosaic-doctor.ps1
+# Audits Mosaic runtime state and detects drift across agent runtimes.
+# PowerShell equivalent of mosaic-doctor (bash).
+$ErrorActionPreference = "Stop"
+
+param(
+    [switch]$FailOnWarn,
+    [switch]$Verbose,
+    [switch]$Help
+)
+
+$MosaicHome = if ($env:MOSAIC_HOME) { $env:MOSAIC_HOME } else { Join-Path $env:USERPROFILE ".config\mosaic" }
+
+if ($Help) {
+    Write-Host @"
+Usage: mosaic-doctor.ps1 [-FailOnWarn] [-Verbose] [-Help]
+
+Audit Mosaic runtime state and detect drift across agent runtimes.
+"@
+    exit 0
+}
+
+$script:warnCount = 0
+
+function Warn {
+    param([string]$Message)
+    $script:warnCount++
+    Write-Host "[WARN] $Message" -ForegroundColor Yellow
+}
+
+function Pass {
+    param([string]$Message)
+    if ($Verbose) { Write-Host "[OK] $Message" -ForegroundColor Green }
+}
+
+function Expect-Dir {
+    param([string]$Path)
+    if (-not (Test-Path $Path -PathType Container)) { Warn "Missing directory: $Path" }
+    else { Pass "Directory present: $Path" }
+}
+
+function Expect-File {
+    param([string]$Path)
+    if (-not (Test-Path $Path -PathType Leaf)) { Warn "Missing file: $Path" }
+    else { Pass "File present: $Path" }
+}
+
+function Check-RuntimeFileCopy {
+    param([string]$Src, [string]$Dst)
+
+    if (-not (Test-Path $Src)) { return }
+
+    if (-not (Test-Path $Dst)) {
+        Warn "Missing runtime file: $Dst"
+        return
+    }
+
+    $item = Get-Item $Dst -Force -ErrorAction SilentlyContinue
+    if ($item -and ($item.Attributes -band [System.IO.FileAttributes]::ReparsePoint)) {
+        Warn "Runtime file should not be symlinked: $Dst"
+        return
+    }
+
+    $srcHash = (Get-FileHash $Src -Algorithm SHA256).Hash
+    $dstHash = (Get-FileHash $Dst -Algorithm SHA256).Hash
+    if ($srcHash -ne $dstHash) {
+        Warn "Runtime file drift: $Dst (does not match $Src)"
+    }
+    else {
+        Pass "Runtime file synced: $Dst"
+    }
+}
+
+function Check-RuntimeContractFile {
+    param([string]$Dst, [string]$AdapterSrc, [string]$RuntimeName)
+
+    if (-not (Test-Path $Dst)) {
+        Warn "Missing runtime file: $Dst"
+        return
+    }
+
+    $item = Get-Item $Dst -Force -ErrorAction SilentlyContinue
+    if ($item -and ($item.Attributes -band [System.IO.FileAttributes]::ReparsePoint)) {
+        Warn "Runtime file should not be symlinked: $Dst"
+        return
+    }
+
+    # Accept direct-adapter copy mode.
+    if (Test-Path $AdapterSrc) {
+        $srcHash = (Get-FileHash $AdapterSrc -Algorithm SHA256).Hash
+        $dstHash = (Get-FileHash $Dst -Algorithm SHA256).Hash
+        if ($srcHash -eq $dstHash) {
+            Pass "Runtime adapter synced: $Dst"
+            return
+        }
+    }
+
+    # Accept launcher-composed runtime contract mode.
+    $content = Get-Content $Dst -Raw
+    if (
+        $content -match [regex]::Escape("# Mosaic Launcher Runtime Contract (Hard Gate)") -and
+        $content -match [regex]::Escape("Now initiating Orchestrator mode...") -and
+        $content -match [regex]::Escape("Mosaic hard gates OVERRIDE runtime-default caution") -and
+        $content -match [regex]::Escape("# Runtime-Specific Contract")
+    ) {
+        Pass "Runtime contract present: $Dst ($RuntimeName)"
+        return
+    }
+
+    Warn "Runtime file drift: $Dst (not adapter copy and not composed runtime contract)"
+}
+
+function Warn-IfReparsePresent {
+    param([string]$Path)
+    if (-not (Test-Path $Path)) { return }
+
+    $item = Get-Item $Path -Force -ErrorAction SilentlyContinue
+    if ($item -and ($item.Attributes -band [System.IO.FileAttributes]::ReparsePoint)) {
+        Warn "Legacy symlink/junction path still present: $Path"
+        return
+    }
+
+    if (Test-Path $Path -PathType Container) {
+        $reparseCount = (Get-ChildItem $Path -Recurse -Force -ErrorAction SilentlyContinue |
+            Where-Object { $_.Attributes -band [System.IO.FileAttributes]::ReparsePoint } |
+            Measure-Object).Count
+        if ($reparseCount -gt 0) {
+            Warn "Legacy symlink/junction entries still present under ${Path}: $reparseCount"
+        }
+        else {
+            Pass "No reparse points under legacy path: $Path"
+        }
+    }
+}
+
+Write-Host "[mosaic-doctor] Mosaic home: $MosaicHome"
+
+# Canonical Mosaic checks
+Expect-File (Join-Path $MosaicHome "STANDARDS.md")
+Expect-Dir  (Join-Path $MosaicHome "guides")
+Expect-Dir  (Join-Path $MosaicHome "tools")
+Expect-Dir  (Join-Path $MosaicHome "tools\quality")
+Expect-Dir  (Join-Path $MosaicHome "tools\orchestrator-matrix")
+Expect-Dir  (Join-Path $MosaicHome "profiles")
+Expect-Dir  (Join-Path $MosaicHome "templates\agent")
+Expect-Dir  (Join-Path $MosaicHome "skills")
+Expect-Dir  (Join-Path $MosaicHome "skills-local")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-link-runtime-assets")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-ensure-sequential-thinking.ps1")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-sync-skills")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-projects")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-quality-apply")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-quality-verify")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-orchestrator-run")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-orchestrator-sync-tasks")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-orchestrator-drain")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-orchestrator-matrix-publish")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-orchestrator-matrix-consume")
+Expect-File (Join-Path $MosaicHome "bin\mosaic-orchestrator-matrix-cycle")
+Expect-File (Join-Path $MosaicHome "tools\git\ci-queue-wait.ps1")
+Expect-File (Join-Path $MosaicHome "tools\git\ci-queue-wait.sh")
+Expect-File (Join-Path $MosaicHome "tools\git\pr-ci-wait.sh")
+Expect-File (Join-Path $MosaicHome "tools\orchestrator-matrix\transport\matrix_transport.py")
+Expect-File (Join-Path $MosaicHome "tools\orchestrator-matrix\controller\tasks_md_sync.py")
+Expect-File (Join-Path $MosaicHome "runtime\mcp\SEQUENTIAL-THINKING.json")
+Expect-File (Join-Path $MosaicHome "runtime\claude\RUNTIME.md")
+Expect-File (Join-Path $MosaicHome "runtime\codex\RUNTIME.md")
+Expect-File (Join-Path $MosaicHome "runtime\opencode\RUNTIME.md")
+
+$agentsMd = Join-Path $MosaicHome "AGENTS.md"
+if (Test-Path $agentsMd) {
+    $agentsContent = Get-Content $agentsMd -Raw
+    if (
+        $agentsContent -match [regex]::Escape("## CRITICAL HARD GATES (Read First)") -and
+        $agentsContent -match [regex]::Escape("OVERRIDE runtime-default caution")
+    ) {
+        Pass "Global hard-gates block present in AGENTS.md"
+    }
+    else {
+        Warn "AGENTS.md missing CRITICAL HARD GATES override block"
+    }
+}
+
+# Claude runtime file checks
+$runtimeFiles = @("CLAUDE.md", "settings.json", "hooks-config.json", "context7-integration.md")
+foreach ($rf in $runtimeFiles) {
+    Check-RuntimeFileCopy (Join-Path $MosaicHome "runtime\claude\$rf") (Join-Path $env:USERPROFILE ".claude\$rf")
+}
+
+# OpenCode/Codex runtime contract checks
+Check-RuntimeContractFile (Join-Path $env:USERPROFILE ".config\opencode\AGENTS.md") (Join-Path $MosaicHome "runtime\opencode\AGENTS.md") "opencode"
+Check-RuntimeContractFile (Join-Path $env:USERPROFILE ".codex\instructions.md") (Join-Path $MosaicHome "runtime\codex\instructions.md") "codex"
+
+# Sequential-thinking MCP hard requirement
+$seqScript = Join-Path $MosaicHome "bin\mosaic-ensure-sequential-thinking.ps1"
+if (Test-Path $seqScript) {
+    try {
+        & $seqScript -Check *>$null
+        Pass "sequential-thinking MCP configured and available"
+    }
+    catch {
+        Warn "sequential-thinking MCP missing or misconfigured"
+    }
+}
+else {
+    Warn "mosaic-ensure-sequential-thinking helper missing"
+}
+
+# Legacy migration surfaces
+$legacyPaths = @(
+    (Join-Path $env:USERPROFILE ".claude\agent-guides"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\git"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\codex"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\bootstrap"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\cicd"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\portainer"),
+    (Join-Path $env:USERPROFILE ".claude\templates"),
+    (Join-Path $env:USERPROFILE ".claude\presets\domains"),
+    (Join-Path $env:USERPROFILE ".claude\presets\tech-stacks"),
+    (Join-Path $env:USERPROFILE ".claude\presets\workflows")
+)
+foreach ($p in $legacyPaths) {
+    Warn-IfReparsePresent $p
+}
+
+# Skills runtime checks (junctions or symlinks into runtime-specific dirs)
+$linkTargets = @(
+    (Join-Path $env:USERPROFILE ".claude\skills"),
+    (Join-Path $env:USERPROFILE ".codex\skills"),
+    (Join-Path $env:USERPROFILE ".config\opencode\skills")
+)
+
+$skillSources = @($MosaicHome + "\skills", $MosaicHome + "\skills-local")
+
+foreach ($runtimeSkills in $linkTargets) {
+    if (-not (Test-Path $runtimeSkills)) { continue }
+
+    foreach ($sourceDir in $skillSources) {
+        if (-not (Test-Path $sourceDir)) { continue }
+
+        Get-ChildItem $sourceDir -Directory | Where-Object { -not $_.Name.StartsWith(".") } | ForEach-Object {
+            $name = $_.Name
+            $skillPath = $_.FullName
+            $target = Join-Path $runtimeSkills $name
+
+            if (-not (Test-Path $target)) {
+                Warn "Missing skill link: $target"
+                return
+            }
+
+            $item = Get-Item $target -Force -ErrorAction SilentlyContinue
+            if (-not ($item.Attributes -band [System.IO.FileAttributes]::ReparsePoint)) {
+                Warn "Non-junction skill entry: $target"
+                return
+            }
+
+            $targetResolved = $item.Target
+            if (-not $targetResolved -or (Resolve-Path $targetResolved -ErrorAction SilentlyContinue).Path -ne (Resolve-Path $skillPath -ErrorAction SilentlyContinue).Path) {
+                Warn "Drifted skill link: $target (expected -> $skillPath)"
+            }
+            else {
+                Pass "Linked skill: $target"
+            }
+        }
+    }
+}
+
+# Broken junctions/symlinks in managed runtime skill dirs
+$brokenLinks = 0
+foreach ($d in $linkTargets) {
+    if (-not (Test-Path $d)) { continue }
+    Get-ChildItem $d -Force -ErrorAction SilentlyContinue | Where-Object {
+        ($_.Attributes -band [System.IO.FileAttributes]::ReparsePoint) -and -not (Test-Path $_.FullName)
+    } | ForEach-Object { $brokenLinks++ }
+}
+if ($brokenLinks -gt 0) {
+    Warn "Broken skill junctions/symlinks detected: $brokenLinks"
+}
+
+Write-Host "[mosaic-doctor] warnings=$($script:warnCount)"
+if ($FailOnWarn -and $script:warnCount -gt 0) {
+    exit 1
+}
--- a/packages/mosaic/framework/tools/_scripts/mosaic-ensure-excalidraw
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-ensure-excalidraw
@@ -0,0 +1,119 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+TOOLS_DIR="$MOSAIC_HOME/tools/excalidraw"
+MODE="apply"
+SCOPE="user"
+
+err() { echo "[mosaic-excalidraw] ERROR: $*" >&2; }
+log() { echo "[mosaic-excalidraw] $*"; }
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --check) MODE="check"; shift ;;
+    --scope)
+      if [[ $# -lt 2 ]]; then
+        err "--scope requires a value: user|local"
+        exit 2
+      fi
+      SCOPE="$2"
+      shift 2
+      ;;
+    *)
+      err "Unknown argument: $1"
+      exit 2
+      ;;
+  esac
+done
+
+require_binary() {
+  local name="$1"
+  if ! command -v "$name" >/dev/null 2>&1; then
+    err "Required binary missing: $name"
+    return 1
+  fi
+}
+
+check_software() {
+  require_binary node
+  require_binary npm
+}
+
+check_tool_dir() {
+  [[ -d "$TOOLS_DIR" ]] || { err "Tool dir not found: $TOOLS_DIR"; return 1; }
+  [[ -f "$TOOLS_DIR/package.json" ]] || { err "package.json not found in $TOOLS_DIR"; return 1; }
+  [[ -f "$TOOLS_DIR/launch.sh" ]] || { err "launch.sh not found in $TOOLS_DIR"; return 1; }
+}
+
+check_npm_deps() {
+  [[ -d "$TOOLS_DIR/node_modules/@modelcontextprotocol" ]] || return 1
+  [[ -d "$TOOLS_DIR/node_modules/@excalidraw" ]] || return 1
+  [[ -d "$TOOLS_DIR/node_modules/jsdom" ]] || return 1
+}
+
+install_npm_deps() {
+  if check_npm_deps; then
+    return 0
+  fi
+  log "Installing npm deps in $TOOLS_DIR..."
+  (cd "$TOOLS_DIR" && npm install --silent) || {
+    err "npm install failed in $TOOLS_DIR"
+    return 1
+  }
+}
+
+check_claude_config() {
+  python3 - <<'PY'
+import json
+from pathlib import Path
+
+p = Path.home() / ".claude.json"
+if not p.exists():
+    raise SystemExit(1)
+try:
+    data = json.loads(p.read_text(encoding="utf-8"))
+except Exception:
+    raise SystemExit(1)
+mcp = data.get("mcpServers")
+if not isinstance(mcp, dict):
+    raise SystemExit(1)
+entry = mcp.get("excalidraw")
+if not isinstance(entry, dict):
+    raise SystemExit(1)
+cmd = entry.get("command", "")
+if not cmd.endswith("launch.sh"):
+    raise SystemExit(1)
+PY
+}
+
+apply_claude_config() {
+  require_binary claude
+  local launch_sh="$TOOLS_DIR/launch.sh"
+  claude mcp add --scope user excalidraw -- "$launch_sh"
+}
+
+# ── Check mode ────────────────────────────────────────────────────────────────
+
+if [[ "$MODE" == "check" ]]; then
+  check_software
+  check_tool_dir
+  if ! check_npm_deps; then
+    err "npm deps not installed in $TOOLS_DIR (run without --check to install)"
+    exit 1
+  fi
+  if ! check_claude_config; then
+    err "excalidraw not registered in ~/.claude.json"
+    exit 1
+  fi
+  log "excalidraw MCP is configured and available"
+  exit 0
+fi
+
+# ── Apply mode ────────────────────────────────────────────────────────────────
+
+check_software
+check_tool_dir
+install_npm_deps
+apply_claude_config
+log "excalidraw MCP configured (scope: $SCOPE)"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-ensure-sequential-thinking
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-ensure-sequential-thinking
@@ -0,0 +1,262 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+MODE="apply"
+RUNTIME="all"
+STRICT_CHECK=0
+
+PKG="@modelcontextprotocol/server-sequential-thinking"
+
+err() { echo "[mosaic-seq] ERROR: $*" >&2; }
+log() { echo "[mosaic-seq] $*"; }
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --check)
+      MODE="check"
+      shift
+      ;;
+    --runtime)
+      if [[ $# -lt 2 ]]; then
+        err "--runtime requires a value: claude|codex|opencode|all"
+        exit 2
+      fi
+      RUNTIME="$2"
+      shift 2
+      ;;
+    --strict)
+      STRICT_CHECK=1
+      shift
+      ;;
+    *)
+      err "Unknown argument: $1"
+      exit 2
+      ;;
+  esac
+done
+
+case "$RUNTIME" in
+  all|claude|codex|opencode) ;;
+  *)
+    err "Invalid runtime: $RUNTIME (expected claude|codex|opencode|all)"
+    exit 2
+    ;;
+esac
+
+require_binary() {
+  local name="$1"
+  if ! command -v "$name" >/dev/null 2>&1; then
+    err "Required binary missing: $name"
+    return 1
+  fi
+}
+
+check_software() {
+  require_binary node
+  require_binary npx
+}
+
+warm_package() {
+  local timeout_sec="${MOSAIC_SEQ_WARM_TIMEOUT_SEC:-15}"
+  if command -v timeout >/dev/null 2>&1; then
+    timeout "$timeout_sec" npx -y "$PKG" --help >/dev/null 2>&1
+  else
+    npx -y "$PKG" --help >/dev/null 2>&1
+  fi
+}
+
+check_claude_config() {
+  python3 - <<'PY'
+import json
+from pathlib import Path
+p = Path.home() / ".claude" / "settings.json"
+if not p.exists():
+    raise SystemExit(1)
+try:
+    data = json.loads(p.read_text(encoding="utf-8"))
+except Exception:
+    raise SystemExit(1)
+mcp = data.get("mcpServers")
+if not isinstance(mcp, dict):
+    raise SystemExit(1)
+entry = mcp.get("sequential-thinking")
+if not isinstance(entry, dict):
+    raise SystemExit(1)
+if entry.get("command") != "npx":
+    raise SystemExit(1)
+args = entry.get("args")
+if args != ["-y", "@modelcontextprotocol/server-sequential-thinking"]:
+    raise SystemExit(1)
+PY
+}
+
+apply_claude_config() {
+  python3 - <<'PY'
+import json
+from pathlib import Path
+p = Path.home() / ".claude" / "settings.json"
+p.parent.mkdir(parents=True, exist_ok=True)
+if p.exists():
+    try:
+        data = json.loads(p.read_text(encoding="utf-8"))
+    except Exception:
+        data = {}
+else:
+    data = {}
+mcp = data.get("mcpServers")
+if not isinstance(mcp, dict):
+    mcp = {}
+mcp["sequential-thinking"] = {
+    "command": "npx",
+    "args": ["-y", "@modelcontextprotocol/server-sequential-thinking"]
+}
+data["mcpServers"] = mcp
+p.write_text(json.dumps(data, indent=2) + "\n", encoding="utf-8")
+PY
+}
+
+check_codex_config() {
+  local cfg="$HOME/.codex/config.toml"
+  [[ -f "$cfg" ]] || return 1
+  grep -Eq '^\[mcp_servers\.(sequential-thinking|sequential_thinking)\]' "$cfg" && \
+  grep -q '^command = "npx"' "$cfg" && \
+  grep -q '@modelcontextprotocol/server-sequential-thinking' "$cfg"
+}
+
+apply_codex_config() {
+  local cfg="$HOME/.codex/config.toml"
+  mkdir -p "$(dirname "$cfg")"
+  [[ -f "$cfg" ]] || touch "$cfg"
+
+  local tmp
+  tmp="$(mktemp)"
+  awk '
+    BEGIN { skip = 0 }
+    /^\[mcp_servers\.(sequential-thinking|sequential_thinking)\]/ { skip = 1; next }
+    skip && /^\[/ { skip = 0 }
+    !skip { print }
+  ' "$cfg" > "$tmp"
+  mv "$tmp" "$cfg"
+
+  {
+    echo ""
+    echo "[mcp_servers.sequential-thinking]"
+    echo "command = \"npx\""
+    echo "args = [\"-y\", \"@modelcontextprotocol/server-sequential-thinking\"]"
+  } >> "$cfg"
+}
+
+check_opencode_config() {
+  python3 - <<'PY'
+import json
+from pathlib import Path
+p = Path.home() / ".config" / "opencode" / "config.json"
+if not p.exists():
+    raise SystemExit(1)
+try:
+    data = json.loads(p.read_text(encoding="utf-8"))
+except Exception:
+    raise SystemExit(1)
+mcp = data.get("mcp")
+if not isinstance(mcp, dict):
+    raise SystemExit(1)
+entry = mcp.get("sequential-thinking")
+if not isinstance(entry, dict):
+    raise SystemExit(1)
+if entry.get("type") != "local":
+    raise SystemExit(1)
+if entry.get("command") != ["npx", "-y", "@modelcontextprotocol/server-sequential-thinking"]:
+    raise SystemExit(1)
+if entry.get("enabled") is not True:
+    raise SystemExit(1)
+PY
+}
+
+apply_opencode_config() {
+  python3 - <<'PY'
+import json
+from pathlib import Path
+p = Path.home() / ".config" / "opencode" / "config.json"
+p.parent.mkdir(parents=True, exist_ok=True)
+if p.exists():
+    try:
+        data = json.loads(p.read_text(encoding="utf-8"))
+    except Exception:
+        data = {}
+else:
+    data = {}
+mcp = data.get("mcp")
+if not isinstance(mcp, dict):
+    mcp = {}
+mcp["sequential-thinking"] = {
+    "type": "local",
+    "command": ["npx", "-y", "@modelcontextprotocol/server-sequential-thinking"],
+    "enabled": True
+}
+data["mcp"] = mcp
+p.write_text(json.dumps(data, indent=2) + "\n", encoding="utf-8")
+PY
+}
+
+check_runtime_config() {
+  case "$RUNTIME" in
+    all)
+      check_claude_config
+      check_codex_config
+      check_opencode_config
+      ;;
+    claude)
+      check_claude_config
+      ;;
+    codex)
+      check_codex_config
+      ;;
+    opencode)
+      check_opencode_config
+      ;;
+  esac
+}
+
+apply_runtime_config() {
+  case "$RUNTIME" in
+    all)
+      apply_claude_config
+      apply_codex_config
+      apply_opencode_config
+      ;;
+    claude)
+      apply_claude_config
+      ;;
+    codex)
+      apply_codex_config
+      ;;
+    opencode)
+      apply_opencode_config
+      ;;
+  esac
+}
+
+if [[ "$MODE" == "check" ]]; then
+  check_software
+  check_runtime_config
+
+  # Runtime launch checks should be local/fast by default.
+  if [[ "$STRICT_CHECK" -eq 1 || "${MOSAIC_SEQ_CHECK_WARM:-0}" == "1" ]]; then
+    if ! warm_package; then
+      err "sequential-thinking package warm-up failed in strict mode"
+      exit 1
+    fi
+  fi
+
+  log "sequential-thinking MCP is configured and available (${RUNTIME})"
+  exit 0
+fi
+
+check_software
+if ! warm_package; then
+  err "Unable to warm sequential-thinking package (npx timeout/failure)"
+  exit 1
+fi
+apply_runtime_config
+log "sequential-thinking MCP configured (${RUNTIME})"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-ensure-sequential-thinking.ps1
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-ensure-sequential-thinking.ps1
@@ -0,0 +1,114 @@
+# mosaic-ensure-sequential-thinking.ps1
+param(
+    [switch]$Check
+)
+
+$ErrorActionPreference = "Stop"
+
+$Pkg = "@modelcontextprotocol/server-sequential-thinking"
+
+function Require-Binary {
+    param([string]$Name)
+    if (-not (Get-Command $Name -ErrorAction SilentlyContinue)) {
+        throw "Required binary missing: $Name"
+    }
+}
+
+function Warm-Package {
+    $null = & npx -y $Pkg --help 2>$null
+}
+
+function Set-ClaudeConfig {
+    $path = Join-Path $env:USERPROFILE ".claude\settings.json"
+    New-Item -ItemType Directory -Path (Split-Path $path -Parent) -Force | Out-Null
+
+    $data = @{}
+    if (Test-Path $path) {
+        try { $data = Get-Content $path -Raw | ConvertFrom-Json -AsHashtable } catch { $data = @{} }
+    }
+    if (-not $data.ContainsKey("mcpServers") -or -not ($data["mcpServers"] -is [hashtable])) {
+        $data["mcpServers"] = @{}
+    }
+    $data["mcpServers"]["sequential-thinking"] = @{
+        command = "npx"
+        args = @("-y", "@modelcontextprotocol/server-sequential-thinking")
+    }
+    $data | ConvertTo-Json -Depth 20 | Set-Content -Path $path -Encoding UTF8
+}
+
+function Set-CodexConfig {
+    $path = Join-Path $env:USERPROFILE ".codex\config.toml"
+    New-Item -ItemType Directory -Path (Split-Path $path -Parent) -Force | Out-Null
+    if (-not (Test-Path $path)) { New-Item -ItemType File -Path $path -Force | Out-Null }
+
+    $content = Get-Content $path -Raw
+    $content = [regex]::Replace($content, "(?ms)^\[mcp_servers\.(sequential-thinking|sequential_thinking)\].*?(?=^\[|\z)", "")
+    $content = $content.TrimEnd() + "`n`n[mcp_servers.sequential-thinking]`ncommand = `"npx`"`nargs = [`"-y`", `"@modelcontextprotocol/server-sequential-thinking`"]`n"
+    Set-Content -Path $path -Value $content -Encoding UTF8
+}
+
+function Set-OpenCodeConfig {
+    $path = Join-Path $env:USERPROFILE ".config\opencode\config.json"
+    New-Item -ItemType Directory -Path (Split-Path $path -Parent) -Force | Out-Null
+
+    $data = @{}
+    if (Test-Path $path) {
+        try { $data = Get-Content $path -Raw | ConvertFrom-Json -AsHashtable } catch { $data = @{} }
+    }
+    if (-not $data.ContainsKey("mcp") -or -not ($data["mcp"] -is [hashtable])) {
+        $data["mcp"] = @{}
+    }
+    $data["mcp"]["sequential-thinking"] = @{
+        type = "local"
+        command = @("npx", "-y", "@modelcontextprotocol/server-sequential-thinking")
+        enabled = $true
+    }
+    $data | ConvertTo-Json -Depth 20 | Set-Content -Path $path -Encoding UTF8
+}
+
+function Test-Configs {
+    $claudeOk = $false
+    $codexOk = $false
+    $opencodeOk = $false
+
+    $claudePath = Join-Path $env:USERPROFILE ".claude\settings.json"
+    if (Test-Path $claudePath) {
+        try {
+            $c = Get-Content $claudePath -Raw | ConvertFrom-Json -AsHashtable
+            $claudeOk = $c.ContainsKey("mcpServers") -and $c["mcpServers"].ContainsKey("sequential-thinking")
+        } catch {}
+    }
+
+    $codexPath = Join-Path $env:USERPROFILE ".codex\config.toml"
+    if (Test-Path $codexPath) {
+        $raw = Get-Content $codexPath -Raw
+        $codexOk = $raw -match "\[mcp_servers\.(sequential-thinking|sequential_thinking)\]" -and $raw -match "@modelcontextprotocol/server-sequential-thinking"
+    }
+
+    $opencodePath = Join-Path $env:USERPROFILE ".config\opencode\config.json"
+    if (Test-Path $opencodePath) {
+        try {
+            $o = Get-Content $opencodePath -Raw | ConvertFrom-Json -AsHashtable
+            $opencodeOk = $o.ContainsKey("mcp") -and $o["mcp"].ContainsKey("sequential-thinking")
+        } catch {}
+    }
+
+    if (-not ($claudeOk -and $codexOk -and $opencodeOk)) {
+        throw "Sequential-thinking MCP runtime config is incomplete"
+    }
+}
+
+Require-Binary node
+Require-Binary npx
+Warm-Package
+
+if ($Check) {
+    Test-Configs
+    Write-Host "[mosaic-seq] sequential-thinking MCP is configured and available"
+    exit 0
+}
+
+Set-ClaudeConfig
+Set-CodexConfig
+Set-OpenCodeConfig
+Write-Host "[mosaic-seq] sequential-thinking MCP configured for Claude, Codex, and OpenCode"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-init
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-init
@@ -0,0 +1,424 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# mosaic-init — Interactive agent identity, user profile, and tool config generator
+#
+# Usage:
+#   mosaic-init                                    # Interactive mode
+#   mosaic-init --name "Jarvis" --style direct     # Flag overrides
+#   mosaic-init --name "Jarvis" --role "memory steward" --style direct \
+#     --accessibility "ADHD-friendly chunking" --guardrails "Never auto-commit"
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+SOUL_TEMPLATE="$MOSAIC_HOME/templates/SOUL.md.template"
+USER_TEMPLATE="$MOSAIC_HOME/templates/USER.md.template"
+TOOLS_TEMPLATE="$MOSAIC_HOME/templates/TOOLS.md.template"
+SOUL_OUTPUT="$MOSAIC_HOME/SOUL.md"
+USER_OUTPUT="$MOSAIC_HOME/USER.md"
+TOOLS_OUTPUT="$MOSAIC_HOME/TOOLS.md"
+
+# Defaults
+AGENT_NAME=""
+ROLE_DESCRIPTION=""
+STYLE=""
+ACCESSIBILITY=""
+CUSTOM_GUARDRAILS=""
+
+# USER.md defaults
+USER_NAME=""
+PRONOUNS=""
+TIMEZONE=""
+BACKGROUND=""
+COMMUNICATION_PREFS=""
+PERSONAL_BOUNDARIES=""
+PROJECTS_TABLE=""
+
+# TOOLS.md defaults
+GIT_PROVIDERS_TABLE=""
+CREDENTIALS_LOCATION=""
+CUSTOM_TOOLS_SECTION=""
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [options]
+
+Generate Mosaic identity and configuration files:
+  - SOUL.md    — Agent identity contract
+  - USER.md    — User profile and accessibility
+  - TOOLS.md   — Machine-level tool reference
+
+Interactive by default. Use flags to skip prompts.
+
+Options:
+  --name <name>            Agent name (e.g., "Jarvis", "Assistant")
+  --role <description>     Role description (e.g., "memory steward, execution partner")
+  --style <style>          Communication style: direct, friendly, or formal
+  --accessibility <prefs>  Accessibility preferences (e.g., "ADHD-friendly chunking")
+  --guardrails <rules>     Custom guardrails (appended to defaults)
+  --user-name <name>       Your name for USER.md
+  --pronouns <pronouns>    Your pronouns (e.g., "He/Him")
+  --timezone <tz>          Your timezone (e.g., "America/Chicago")
+  --non-interactive        Fail if any required value is missing (no prompts)
+  --soul-only              Only generate SOUL.md
+  -h, --help               Show help
+USAGE
+}
+
+NON_INTERACTIVE=0
+SOUL_ONLY=0
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --name) AGENT_NAME="$2"; shift 2 ;;
+    --role) ROLE_DESCRIPTION="$2"; shift 2 ;;
+    --style) STYLE="$2"; shift 2 ;;
+    --accessibility) ACCESSIBILITY="$2"; shift 2 ;;
+    --guardrails) CUSTOM_GUARDRAILS="$2"; shift 2 ;;
+    --user-name) USER_NAME="$2"; shift 2 ;;
+    --pronouns) PRONOUNS="$2"; shift 2 ;;
+    --timezone) TIMEZONE="$2"; shift 2 ;;
+    --non-interactive) NON_INTERACTIVE=1; shift ;;
+    --soul-only) SOUL_ONLY=1; shift ;;
+    -h|--help) usage; exit 0 ;;
+    *) echo "Unknown argument: $1" >&2; usage >&2; exit 1 ;;
+  esac
+done
+
+prompt_if_empty() {
+  local var_name="$1"
+  local prompt_text="$2"
+  local default_value="${3:-}"
+  local current_value="${!var_name}"
+
+  if [[ -n "$current_value" ]]; then
+    return
+  fi
+
+  if [[ $NON_INTERACTIVE -eq 1 ]]; then
+    if [[ -n "$default_value" ]]; then
+      eval "$var_name=\"$default_value\""
+      return
+    fi
+    echo "[mosaic-init] ERROR: --$var_name is required in non-interactive mode" >&2
+    exit 1
+  fi
+
+  if [[ -n "$default_value" ]]; then
+    prompt_text="$prompt_text [$default_value]"
+  fi
+
+  printf "%s: " "$prompt_text"
+  read -r value
+  if [[ -z "$value" && -n "$default_value" ]]; then
+    value="$default_value"
+  fi
+  eval "$var_name=\"$value\""
+}
+
+prompt_multiline() {
+  local var_name="$1"
+  local prompt_text="$2"
+  local default_value="${3:-}"
+  local current_value="${!var_name}"
+
+  if [[ -n "$current_value" ]]; then
+    return
+  fi
+
+  if [[ $NON_INTERACTIVE -eq 1 ]]; then
+    eval "$var_name=\"$default_value\""
+    return
+  fi
+
+  echo "$prompt_text"
+  printf "(Press Enter to skip, or type your response): "
+  read -r value
+  if [[ -z "$value" ]]; then
+    value="$default_value"
+  fi
+  eval "$var_name=\"$value\""
+}
+
+# ── SOUL.md Generation ────────────────────────────────────────
+echo "[mosaic-init] Generating SOUL.md — agent identity contract"
+echo ""
+
+prompt_if_empty AGENT_NAME "What name should agents use" "Assistant"
+prompt_if_empty ROLE_DESCRIPTION "Agent role description" "execution partner and visibility engine"
+
+if [[ -z "$STYLE" && $NON_INTERACTIVE -eq 0 ]]; then
+  echo ""
+  echo "Communication style:"
+  echo "  1) direct  — Concise, no fluff, actionable"
+  echo "  2) friendly — Warm but efficient, conversational"
+  echo "  3) formal  — Professional, structured, thorough"
+  printf "Choose [1/2/3] (default: 1): "
+  read -r style_choice
+  case "${style_choice:-1}" in
+    1|direct) STYLE="direct" ;;
+    2|friendly) STYLE="friendly" ;;
+    3|formal) STYLE="formal" ;;
+    *) STYLE="direct" ;;
+  esac
+elif [[ -z "$STYLE" ]]; then
+  STYLE="direct"
+fi
+
+prompt_if_empty ACCESSIBILITY "Accessibility preferences (or 'none')" "none"
+
+if [[ $NON_INTERACTIVE -eq 0 && -z "$CUSTOM_GUARDRAILS" ]]; then
+  echo ""
+  printf "Custom guardrails (optional, press Enter to skip): "
+  read -r CUSTOM_GUARDRAILS
+fi
+
+# Build behavioral principles based on style + accessibility
+BEHAVIORAL_PRINCIPLES=""
+case "$STYLE" in
+  direct)
+    BEHAVIORAL_PRINCIPLES="1. Clarity over performance theater.
+2. Practical execution over abstract planning.
+3. Truthfulness over confidence: state uncertainty explicitly.
+4. Visible state over hidden assumptions.
+5. Accessibility-aware — see \`~/.config/mosaic/USER.md\` for user-specific accommodations."
+    ;;
+  friendly)
+    BEHAVIORAL_PRINCIPLES="1. Be helpful and approachable while staying efficient.
+2. Provide context and explain reasoning when helpful.
+3. Truthfulness over confidence: state uncertainty explicitly.
+4. Visible state over hidden assumptions.
+5. Accessibility-aware — see \`~/.config/mosaic/USER.md\` for user-specific accommodations."
+    ;;
+  formal)
+    BEHAVIORAL_PRINCIPLES="1. Maintain professional, structured communication.
+2. Provide thorough analysis with explicit tradeoffs.
+3. Truthfulness over confidence: state uncertainty explicitly.
+4. Document decisions and rationale clearly.
+5. Accessibility-aware — see \`~/.config/mosaic/USER.md\` for user-specific accommodations."
+    ;;
+esac
+
+if [[ "$ACCESSIBILITY" != "none" && -n "$ACCESSIBILITY" ]]; then
+  BEHAVIORAL_PRINCIPLES="$BEHAVIORAL_PRINCIPLES
+6. $ACCESSIBILITY."
+fi
+
+# Build communication style section
+COMMUNICATION_STYLE=""
+case "$STYLE" in
+  direct)
+    COMMUNICATION_STYLE="- Be direct, concise, and concrete.
+- Avoid fluff, hype, and anthropomorphic roleplay.
+- Do not simulate certainty when facts are missing.
+- Prefer actionable next steps and explicit tradeoffs."
+    ;;
+  friendly)
+    COMMUNICATION_STYLE="- Be warm and conversational while staying focused.
+- Explain your reasoning when it helps the user.
+- Do not simulate certainty when facts are missing.
+- Prefer actionable next steps with clear context."
+    ;;
+  formal)
+    COMMUNICATION_STYLE="- Use professional, structured language.
+- Provide thorough explanations with supporting detail.
+- Do not simulate certainty when facts are missing.
+- Present options with explicit tradeoffs and recommendations."
+    ;;
+esac
+
+# Format custom guardrails
+FORMATTED_GUARDRAILS=""
+if [[ -n "$CUSTOM_GUARDRAILS" ]]; then
+  FORMATTED_GUARDRAILS="- $CUSTOM_GUARDRAILS"
+fi
+
+# Verify template exists
+if [[ ! -f "$SOUL_TEMPLATE" ]]; then
+  echo "[mosaic-init] ERROR: Template not found: $SOUL_TEMPLATE" >&2
+  echo "[mosaic-init] Run the Mosaic installer first." >&2
+  exit 1
+fi
+
+# Generate SOUL.md from template using awk (handles multi-line values)
+awk -v name="$AGENT_NAME" \
+    -v role="$ROLE_DESCRIPTION" \
+    -v principles="$BEHAVIORAL_PRINCIPLES" \
+    -v comms="$COMMUNICATION_STYLE" \
+    -v guardrails="$FORMATTED_GUARDRAILS" \
+    '{
+      gsub(/\{\{AGENT_NAME\}\}/, name)
+      gsub(/\{\{ROLE_DESCRIPTION\}\}/, role)
+      gsub(/\{\{BEHAVIORAL_PRINCIPLES\}\}/, principles)
+      gsub(/\{\{COMMUNICATION_STYLE\}\}/, comms)
+      gsub(/\{\{CUSTOM_GUARDRAILS\}\}/, guardrails)
+      print
+    }' "$SOUL_TEMPLATE" > "$SOUL_OUTPUT"
+
+echo ""
+echo "[mosaic-init] Generated: $SOUL_OUTPUT"
+echo "[mosaic-init] Agent name: $AGENT_NAME"
+echo "[mosaic-init] Style: $STYLE"
+
+if [[ $SOUL_ONLY -eq 1 ]]; then
+  # Push to runtime adapters and exit
+  if [[ -x "$MOSAIC_HOME/tools/_scripts/mosaic-link-runtime-assets" ]]; then
+    echo "[mosaic-init] Updating runtime adapters..."
+    "$MOSAIC_HOME/tools/_scripts/mosaic-link-runtime-assets"
+  fi
+  echo "[mosaic-init] Done. Launch with: mosaic claude"
+  exit 0
+fi
+
+# ── USER.md Generation ────────────────────────────────────────
+echo ""
+echo "[mosaic-init] Generating USER.md — user profile"
+echo ""
+
+prompt_if_empty USER_NAME "Your name" ""
+prompt_if_empty PRONOUNS "Your pronouns" "They/Them"
+prompt_if_empty TIMEZONE "Your timezone" "UTC"
+
+prompt_multiline BACKGROUND "Your professional background (brief summary)" "(not configured)"
+
+# Build accessibility section
+ACCESSIBILITY_SECTION=""
+if [[ "$ACCESSIBILITY" != "none" && -n "$ACCESSIBILITY" ]]; then
+  ACCESSIBILITY_SECTION="$ACCESSIBILITY"
+else
+  if [[ $NON_INTERACTIVE -eq 0 ]]; then
+    echo ""
+    prompt_multiline ACCESSIBILITY_SECTION \
+      "Accessibility or neurodivergence accommodations (or press Enter to skip)" \
+      "(No specific accommodations configured. Edit this section to add any.)"
+  else
+    ACCESSIBILITY_SECTION="(No specific accommodations configured. Edit this section to add any.)"
+  fi
+fi
+
+# Build communication preferences
+if [[ -z "$COMMUNICATION_PREFS" ]]; then
+  case "$STYLE" in
+    direct)
+      COMMUNICATION_PREFS="- Direct and concise
+- No sycophancy
+- Executive summaries and tables for overview"
+      ;;
+    friendly)
+      COMMUNICATION_PREFS="- Warm and conversational
+- Explain reasoning when helpful
+- Balance thoroughness with brevity"
+      ;;
+    formal)
+      COMMUNICATION_PREFS="- Professional and structured
+- Thorough explanations with supporting detail
+- Formal tone with explicit recommendations"
+      ;;
+  esac
+fi
+
+prompt_multiline PERSONAL_BOUNDARIES \
+  "Personal boundaries or preferences agents should respect" \
+  "(Edit this section to add any personal boundaries.)"
+
+if [[ -z "$PROJECTS_TABLE" ]]; then
+  PROJECTS_TABLE="| Project | Stack | Registry |
+|---------|-------|----------|
+| (none configured) | | |"
+fi
+
+if [[ ! -f "$USER_TEMPLATE" ]]; then
+  echo "[mosaic-init] WARN: USER.md template not found: $USER_TEMPLATE" >&2
+  echo "[mosaic-init] Skipping USER.md generation." >&2
+else
+  awk -v user_name="$USER_NAME" \
+      -v pronouns="$PRONOUNS" \
+      -v timezone="$TIMEZONE" \
+      -v background="$BACKGROUND" \
+      -v accessibility="$ACCESSIBILITY_SECTION" \
+      -v comms="$COMMUNICATION_PREFS" \
+      -v boundaries="$PERSONAL_BOUNDARIES" \
+      -v projects="$PROJECTS_TABLE" \
+      '{
+        gsub(/\{\{USER_NAME\}\}/, user_name)
+        gsub(/\{\{PRONOUNS\}\}/, pronouns)
+        gsub(/\{\{TIMEZONE\}\}/, timezone)
+        gsub(/\{\{BACKGROUND\}\}/, background)
+        gsub(/\{\{ACCESSIBILITY_SECTION\}\}/, accessibility)
+        gsub(/\{\{COMMUNICATION_PREFS\}\}/, comms)
+        gsub(/\{\{PERSONAL_BOUNDARIES\}\}/, boundaries)
+        gsub(/\{\{PROJECTS_TABLE\}\}/, projects)
+        print
+      }' "$USER_TEMPLATE" > "$USER_OUTPUT"
+
+  echo "[mosaic-init] Generated: $USER_OUTPUT"
+fi
+
+# ── TOOLS.md Generation ───────────────────────────────────────
+echo ""
+echo "[mosaic-init] Generating TOOLS.md — machine-level tool reference"
+echo ""
+
+if [[ -z "$GIT_PROVIDERS_TABLE" ]]; then
+  if [[ $NON_INTERACTIVE -eq 0 ]]; then
+    echo "Git providers (add rows for your Gitea/GitHub/GitLab instances):"
+    printf "Primary git provider URL (or press Enter to skip): "
+    read -r git_url
+    if [[ -n "$git_url" ]]; then
+      printf "Provider name: "
+      read -r git_name
+      printf "CLI tool (tea/gh/glab): "
+      read -r git_cli
+      printf "Purpose: "
+      read -r git_purpose
+      GIT_PROVIDERS_TABLE="| Instance | URL | CLI | Purpose |
+|----------|-----|-----|---------|
+| $git_name | $git_url | \`$git_cli\` | $git_purpose |"
+    else
+      GIT_PROVIDERS_TABLE="| Instance | URL | CLI | Purpose |
+|----------|-----|-----|---------|
+| (add your git providers here) | | | |"
+    fi
+  else
+    GIT_PROVIDERS_TABLE="| Instance | URL | CLI | Purpose |
+|----------|-----|-----|---------|
+| (add your git providers here) | | | |"
+  fi
+fi
+
+prompt_if_empty CREDENTIALS_LOCATION "Credential file path (or 'none')" "none"
+
+if [[ -z "$CUSTOM_TOOLS_SECTION" ]]; then
+  CUSTOM_TOOLS_SECTION="## Custom Tools
+
+(Add any machine-specific tools, scripts, or workflows here.)"
+fi
+
+if [[ ! -f "$TOOLS_TEMPLATE" ]]; then
+  echo "[mosaic-init] WARN: TOOLS.md template not found: $TOOLS_TEMPLATE" >&2
+  echo "[mosaic-init] Skipping TOOLS.md generation." >&2
+else
+  awk -v providers="$GIT_PROVIDERS_TABLE" \
+      -v creds="$CREDENTIALS_LOCATION" \
+      -v custom="$CUSTOM_TOOLS_SECTION" \
+      '{
+        gsub(/\{\{GIT_PROVIDERS_TABLE\}\}/, providers)
+        gsub(/\{\{CREDENTIALS_LOCATION\}\}/, creds)
+        gsub(/\{\{CUSTOM_TOOLS_SECTION\}\}/, custom)
+        print
+      }' "$TOOLS_TEMPLATE" > "$TOOLS_OUTPUT"
+
+  echo "[mosaic-init] Generated: $TOOLS_OUTPUT"
+fi
+
+# ── Finalize ──────────────────────────────────────────────────
+
+# Push to runtime adapters
+if [[ -x "$MOSAIC_HOME/tools/_scripts/mosaic-link-runtime-assets" ]]; then
+  echo ""
+  echo "[mosaic-init] Updating runtime adapters..."
+  "$MOSAIC_HOME/tools/_scripts/mosaic-link-runtime-assets"
+fi
+
+echo ""
+echo "[mosaic-init] Done. Launch with: mosaic claude"
+echo "[mosaic-init] Edit USER.md and TOOLS.md directly for further customization."
--- a/packages/mosaic/framework/tools/_scripts/mosaic-init.ps1
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-init.ps1
@@ -0,0 +1,144 @@
+# mosaic-init.ps1 — Interactive SOUL.md generator (Windows)
+#
+# Usage:
+#   mosaic-init.ps1                                    # Interactive mode
+#   mosaic-init.ps1 -Name "Jarvis" -Style direct       # Flag overrides
+$ErrorActionPreference = "Stop"
+
+param(
+    [string]$Name,
+    [string]$Role,
+    [ValidateSet("direct", "friendly", "formal")]
+    [string]$Style,
+    [string]$Accessibility,
+    [string]$Guardrails,
+    [switch]$NonInteractive,
+    [switch]$Help
+)
+
+$MosaicHome = if ($env:MOSAIC_HOME) { $env:MOSAIC_HOME } else { Join-Path $env:USERPROFILE ".config\mosaic" }
+$Template = Join-Path $MosaicHome "templates\SOUL.md.template"
+$Output = Join-Path $MosaicHome "SOUL.md"
+
+if ($Help) {
+    Write-Host @"
+Usage: mosaic-init.ps1 [-Name <name>] [-Role <desc>] [-Style direct|friendly|formal]
+                       [-Accessibility <prefs>] [-Guardrails <rules>] [-NonInteractive]
+
+Generate ~/.config/mosaic/SOUL.md - the universal agent identity contract.
+Interactive by default. Use flags to skip prompts.
+"@
+    exit 0
+}
+
+function Prompt-IfEmpty {
+    param([string]$Current, [string]$PromptText, [string]$Default = "")
+
+    if ($Current) { return $Current }
+
+    if ($NonInteractive) {
+        if ($Default) { return $Default }
+        Write-Host "[mosaic-init] ERROR: Value required in non-interactive mode: $PromptText" -ForegroundColor Red
+        exit 1
+    }
+
+    $display = if ($Default) { "$PromptText [$Default]" } else { $PromptText }
+    $value = Read-Host $display
+    if (-not $value -and $Default) { return $Default }
+    return $value
+}
+
+Write-Host "[mosaic-init] Generating SOUL.md - your universal agent identity contract"
+Write-Host ""
+
+$Name = Prompt-IfEmpty $Name "What name should agents use" "Assistant"
+$Role = Prompt-IfEmpty $Role "Agent role description" "execution partner and visibility engine"
+
+if (-not $Style) {
+    if ($NonInteractive) {
+        $Style = "direct"
+    }
+    else {
+        Write-Host ""
+        Write-Host "Communication style:"
+        Write-Host "  1) direct  - Concise, no fluff, actionable"
+        Write-Host "  2) friendly - Warm but efficient, conversational"
+        Write-Host "  3) formal  - Professional, structured, thorough"
+        $choice = Read-Host "Choose [1/2/3] (default: 1)"
+        $Style = switch ($choice) {
+            "2" { "friendly" }
+            "3" { "formal" }
+            default { "direct" }
+        }
+    }
+}
+
+$Accessibility = Prompt-IfEmpty $Accessibility "Accessibility preferences (or 'none')" "none"
+
+if (-not $Guardrails -and -not $NonInteractive) {
+    Write-Host ""
+    $Guardrails = Read-Host "Custom guardrails (optional, press Enter to skip)"
+}
+
+# Build behavioral principles
+$BehavioralPrinciples = switch ($Style) {
+    "direct" {
+        "1. Clarity over performance theater.`n2. Practical execution over abstract planning.`n3. Truthfulness over confidence: state uncertainty explicitly.`n4. Visible state over hidden assumptions."
+    }
+    "friendly" {
+        "1. Be helpful and approachable while staying efficient.`n2. Provide context and explain reasoning when helpful.`n3. Truthfulness over confidence: state uncertainty explicitly.`n4. Visible state over hidden assumptions."
+    }
+    "formal" {
+        "1. Maintain professional, structured communication.`n2. Provide thorough analysis with explicit tradeoffs.`n3. Truthfulness over confidence: state uncertainty explicitly.`n4. Document decisions and rationale clearly."
+    }
+}
+
+if ($Accessibility -and $Accessibility -ne "none") {
+    $BehavioralPrinciples += "`n5. $Accessibility."
+}
+
+# Build communication style
+$CommunicationStyle = switch ($Style) {
+    "direct" {
+        "- Be direct, concise, and concrete.`n- Avoid fluff, hype, and anthropomorphic roleplay.`n- Do not simulate certainty when facts are missing.`n- Prefer actionable next steps and explicit tradeoffs."
+    }
+    "friendly" {
+        "- Be warm and conversational while staying focused.`n- Explain your reasoning when it helps the user.`n- Do not simulate certainty when facts are missing.`n- Prefer actionable next steps with clear context."
+    }
+    "formal" {
+        "- Use professional, structured language.`n- Provide thorough explanations with supporting detail.`n- Do not simulate certainty when facts are missing.`n- Present options with explicit tradeoffs and recommendations."
+    }
+}
+
+# Format custom guardrails
+$FormattedGuardrails = if ($Guardrails) { "- $Guardrails" } else { "" }
+
+# Verify template
+if (-not (Test-Path $Template)) {
+    Write-Host "[mosaic-init] ERROR: Template not found: $Template" -ForegroundColor Red
+    exit 1
+}
+
+# Generate SOUL.md
+$content = Get-Content $Template -Raw
+$content = $content -replace '\{\{AGENT_NAME\}\}', $Name
+$content = $content -replace '\{\{ROLE_DESCRIPTION\}\}', $Role
+$content = $content -replace '\{\{BEHAVIORAL_PRINCIPLES\}\}', $BehavioralPrinciples
+$content = $content -replace '\{\{COMMUNICATION_STYLE\}\}', $CommunicationStyle
+$content = $content -replace '\{\{CUSTOM_GUARDRAILS\}\}', $FormattedGuardrails
+
+Set-Content -Path $Output -Value $content -Encoding UTF8
+
+Write-Host ""
+Write-Host "[mosaic-init] Generated: $Output"
+Write-Host "[mosaic-init] Agent name: $Name"
+Write-Host "[mosaic-init] Style: $Style"
+
+# Push to runtime adapters
+$linkScript = Join-Path $MosaicHome "bin\mosaic-link-runtime-assets.ps1"
+if (Test-Path $linkScript) {
+    Write-Host "[mosaic-init] Updating runtime adapters..."
+    & $linkScript
+}
+
+Write-Host "[mosaic-init] Done. Launch with: mosaic claude"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-link-runtime-assets
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-link-runtime-assets
@@ -0,0 +1,136 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+backup_stamp="$(date +%Y%m%d%H%M%S)"
+
+copy_file_managed() {
+  local src="$1"
+  local dst="$2"
+
+  mkdir -p "$(dirname "$dst")"
+
+  if [[ -L "$dst" ]]; then
+    rm -f "$dst"
+  fi
+
+  if [[ -f "$dst" ]]; then
+    if cmp -s "$src" "$dst"; then
+      return
+    fi
+    mv "$dst" "${dst}.mosaic-bak-${backup_stamp}"
+  fi
+
+  cp "$src" "$dst"
+}
+
+remove_legacy_path() {
+  local p="$1"
+
+  if [[ -L "$p" ]]; then
+    rm -f "$p"
+    return
+  fi
+
+  if [[ -d "$p" ]]; then
+    find "$p" -depth -type l -delete 2>/dev/null || true
+    find "$p" -depth -type d -empty -delete 2>/dev/null || true
+    return
+  fi
+
+  # Remove stale symlinked files if present.
+  if [[ -e "$p" && -L "$p" ]]; then
+    rm -f "$p"
+  fi
+}
+
+# Remove compatibility symlink surfaces for migrated content.
+legacy_paths=(
+  "$HOME/.claude/agent-guides"
+  "$HOME/.claude/scripts/git"
+  "$HOME/.claude/scripts/codex"
+  "$HOME/.claude/scripts/bootstrap"
+  "$HOME/.claude/scripts/cicd"
+  "$HOME/.claude/scripts/portainer"
+  "$HOME/.claude/scripts/debug-hook.sh"
+  "$HOME/.claude/scripts/qa-hook-handler.sh"
+  "$HOME/.claude/scripts/qa-hook-stdin.sh"
+  "$HOME/.claude/scripts/qa-hook-wrapper.sh"
+  "$HOME/.claude/scripts/qa-queue-monitor.sh"
+  "$HOME/.claude/scripts/remediation-hook-handler.sh"
+  "$HOME/.claude/templates"
+  "$HOME/.claude/presets/domains"
+  "$HOME/.claude/presets/tech-stacks"
+  "$HOME/.claude/presets/workflows"
+  "$HOME/.claude/presets/jarvis-loop.json"
+)
+
+for p in "${legacy_paths[@]}"; do
+  remove_legacy_path "$p"
+done
+
+# Claude-specific runtime files (settings, hooks — NOT CLAUDE.md which is now a thin pointer)
+for runtime_file in \
+  CLAUDE.md \
+  settings.json \
+  hooks-config.json \
+  context7-integration.md; do
+  src="$MOSAIC_HOME/runtime/claude/$runtime_file"
+  [[ -f "$src" ]] || continue
+  copy_file_managed "$src" "$HOME/.claude/$runtime_file"
+done
+
+# OpenCode runtime adapter (thin pointer to AGENTS.md)
+opencode_adapter="$MOSAIC_HOME/runtime/opencode/AGENTS.md"
+if [[ -f "$opencode_adapter" ]]; then
+  copy_file_managed "$opencode_adapter" "$HOME/.config/opencode/AGENTS.md"
+fi
+
+# Codex runtime adapter (thin pointer to AGENTS.md)
+codex_adapter="$MOSAIC_HOME/runtime/codex/instructions.md"
+if [[ -f "$codex_adapter" ]]; then
+  mkdir -p "$HOME/.codex"
+  copy_file_managed "$codex_adapter" "$HOME/.codex/instructions.md"
+fi
+
+# Pi runtime settings (MCP + skills paths)
+pi_settings_dir="$HOME/.pi/agent"
+pi_settings_file="$pi_settings_dir/settings.json"
+mkdir -p "$pi_settings_dir"
+
+if [[ ! -f "$pi_settings_file" ]]; then
+  echo '{}' > "$pi_settings_file"
+fi
+
+# Ensure Pi settings.json has Mosaic skills paths
+mosaic_skills_path="$MOSAIC_HOME/skills"
+mosaic_local_path="$MOSAIC_HOME/skills-local"
+if ! grep -q "$mosaic_skills_path" "$pi_settings_file" 2>/dev/null; then
+  if command -v python3 >/dev/null 2>&1; then
+    python3 -c "
+import json
+with open('$pi_settings_file', 'r') as f:
+    data = json.load(f)
+skills = data.get('skills', [])
+if not isinstance(skills, list):
+    skills = []
+for p in ['$mosaic_skills_path', '$mosaic_local_path']:
+    if p not in skills:
+        skills.append(p)
+data['skills'] = skills
+with open('$pi_settings_file', 'w') as f:
+    json.dump(data, f, indent=2)
+    f.write('\\n')
+" 2>/dev/null
+  fi
+fi
+
+# Pi extension is loaded via --extension flag in the mosaic launcher.
+# Do NOT copy into ~/.pi/agent/extensions/ — that causes duplicate loading.
+
+if [[ -x "$MOSAIC_HOME/tools/_scripts/mosaic-ensure-sequential-thinking" ]]; then
+  "$MOSAIC_HOME/tools/_scripts/mosaic-ensure-sequential-thinking"
+fi
+
+echo "[mosaic-link] Runtime assets synced (non-symlink mode)"
+echo "[mosaic-link] Canonical source: $MOSAIC_HOME"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-link-runtime-assets.ps1
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-link-runtime-assets.ps1
@@ -0,0 +1,111 @@
+# mosaic-link-runtime-assets.ps1
+# Syncs Mosaic runtime config files into agent runtime directories.
+# PowerShell equivalent of mosaic-link-runtime-assets (bash).
+$ErrorActionPreference = "Stop"
+
+$MosaicHome = if ($env:MOSAIC_HOME) { $env:MOSAIC_HOME } else { Join-Path $env:USERPROFILE ".config\mosaic" }
+$BackupStamp = Get-Date -Format "yyyyMMddHHmmss"
+
+function Copy-FileManaged {
+    param([string]$Src, [string]$Dst)
+
+    $parent = Split-Path $Dst -Parent
+    if (-not (Test-Path $parent)) { New-Item -ItemType Directory -Path $parent -Force | Out-Null }
+
+    # Remove existing symlink/junction
+    $item = Get-Item $Dst -Force -ErrorAction SilentlyContinue
+    if ($item -and $item.Attributes -band [System.IO.FileAttributes]::ReparsePoint) {
+        Remove-Item $Dst -Force
+    }
+
+    if (Test-Path $Dst) {
+        $srcHash = (Get-FileHash $Src -Algorithm SHA256).Hash
+        $dstHash = (Get-FileHash $Dst -Algorithm SHA256).Hash
+        if ($srcHash -eq $dstHash) { return }
+        Rename-Item $Dst "$Dst.mosaic-bak-$BackupStamp"
+    }
+
+    Copy-Item $Src $Dst -Force
+}
+
+function Remove-LegacyPath {
+    param([string]$Path)
+
+    if (-not (Test-Path $Path)) { return }
+
+    $item = Get-Item $Path -Force -ErrorAction SilentlyContinue
+    if ($item -and $item.Attributes -band [System.IO.FileAttributes]::ReparsePoint) {
+        Remove-Item $Path -Force
+        return
+    }
+
+    if (Test-Path $Path -PathType Container) {
+        # Remove symlinks/junctions inside, then empty dirs
+        Get-ChildItem $Path -Recurse -Force | Where-Object {
+            $_.Attributes -band [System.IO.FileAttributes]::ReparsePoint
+        } | Remove-Item -Force
+
+        Get-ChildItem $Path -Recurse -Directory -Force |
+            Sort-Object { $_.FullName.Length } -Descending |
+            Where-Object { (Get-ChildItem $_.FullName -Force | Measure-Object).Count -eq 0 } |
+            Remove-Item -Force
+    }
+}
+
+# Remove legacy compatibility paths
+$legacyPaths = @(
+    (Join-Path $env:USERPROFILE ".claude\agent-guides"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\git"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\codex"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\bootstrap"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\cicd"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\portainer"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\debug-hook.sh"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\qa-hook-handler.sh"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\qa-hook-stdin.sh"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\qa-hook-wrapper.sh"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\qa-queue-monitor.sh"),
+    (Join-Path $env:USERPROFILE ".claude\scripts\remediation-hook-handler.sh"),
+    (Join-Path $env:USERPROFILE ".claude\templates"),
+    (Join-Path $env:USERPROFILE ".claude\presets\domains"),
+    (Join-Path $env:USERPROFILE ".claude\presets\tech-stacks"),
+    (Join-Path $env:USERPROFILE ".claude\presets\workflows"),
+    (Join-Path $env:USERPROFILE ".claude\presets\jarvis-loop.json")
+)
+
+foreach ($p in $legacyPaths) {
+    Remove-LegacyPath $p
+}
+
+# Claude-specific runtime files (settings, hooks — CLAUDE.md is now a thin pointer)
+$runtimeFiles = @("CLAUDE.md", "settings.json", "hooks-config.json", "context7-integration.md")
+foreach ($rf in $runtimeFiles) {
+    $src = Join-Path $MosaicHome "runtime\claude\$rf"
+    if (-not (Test-Path $src)) { continue }
+    $dst = Join-Path $env:USERPROFILE ".claude\$rf"
+    Copy-FileManaged $src $dst
+}
+
+# OpenCode runtime adapter
+$opencodeSrc = Join-Path $MosaicHome "runtime\opencode\AGENTS.md"
+if (Test-Path $opencodeSrc) {
+    $opencodeDst = Join-Path $env:USERPROFILE ".config\opencode\AGENTS.md"
+    Copy-FileManaged $opencodeSrc $opencodeDst
+}
+
+# Codex runtime adapter
+$codexSrc = Join-Path $MosaicHome "runtime\codex\instructions.md"
+if (Test-Path $codexSrc) {
+    $codexDir = Join-Path $env:USERPROFILE ".codex"
+    if (-not (Test-Path $codexDir)) { New-Item -ItemType Directory -Path $codexDir -Force | Out-Null }
+    $codexDst = Join-Path $codexDir "instructions.md"
+    Copy-FileManaged $codexSrc $codexDst
+}
+
+$seqScript = Join-Path $MosaicHome "bin\mosaic-ensure-sequential-thinking.ps1"
+if (Test-Path $seqScript) {
+    & $seqScript
+}
+
+Write-Host "[mosaic-link] Runtime assets synced (non-symlink mode)"
+Write-Host "[mosaic-link] Canonical source: $MosaicHome"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-log-limitation
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-log-limitation
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [[ -x "scripts/agent/log-limitation.sh" ]]; then
+  exec bash scripts/agent/log-limitation.sh "$@"
+fi
+
+echo "[mosaic] Missing scripts/agent/log-limitation.sh in $(pwd)" >&2
+exit 1
--- a/packages/mosaic/framework/tools/_scripts/mosaic-migrate-local-skills
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-migrate-local-skills
@@ -0,0 +1,88 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+APPLY=0
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [--apply]
+
+Migrate runtime-local skill directories (e.g. ~/.claude/skills/jarvis) to Mosaic-managed
+skills by replacing local directories with symlinks to ~/.config/mosaic/skills-local.
+
+Default mode is dry-run.
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --apply)
+      APPLY=1
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+skill_roots=(
+  "$HOME/.claude/skills"
+  "$HOME/.codex/skills"
+  "$HOME/.config/opencode/skills"
+  "$HOME/.pi/agent/skills"
+)
+
+if [[ ! -d "$MOSAIC_HOME/skills-local" ]]; then
+  echo "[mosaic-local-skills] Missing local skills dir: $MOSAIC_HOME/skills-local" >&2
+  exit 1
+fi
+
+count=0
+
+while IFS= read -r -d '' local_skill; do
+  name="$(basename "$local_skill")"
+  src="$MOSAIC_HOME/skills-local/$name"
+  [[ -d "$src" ]] || continue
+
+  for root in "${skill_roots[@]}"; do
+    [[ -d "$root" ]] || continue
+    target="$root/$name"
+
+    # Already linked correctly.
+    if [[ -L "$target" ]]; then
+      target_real="$(readlink -f "$target" 2>/dev/null || true)"
+      src_real="$(readlink -f "$src" 2>/dev/null || true)"
+      if [[ -n "$target_real" && -n "$src_real" && "$target_real" == "$src_real" ]]; then
+        continue
+      fi
+    fi
+
+    # Only migrate local directories containing SKILL.md
+    if [[ -d "$target" && -f "$target/SKILL.md" && ! -L "$target" ]]; then
+      count=$((count + 1))
+      if [[ $APPLY -eq 1 ]]; then
+        stamp="$(date +%Y%m%d%H%M%S)"
+        mv "$target" "${target}.mosaic-bak-${stamp}"
+        ln -s "$src" "$target"
+        echo "[mosaic-local-skills] migrated: $target -> $src"
+      else
+        echo "[mosaic-local-skills] would migrate: $target -> $src"
+      fi
+    fi
+  done
+done < <(find "$MOSAIC_HOME/skills-local" -mindepth 1 -maxdepth 1 \( -type d -o -type l \) -print0)
+
+if [[ $APPLY -eq 1 ]]; then
+  echo "[mosaic-local-skills] complete: migrated=$count"
+else
+  echo "[mosaic-local-skills] dry-run: migratable=$count"
+  echo "[mosaic-local-skills] re-run with --apply to migrate"
+fi
--- a/packages/mosaic/framework/tools/_scripts/mosaic-migrate-local-skills.ps1
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-migrate-local-skills.ps1
@@ -0,0 +1,90 @@
+# mosaic-migrate-local-skills.ps1
+# Migrates runtime-local skill directories to Mosaic-managed junctions.
+# Uses directory junctions (no elevation required) with fallback to copies.
+# PowerShell equivalent of mosaic-migrate-local-skills (bash).
+$ErrorActionPreference = "Stop"
+
+param(
+    [switch]$Apply,
+    [switch]$Help
+)
+
+$MosaicHome = if ($env:MOSAIC_HOME) { $env:MOSAIC_HOME } else { Join-Path $env:USERPROFILE ".config\mosaic" }
+$LocalSkillsDir = Join-Path $MosaicHome "skills-local"
+
+if ($Help) {
+    Write-Host @"
+Usage: mosaic-migrate-local-skills.ps1 [-Apply] [-Help]
+
+Migrate runtime-local skill directories (e.g. ~/.claude/skills/jarvis) to
+Mosaic-managed skills by replacing local directories with junctions to
+~/.config/mosaic/skills-local.
+
+Default mode is dry-run.
+"@
+    exit 0
+}
+
+if (-not (Test-Path $LocalSkillsDir)) {
+    Write-Host "[mosaic-local-skills] Missing local skills dir: $LocalSkillsDir" -ForegroundColor Red
+    exit 1
+}
+
+$skillRoots = @(
+    (Join-Path $env:USERPROFILE ".claude\skills"),
+    (Join-Path $env:USERPROFILE ".codex\skills"),
+    (Join-Path $env:USERPROFILE ".config\opencode\skills")
+)
+
+$count = 0
+
+Get-ChildItem $LocalSkillsDir -Directory | ForEach-Object {
+    $name = $_.Name
+    $src = $_.FullName
+
+    foreach ($root in $skillRoots) {
+        if (-not (Test-Path $root)) { continue }
+        $target = Join-Path $root $name
+
+        # Already a junction/symlink — check if it points to the right place
+        $existing = Get-Item $target -Force -ErrorAction SilentlyContinue
+        if ($existing -and ($existing.Attributes -band [System.IO.FileAttributes]::ReparsePoint)) {
+            $currentTarget = $existing.Target
+            if ($currentTarget -and ($currentTarget -eq $src -or (Resolve-Path $currentTarget -ErrorAction SilentlyContinue).Path -eq (Resolve-Path $src -ErrorAction SilentlyContinue).Path)) {
+                continue
+            }
+        }
+
+        # Only migrate local directories containing SKILL.md
+        if ((Test-Path $target -PathType Container) -and
+            (Test-Path (Join-Path $target "SKILL.md")) -and
+            -not ($existing -and ($existing.Attributes -band [System.IO.FileAttributes]::ReparsePoint))) {
+
+            $count++
+            if ($Apply) {
+                $stamp = Get-Date -Format "yyyyMMddHHmmss"
+                Rename-Item $target "$target.mosaic-bak-$stamp"
+                try {
+                    New-Item -ItemType Junction -Path $target -Target $src -ErrorAction Stop | Out-Null
+                    Write-Host "[mosaic-local-skills] migrated: $target -> $src"
+                }
+                catch {
+                    Write-Host "[mosaic-local-skills] Junction failed for $name, falling back to copy"
+                    Copy-Item $src $target -Recurse -Force
+                    Write-Host "[mosaic-local-skills] copied: $target <- $src"
+                }
+            }
+            else {
+                Write-Host "[mosaic-local-skills] would migrate: $target -> $src"
+            }
+        }
+    }
+}
+
+if ($Apply) {
+    Write-Host "[mosaic-local-skills] complete: migrated=$count"
+}
+else {
+    Write-Host "[mosaic-local-skills] dry-run: migratable=$count"
+    Write-Host "[mosaic-local-skills] re-run with -Apply to migrate"
+}
--- a/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-drain
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-drain
@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+sync_cmd="$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-sync-tasks"
+run_cmd="$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-run"
+
+do_sync=1
+poll_sec=15
+extra_args=()
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --no-sync)
+      do_sync=0
+      shift
+      ;;
+    --poll-sec)
+      poll_sec="${2:-15}"
+      shift 2
+      ;;
+    *)
+      extra_args+=("$1")
+      shift
+      ;;
+  esac
+done
+
+if [[ $do_sync -eq 1 ]]; then
+  "$sync_cmd" --apply
+fi
+
+exec "$run_cmd" --until-drained --poll-sec "$poll_sec" "${extra_args[@]}"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-matrix-consume
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-matrix-consume
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+BRIDGE="$MOSAIC_HOME/tools/orchestrator-matrix/transport/matrix_transport.py"
+
+if [[ ! -f "$BRIDGE" ]]; then
+  echo "[mosaic-orch-matrix] missing transport bridge: $BRIDGE" >&2
+  exit 1
+fi
+
+exec python3 "$BRIDGE" --repo "$(pwd)" --mode consume "$@"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-matrix-cycle
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-matrix-cycle
@@ -0,0 +1,19 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+
+consume="$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-matrix-consume"
+run="$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-run"
+publish="$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-matrix-publish"
+
+for cmd in "$consume" "$run" "$publish"; do
+  if [[ ! -x "$cmd" ]]; then
+    echo "[mosaic-orch-cycle] missing executable: $cmd" >&2
+    exit 1
+  fi
+done
+
+"$consume"
+"$run" --once "$@"
+"$publish"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-matrix-publish
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-matrix-publish
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+BRIDGE="$MOSAIC_HOME/tools/orchestrator-matrix/transport/matrix_transport.py"
+
+if [[ ! -f "$BRIDGE" ]]; then
+  echo "[mosaic-orch-matrix] missing transport bridge: $BRIDGE" >&2
+  exit 1
+fi
+
+exec python3 "$BRIDGE" --repo "$(pwd)" --mode publish "$@"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-run
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-run
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+CTRL="$MOSAIC_HOME/tools/orchestrator-matrix/controller/mosaic_orchestrator.py"
+
+if [[ ! -f "$CTRL" ]]; then
+  echo "[mosaic-orchestrator] missing controller: $CTRL" >&2
+  exit 1
+fi
+
+exec python3 "$CTRL" --repo "$(pwd)" "$@"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-sync-tasks
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-orchestrator-sync-tasks
@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+SYNC="$MOSAIC_HOME/tools/orchestrator-matrix/controller/tasks_md_sync.py"
+
+if [[ ! -f "$SYNC" ]]; then
+  echo "[mosaic-orchestrator-sync] missing sync script: $SYNC" >&2
+  exit 1
+fi
+
+exec python3 "$SYNC" --repo "$(pwd)" "$@"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-projects
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-projects
@@ -0,0 +1,218 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+PROJECTS_FILE="$MOSAIC_HOME/projects.txt"
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") <command> [options]
+
+Commands:
+  init
+      Create projects registry file at ~/.config/mosaic/projects.txt
+
+  add <repo-path> [repo-path...]
+      Add one or more repos to the registry
+
+  remove <repo-path> [repo-path...]
+      Remove one or more repos from the registry
+
+  list
+      Show registered repos
+
+  bootstrap [--all|repo-path...] [--force] [--quality-template <name>]
+      Bootstrap registered repos or explicit repo paths
+
+  orchestrate <drain|start|status|stop> [--all|repo-path...] [--poll-sec N] [--no-sync] [--worker-cmd "cmd"]
+      Run orchestrator actions across repos from one command
+
+Examples:
+  mosaic-projects init
+  mosaic-projects add ~/src/syncagent ~/src/inventory-stickers
+  mosaic-projects bootstrap --all
+  mosaic-projects orchestrate drain --all --worker-cmd "codex -p"
+  mosaic-projects orchestrate start ~/src/syncagent --worker-cmd "opencode -p"
+USAGE
+}
+
+ensure_registry() {
+  mkdir -p "$MOSAIC_HOME"
+  if [[ ! -f "$PROJECTS_FILE" ]]; then
+    cat > "$PROJECTS_FILE" <<EOF
+# Mosaic managed projects (one absolute path per line)
+# Lines starting with # are ignored.
+EOF
+  fi
+}
+
+norm_path() {
+  local p="$1"
+  if [[ -d "$p" ]]; then
+    (cd "$p" && pwd)
+  else
+    return 1
+  fi
+}
+
+read_registry() {
+  ensure_registry
+  grep -vE '^\s*#|^\s*$' "$PROJECTS_FILE" | while read -r p; do
+    [[ -d "$p" ]] && echo "$p"
+  done
+}
+
+add_repo() {
+  local p="$1"
+  ensure_registry
+  local np
+  np="$(norm_path "$p")" || { echo "[mosaic-projects] skip missing dir: $p" >&2; return 1; }
+  if grep -Fxq "$np" "$PROJECTS_FILE"; then
+    echo "[mosaic-projects] already registered: $np"
+    return 0
+  fi
+  echo "$np" >> "$PROJECTS_FILE"
+  echo "[mosaic-projects] added: $np"
+}
+
+remove_repo() {
+  local p="$1"
+  ensure_registry
+  local np
+  np="$(norm_path "$p" 2>/dev/null || echo "$p")"
+  tmp="$(mktemp)"
+  grep -vFx "$np" "$PROJECTS_FILE" > "$tmp" || true
+  mv "$tmp" "$PROJECTS_FILE"
+  echo "[mosaic-projects] removed: $np"
+}
+
+resolve_targets() {
+  local use_all="$1"
+  shift
+  if [[ "$use_all" == "1" ]]; then
+    read_registry
+    return 0
+  fi
+  if [[ $# -gt 0 ]]; then
+    for p in "$@"; do
+      norm_path "$p" || { echo "[mosaic-projects] missing target: $p" >&2; exit 1; }
+    done
+    return 0
+  fi
+  if git rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+    git rev-parse --show-toplevel
+    return 0
+  fi
+  echo "[mosaic-projects] no targets provided. Use --all or pass repo paths." >&2
+  exit 1
+}
+
+cmd="${1:-}"
+if [[ -z "$cmd" ]]; then
+  usage
+  exit 1
+fi
+shift || true
+
+case "$cmd" in
+  init)
+    ensure_registry
+    echo "[mosaic-projects] registry ready: $PROJECTS_FILE"
+    ;;
+  add)
+    [[ $# -gt 0 ]] || { echo "[mosaic-projects] add requires repo path(s)" >&2; exit 1; }
+    for p in "$@"; do add_repo "$p"; done
+    ;;
+  remove)
+    [[ $# -gt 0 ]] || { echo "[mosaic-projects] remove requires repo path(s)" >&2; exit 1; }
+    for p in "$@"; do remove_repo "$p"; done
+    ;;
+  list)
+    read_registry
+    ;;
+  bootstrap)
+    use_all=0
+    force=0
+    quality_template=""
+    targets=()
+    while [[ $# -gt 0 ]]; do
+      case "$1" in
+        --all) use_all=1; shift ;;
+        --force) force=1; shift ;;
+        --quality-template) quality_template="${2:-}"; shift 2 ;;
+        *) targets+=("$1"); shift ;;
+      esac
+    done
+    mapfile -t repos < <(resolve_targets "$use_all" "${targets[@]}")
+    [[ ${#repos[@]} -gt 0 ]] || { echo "[mosaic-projects] no repos resolved"; exit 1; }
+    for repo in "${repos[@]}"; do
+      args=()
+      [[ $force -eq 1 ]] && args+=(--force)
+      [[ -n "$quality_template" ]] && args+=(--quality-template "$quality_template")
+      args+=("$repo")
+      echo "[mosaic-projects] bootstrap: $repo"
+      "$MOSAIC_HOME/tools/_scripts/mosaic-bootstrap-repo" "${args[@]}"
+      add_repo "$repo" || true
+    done
+    ;;
+  orchestrate)
+    action="${1:-}"
+    [[ -n "$action" ]] || { echo "[mosaic-projects] orchestrate requires action: drain|start|status|stop" >&2; exit 1; }
+    shift || true
+    use_all=0
+    poll_sec=15
+    no_sync=0
+    worker_cmd=""
+    targets=()
+    while [[ $# -gt 0 ]]; do
+      case "$1" in
+        --all) use_all=1; shift ;;
+        --poll-sec) poll_sec="${2:-15}"; shift 2 ;;
+        --no-sync) no_sync=1; shift ;;
+        --worker-cmd) worker_cmd="${2:-}"; shift 2 ;;
+        *) targets+=("$1"); shift ;;
+      esac
+    done
+    mapfile -t repos < <(resolve_targets "$use_all" "${targets[@]}")
+    [[ ${#repos[@]} -gt 0 ]] || { echo "[mosaic-projects] no repos resolved"; exit 1; }
+
+    for repo in "${repos[@]}"; do
+      echo "[mosaic-projects] orchestrate:$action -> $repo"
+      (
+        cd "$repo"
+        if [[ -n "$worker_cmd" ]]; then
+          export MOSAIC_WORKER_EXEC="$worker_cmd"
+        fi
+        if [[ -x "scripts/agent/orchestrator-daemon.sh" ]]; then
+          args=()
+          [[ "$action" == "start" || "$action" == "drain" ]] && args+=(--poll-sec "$poll_sec")
+          [[ $no_sync -eq 1 ]] && args+=(--no-sync)
+          bash scripts/agent/orchestrator-daemon.sh "$action" "${args[@]}"
+        else
+          case "$action" in
+            drain)
+              args=(--poll-sec "$poll_sec")
+              [[ $no_sync -eq 1 ]] && args+=(--no-sync)
+              "$MOSAIC_HOME/tools/_scripts/mosaic-orchestrator-drain" "${args[@]}"
+              ;;
+            status)
+              echo "[mosaic-projects] no daemon script in repo; run from bootstrapped repo or re-bootstrap"
+              ;;
+            start|stop)
+              echo "[mosaic-projects] action '$action' requires scripts/agent/orchestrator-daemon.sh (run bootstrap first)" >&2
+              exit 1
+              ;;
+            *)
+              echo "[mosaic-projects] unsupported action: $action" >&2
+              exit 1
+              ;;
+          esac
+        fi
+      )
+    done
+    ;;
+  *)
+    usage
+    exit 1
+    ;;
+esac
--- a/packages/mosaic/framework/tools/_scripts/mosaic-prune-legacy-runtime
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-prune-legacy-runtime
@@ -0,0 +1,95 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+RUNTIME="claude"
+APPLY=0
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [options]
+
+Remove legacy runtime files that were preserved as *.mosaic-bak-* after Mosaic linking.
+Only removes backups when the active file is a symlink to ~/.config/mosaic.
+
+Options:
+  --runtime <name>   Runtime to prune (default: claude)
+  --apply            Perform deletions (default: dry-run)
+  -h, --help         Show help
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --runtime)
+      [[ $# -lt 2 ]] && { echo "Missing value for --runtime" >&2; exit 1; }
+      RUNTIME="$2"
+      shift 2
+      ;;
+    --apply)
+      APPLY=1
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+case "$RUNTIME" in
+  claude)
+    TARGET_ROOT="$HOME/.claude"
+    ;;
+  *)
+    echo "Unsupported runtime: $RUNTIME" >&2
+    exit 1
+    ;;
+esac
+
+if [[ ! -d "$TARGET_ROOT" ]]; then
+  echo "[mosaic-prune] Runtime directory not found: $TARGET_ROOT" >&2
+  exit 1
+fi
+
+mosaic_real="$(readlink -f "$MOSAIC_HOME")"
+count_candidates=0
+count_deletable=0
+
+while IFS= read -r -d '' bak; do
+  count_candidates=$((count_candidates + 1))
+
+  base="${bak%%.mosaic-bak-*}"
+  if [[ ! -L "$base" ]]; then
+    continue
+  fi
+
+  base_real="$(readlink -f "$base" 2>/dev/null || true)"
+  if [[ -z "$base_real" ]]; then
+    continue
+  fi
+
+  if [[ "$base_real" != "$mosaic_real"/* ]]; then
+    continue
+  fi
+
+  count_deletable=$((count_deletable + 1))
+  if [[ $APPLY -eq 1 ]]; then
+    rm -rf "$bak"
+    echo "[mosaic-prune] deleted: $bak"
+  else
+    echo "[mosaic-prune] would delete: $bak"
+  fi
+done < <(find "$TARGET_ROOT" \( -type f -o -type d \) -name '*.mosaic-bak-*' -print0)
+
+if [[ $APPLY -eq 1 ]]; then
+  echo "[mosaic-prune] complete: deleted=$count_deletable candidates=$count_candidates runtime=$RUNTIME"
+else
+  echo "[mosaic-prune] dry-run: deletable=$count_deletable candidates=$count_candidates runtime=$RUNTIME"
+  echo "[mosaic-prune] re-run with --apply to delete"
+fi
--- a/packages/mosaic/framework/tools/_scripts/mosaic-quality-apply
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-quality-apply
@@ -0,0 +1,65 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+TARGET_DIR="$(pwd)"
+TEMPLATE=""
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") --template <name> [--target <dir>]
+
+Apply Mosaic quality tools templates into a project.
+
+Templates:
+  typescript-node
+  typescript-nextjs
+  monorepo
+
+Examples:
+  $(basename "$0") --template typescript-node --target ~/src/my-project
+  $(basename "$0") --template monorepo
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --template)
+      TEMPLATE="${2:-}"
+      shift 2
+      ;;
+    --target)
+      TARGET_DIR="${2:-}"
+      shift 2
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+if [[ -z "$TEMPLATE" ]]; then
+  echo "[mosaic-quality] Missing required --template" >&2
+  usage >&2
+  exit 1
+fi
+
+if [[ ! -d "$TARGET_DIR" ]]; then
+  echo "[mosaic-quality] Target directory does not exist: $TARGET_DIR" >&2
+  exit 1
+fi
+
+SCRIPT="$MOSAIC_HOME/tools/quality/scripts/install.sh"
+if [[ ! -x "$SCRIPT" ]]; then
+  echo "[mosaic-quality] Missing install script: $SCRIPT" >&2
+  exit 1
+fi
+
+echo "[mosaic-quality] Applying template '$TEMPLATE' to $TARGET_DIR"
+"$SCRIPT" --template "$TEMPLATE" --target "$TARGET_DIR"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-quality-verify
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-quality-verify
@@ -0,0 +1,52 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+TARGET_DIR="$(pwd)"
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [--target <dir>]
+
+Run quality-rails verification checks inside a target repository.
+
+Examples:
+  $(basename "$0")
+  $(basename "$0") --target ~/src/my-project
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --target)
+      TARGET_DIR="${2:-}"
+      shift 2
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+if [[ ! -d "$TARGET_DIR" ]]; then
+  echo "[mosaic-quality] Target directory does not exist: $TARGET_DIR" >&2
+  exit 1
+fi
+
+SCRIPT="$MOSAIC_HOME/tools/quality/scripts/verify.sh"
+if [[ ! -x "$SCRIPT" ]]; then
+  echo "[mosaic-quality] Missing verify script: $SCRIPT" >&2
+  exit 1
+fi
+
+echo "[mosaic-quality] Running verification in $TARGET_DIR"
+(
+  cd "$TARGET_DIR"
+  "$SCRIPT"
+)
--- a/packages/mosaic/framework/tools/_scripts/mosaic-release-upgrade
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-release-upgrade
@@ -0,0 +1,124 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# mosaic-release-upgrade — Upgrade installed Mosaic framework release.
+#
+# This re-runs the remote installer with explicit install mode controls.
+# Default behavior is safe/idempotent (keep SOUL.md + memory).
+#
+# Usage:
+#   mosaic-release-upgrade
+#   mosaic-release-upgrade --ref main --keep
+#   mosaic-release-upgrade --ref v0.2.0 --overwrite --yes
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+REMOTE_SCRIPT_URL="${MOSAIC_REMOTE_INSTALL_URL:-https://git.mosaicstack.dev/mosaic/mosaic-stack/raw/branch/main/tools/install.sh}"
+BOOTSTRAP_REF="${MOSAIC_BOOTSTRAP_REF:-main}"
+INSTALL_MODE="${MOSAIC_INSTALL_MODE:-keep}" # keep|overwrite
+YES=false
+DRY_RUN=false
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [options]
+
+Upgrade the installed Mosaic framework release.
+
+Options:
+  --ref <name>         Bootstrap archive ref (branch/tag/commit). Default: main
+  --keep               Keep local files (SOUL.md, memory/) during upgrade (default)
+  --overwrite          Overwrite target install directory contents
+  -y, --yes            Skip confirmation prompt
+  --dry-run            Show actions without executing
+  -h, --help           Show this help
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --ref)
+      [[ $# -lt 2 ]] && { echo "Missing value for --ref" >&2; exit 1; }
+      BOOTSTRAP_REF="$2"
+      shift 2
+      ;;
+    --keep)
+      INSTALL_MODE="keep"
+      shift
+      ;;
+    --overwrite)
+      INSTALL_MODE="overwrite"
+      shift
+      ;;
+    -y|--yes)
+      YES=true
+      shift
+      ;;
+    --dry-run)
+      DRY_RUN=true
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+case "$INSTALL_MODE" in
+  keep|overwrite) ;;
+  *)
+    echo "[mosaic-release-upgrade] Invalid install mode: $INSTALL_MODE" >&2
+    exit 1
+    ;;
+esac
+
+current_version="unknown"
+if [[ -x "$MOSAIC_HOME/bin/mosaic" ]]; then
+  current_version="$("$MOSAIC_HOME/bin/mosaic" --version 2>/dev/null | awk '{print $2}' || true)"
+  [[ -n "$current_version" ]] || current_version="unknown"
+fi
+
+echo "[mosaic-release-upgrade] Current version: $current_version"
+echo "[mosaic-release-upgrade] Target ref: $BOOTSTRAP_REF"
+echo "[mosaic-release-upgrade] Install mode: $INSTALL_MODE"
+echo "[mosaic-release-upgrade] Installer URL: $REMOTE_SCRIPT_URL"
+
+if [[ "$DRY_RUN" == "true" ]]; then
+  echo "[mosaic-release-upgrade] Dry run: no changes applied."
+  exit 0
+fi
+
+if [[ "$YES" != "true" && -t 0 ]]; then
+  printf "Proceed with Mosaic release upgrade? [y/N]: "
+  read -r confirm
+  case "${confirm:-n}" in
+    y|Y|yes|YES) ;;
+    *)
+      echo "[mosaic-release-upgrade] Aborted."
+      exit 1
+      ;;
+  esac
+fi
+
+if command -v curl >/dev/null 2>&1; then
+  curl -sL "$REMOTE_SCRIPT_URL" | \
+    MOSAIC_BOOTSTRAP_REF="$BOOTSTRAP_REF" \
+    MOSAIC_INSTALL_MODE="$INSTALL_MODE" \
+    MOSAIC_HOME="$MOSAIC_HOME" \
+    sh
+elif command -v wget >/dev/null 2>&1; then
+  wget -qO- "$REMOTE_SCRIPT_URL" | \
+    MOSAIC_BOOTSTRAP_REF="$BOOTSTRAP_REF" \
+    MOSAIC_INSTALL_MODE="$INSTALL_MODE" \
+    MOSAIC_HOME="$MOSAIC_HOME" \
+    sh
+else
+  echo "[mosaic-release-upgrade] ERROR: curl or wget required." >&2
+  exit 1
+fi
+
--- a/packages/mosaic/framework/tools/_scripts/mosaic-release-upgrade.ps1
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-release-upgrade.ps1
@@ -0,0 +1,65 @@
+# mosaic-release-upgrade.ps1 — Upgrade installed Mosaic framework release (Windows)
+#
+# Usage:
+#   mosaic-release-upgrade.ps1
+#   mosaic-release-upgrade.ps1 -Ref main -Keep
+#   mosaic-release-upgrade.ps1 -Ref v0.2.0 -Overwrite -Yes
+#
+param(
+    [string]$Ref = $(if ($env:MOSAIC_BOOTSTRAP_REF) { $env:MOSAIC_BOOTSTRAP_REF } else { "main" }),
+    [switch]$Keep,
+    [switch]$Overwrite,
+    [switch]$Yes,
+    [switch]$DryRun
+)
+
+$ErrorActionPreference = "Stop"
+
+$MosaicHome = if ($env:MOSAIC_HOME) { $env:MOSAIC_HOME } else { Join-Path $env:USERPROFILE ".config\mosaic" }
+$RemoteInstallerUrl = if ($env:MOSAIC_REMOTE_INSTALL_URL) {
+    $env:MOSAIC_REMOTE_INSTALL_URL
+} else {
+    "https://git.mosaicstack.dev/mosaic/mosaic-stack/raw/branch/main/tools/install.sh"
+}
+
+$installMode = if ($Overwrite) { "overwrite" } elseif ($Keep) { "keep" } elseif ($env:MOSAIC_INSTALL_MODE) { $env:MOSAIC_INSTALL_MODE } else { "keep" }
+if ($installMode -notin @("keep", "overwrite")) {
+    Write-Host "[mosaic-release-upgrade] Invalid install mode: $installMode" -ForegroundColor Red
+    exit 1
+}
+
+$currentVersion = "unknown"
+$mosaicCmd = Join-Path $MosaicHome "bin\mosaic.ps1"
+if (Test-Path $mosaicCmd) {
+    try {
+        $currentVersion = (& $mosaicCmd --version) -replace '^mosaic\s+', ''
+    }
+    catch {
+        $currentVersion = "unknown"
+    }
+}
+
+Write-Host "[mosaic-release-upgrade] Current version: $currentVersion"
+Write-Host "[mosaic-release-upgrade] Target ref: $Ref"
+Write-Host "[mosaic-release-upgrade] Install mode: $installMode"
+Write-Host "[mosaic-release-upgrade] Installer URL: $RemoteInstallerUrl"
+
+if ($DryRun) {
+    Write-Host "[mosaic-release-upgrade] Dry run: no changes applied."
+    exit 0
+}
+
+if (-not $Yes) {
+    $confirmation = Read-Host "Proceed with Mosaic release upgrade? [y/N]"
+    if ($confirmation -notin @("y", "Y", "yes", "YES")) {
+        Write-Host "[mosaic-release-upgrade] Aborted."
+        exit 1
+    }
+}
+
+$env:MOSAIC_BOOTSTRAP_REF = $Ref
+$env:MOSAIC_INSTALL_MODE = $installMode
+$env:MOSAIC_HOME = $MosaicHome
+
+Invoke-RestMethod -Uri $RemoteInstallerUrl | Invoke-Expression
+
--- a/packages/mosaic/framework/tools/_scripts/mosaic-session-end
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-session-end
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [[ -x "scripts/agent/session-end.sh" ]]; then
+  exec bash scripts/agent/session-end.sh "$@"
+fi
+
+echo "[mosaic] Missing scripts/agent/session-end.sh in $(pwd)" >&2
+exit 1
--- a/packages/mosaic/framework/tools/_scripts/mosaic-session-start
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-session-start
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+if [[ -x "scripts/agent/session-start.sh" ]]; then
+  exec bash scripts/agent/session-start.sh
+fi
+
+echo "[mosaic] Missing scripts/agent/session-start.sh in $(pwd)" >&2
+exit 1
--- a/packages/mosaic/framework/tools/_scripts/mosaic-sync-skills
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-sync-skills
@@ -0,0 +1,183 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+SKILLS_REPO_URL="${MOSAIC_SKILLS_REPO_URL:-https://git.mosaicstack.dev/mosaic/agent-skills.git}"
+SKILLS_REPO_DIR="${MOSAIC_SKILLS_REPO_DIR:-$MOSAIC_HOME/sources/agent-skills}"
+MOSAIC_SKILLS_DIR="$MOSAIC_HOME/skills"
+MOSAIC_LOCAL_SKILLS_DIR="$MOSAIC_HOME/skills-local"
+
+fetch=1
+link_only=0
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [options]
+
+Sync canonical skills into ~/.config/mosaic/skills and link all Mosaic skills into runtime skill directories.
+
+Options:
+  --link-only     Skip git clone/pull and only relink from ~/.config/mosaic/{skills,skills-local}
+  --no-link       Sync canonical skills but do not update runtime links
+  -h, --help      Show help
+
+Env:
+  MOSAIC_HOME               Default: ~/.config/mosaic
+  MOSAIC_SKILLS_REPO_URL    Default: https://git.mosaicstack.dev/mosaic/agent-skills.git
+  MOSAIC_SKILLS_REPO_DIR    Default: ~/.config/mosaic/sources/agent-skills
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --link-only)
+      fetch=0
+      shift
+      ;;
+    --no-link)
+      link_only=1
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+mkdir -p "$MOSAIC_HOME" "$MOSAIC_SKILLS_DIR" "$MOSAIC_LOCAL_SKILLS_DIR"
+
+if [[ $fetch -eq 1 ]]; then
+  if [[ -d "$SKILLS_REPO_DIR/.git" ]]; then
+    echo "[mosaic-skills] Updating skills source: $SKILLS_REPO_DIR"
+    git -C "$SKILLS_REPO_DIR" pull --rebase
+  else
+    echo "[mosaic-skills] Cloning skills source to: $SKILLS_REPO_DIR"
+    mkdir -p "$(dirname "$SKILLS_REPO_DIR")"
+    git clone "$SKILLS_REPO_URL" "$SKILLS_REPO_DIR"
+  fi
+
+  SOURCE_SKILLS_DIR="$SKILLS_REPO_DIR/skills"
+  if [[ ! -d "$SOURCE_SKILLS_DIR" ]]; then
+    echo "[mosaic-skills] Missing source skills dir: $SOURCE_SKILLS_DIR" >&2
+    exit 1
+  fi
+
+  if command -v rsync >/dev/null 2>&1; then
+    rsync -a --delete "$SOURCE_SKILLS_DIR/" "$MOSAIC_SKILLS_DIR/"
+  else
+    rm -rf "$MOSAIC_SKILLS_DIR"/*
+    cp -R "$SOURCE_SKILLS_DIR"/* "$MOSAIC_SKILLS_DIR"/
+  fi
+fi
+
+if [[ ! -d "$MOSAIC_SKILLS_DIR" ]]; then
+  echo "[mosaic-skills] Canonical skills dir missing: $MOSAIC_SKILLS_DIR" >&2
+  exit 1
+fi
+
+if [[ $link_only -eq 1 ]]; then
+  echo "[mosaic-skills] Canonical sync completed (link update skipped)"
+  exit 0
+fi
+
+link_targets=(
+  "$HOME/.claude/skills"
+  "$HOME/.codex/skills"
+  "$HOME/.config/opencode/skills"
+  "$HOME/.pi/agent/skills"
+)
+
+canonical_real="$(readlink -f "$MOSAIC_SKILLS_DIR")"
+
+link_skill_into_target() {
+  local skill_path="$1"
+  local target_dir="$2"
+
+  local name link_path
+  name="$(basename "$skill_path")"
+
+  # Do not distribute hidden/system skill directories globally.
+  if [[ "$name" == .* ]]; then
+    return
+  fi
+
+  link_path="$target_dir/$name"
+
+  if [[ -L "$link_path" ]]; then
+    ln -sfn "$skill_path" "$link_path"
+    return
+  fi
+
+  if [[ -e "$link_path" ]]; then
+    echo "[mosaic-skills] Preserve existing runtime-specific entry: $link_path"
+    return
+  fi
+
+  ln -s "$skill_path" "$link_path"
+}
+
+is_mosaic_skill_name() {
+  local name="$1"
+  # -d follows symlinks; -L catches broken symlinks that still indicate ownership
+  [[ -d "$MOSAIC_SKILLS_DIR/$name" || -L "$MOSAIC_SKILLS_DIR/$name" ]] && return 0
+  [[ -d "$MOSAIC_LOCAL_SKILLS_DIR/$name" || -L "$MOSAIC_LOCAL_SKILLS_DIR/$name" ]] && return 0
+  return 1
+}
+
+prune_stale_links_in_target() {
+  local target_dir="$1"
+
+  while IFS= read -r -d '' link_path; do
+    local name resolved
+    name="$(basename "$link_path")"
+
+    if is_mosaic_skill_name "$name"; then
+      continue
+    fi
+
+    resolved="$(readlink -f "$link_path" 2>/dev/null || true)"
+    if [[ -z "$resolved" ]]; then
+      rm -f "$link_path"
+      echo "[mosaic-skills] Removed stale broken skill link: $link_path"
+      continue
+    fi
+
+    if [[ "$resolved" == "$MOSAIC_HOME/"* ]]; then
+      rm -f "$link_path"
+      echo "[mosaic-skills] Removed stale retired skill link: $link_path"
+    fi
+  done < <(find "$target_dir" -mindepth 1 -maxdepth 1 -type l -print0)
+}
+
+for target in "${link_targets[@]}"; do
+  mkdir -p "$target"
+
+  # If target already resolves to canonical dir, skip to avoid self-link recursion/corruption.
+  target_real="$(readlink -f "$target" 2>/dev/null || true)"
+  if [[ -n "$target_real" && "$target_real" == "$canonical_real" ]]; then
+    echo "[mosaic-skills] Skip target (already canonical): $target"
+    continue
+  fi
+
+  prune_stale_links_in_target "$target"
+
+  while IFS= read -r -d '' skill; do
+    link_skill_into_target "$skill" "$target"
+  done < <(find "$MOSAIC_SKILLS_DIR" -mindepth 1 -maxdepth 1 -type d -print0)
+
+  if [[ -d "$MOSAIC_LOCAL_SKILLS_DIR" ]]; then
+    while IFS= read -r -d '' skill; do
+      link_skill_into_target "$skill" "$target"
+    done < <(find "$MOSAIC_LOCAL_SKILLS_DIR" -mindepth 1 -maxdepth 1 \( -type d -o -type l \) -print0)
+  fi
+
+  echo "[mosaic-skills] Linked skills into: $target"
+done
+
+echo "[mosaic-skills] Complete"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-sync-skills.ps1
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-sync-skills.ps1
@@ -0,0 +1,126 @@
+# mosaic-sync-skills.ps1
+# Syncs canonical skills and links them into agent runtime skill directories.
+# Uses directory junctions (no elevation required) with fallback to copies.
+# PowerShell equivalent of mosaic-sync-skills (bash).
+$ErrorActionPreference = "Stop"
+
+param(
+    [switch]$LinkOnly,
+    [switch]$NoLink,
+    [switch]$Help
+)
+
+$MosaicHome = if ($env:MOSAIC_HOME) { $env:MOSAIC_HOME } else { Join-Path $env:USERPROFILE ".config\mosaic" }
+$SkillsRepoUrl = if ($env:MOSAIC_SKILLS_REPO_URL) { $env:MOSAIC_SKILLS_REPO_URL } else { "https://git.mosaicstack.dev/mosaic/agent-skills.git" }
+$SkillsRepoDir = if ($env:MOSAIC_SKILLS_REPO_DIR) { $env:MOSAIC_SKILLS_REPO_DIR } else { Join-Path $MosaicHome "sources\agent-skills" }
+$MosaicSkillsDir = Join-Path $MosaicHome "skills"
+$MosaicLocalSkillsDir = Join-Path $MosaicHome "skills-local"
+
+if ($Help) {
+    Write-Host @"
+Usage: mosaic-sync-skills.ps1 [-LinkOnly] [-NoLink] [-Help]
+
+Sync canonical skills into ~/.config/mosaic/skills and link all Mosaic skills
+into runtime skill directories using directory junctions.
+
+Options:
+  -LinkOnly     Skip git clone/pull and only relink
+  -NoLink       Sync canonical skills but do not update runtime links
+  -Help         Show help
+"@
+    exit 0
+}
+
+foreach ($d in @($MosaicHome, $MosaicSkillsDir, $MosaicLocalSkillsDir)) {
+    if (-not (Test-Path $d)) { New-Item -ItemType Directory -Path $d -Force | Out-Null }
+}
+
+# Fetch skills from git
+if (-not $LinkOnly) {
+    if (Test-Path (Join-Path $SkillsRepoDir ".git")) {
+        Write-Host "[mosaic-skills] Updating skills source: $SkillsRepoDir"
+        git -C $SkillsRepoDir pull --rebase
+    }
+    else {
+        Write-Host "[mosaic-skills] Cloning skills source to: $SkillsRepoDir"
+        $parentDir = Split-Path $SkillsRepoDir -Parent
+        if (-not (Test-Path $parentDir)) { New-Item -ItemType Directory -Path $parentDir -Force | Out-Null }
+        git clone $SkillsRepoUrl $SkillsRepoDir
+    }
+
+    $sourceSkillsDir = Join-Path $SkillsRepoDir "skills"
+    if (-not (Test-Path $sourceSkillsDir)) {
+        Write-Host "[mosaic-skills] Missing source skills dir: $sourceSkillsDir" -ForegroundColor Red
+        exit 1
+    }
+
+    # Sync: remove old, copy new
+    if (Test-Path $MosaicSkillsDir) {
+        Get-ChildItem $MosaicSkillsDir | Remove-Item -Recurse -Force
+    }
+    Copy-Item "$sourceSkillsDir\*" $MosaicSkillsDir -Recurse -Force
+}
+
+if (-not (Test-Path $MosaicSkillsDir)) {
+    Write-Host "[mosaic-skills] Canonical skills dir missing: $MosaicSkillsDir" -ForegroundColor Red
+    exit 1
+}
+
+if ($NoLink) {
+    Write-Host "[mosaic-skills] Canonical sync completed (link update skipped)"
+    exit 0
+}
+
+function Link-SkillIntoTarget {
+    param([string]$SkillPath, [string]$TargetDir)
+
+    $name = Split-Path $SkillPath -Leaf
+    if ($name.StartsWith(".")) { return }
+
+    $linkPath = Join-Path $TargetDir $name
+
+    # Already a junction/symlink — recreate
+    $existing = Get-Item $linkPath -Force -ErrorAction SilentlyContinue
+    if ($existing -and ($existing.Attributes -band [System.IO.FileAttributes]::ReparsePoint)) {
+        Remove-Item $linkPath -Force
+    }
+    elseif ($existing) {
+        Write-Host "[mosaic-skills] Preserve existing runtime-specific entry: $linkPath"
+        return
+    }
+
+    # Try junction first, fall back to copy
+    try {
+        New-Item -ItemType Junction -Path $linkPath -Target $SkillPath -ErrorAction Stop | Out-Null
+    }
+    catch {
+        Write-Host "[mosaic-skills] Junction failed for $name, falling back to copy"
+        Copy-Item $SkillPath $linkPath -Recurse -Force
+    }
+}
+
+$linkTargets = @(
+    (Join-Path $env:USERPROFILE ".claude\skills"),
+    (Join-Path $env:USERPROFILE ".codex\skills"),
+    (Join-Path $env:USERPROFILE ".config\opencode\skills")
+)
+
+foreach ($target in $linkTargets) {
+    if (-not (Test-Path $target)) { New-Item -ItemType Directory -Path $target -Force | Out-Null }
+
+    # Link canonical skills
+    Get-ChildItem $MosaicSkillsDir -Directory | ForEach-Object {
+        Link-SkillIntoTarget $_.FullName $target
+    }
+
+    # Link local skills
+    if (Test-Path $MosaicLocalSkillsDir) {
+        Get-ChildItem $MosaicLocalSkillsDir -Directory | ForEach-Object {
+            Link-SkillIntoTarget $_.FullName $target
+        }
+    }
+
+    Write-Host "[mosaic-skills] Linked skills into: $target"
+}
+
+Write-Host "[mosaic-skills] Complete"
--- a/packages/mosaic/framework/tools/_scripts/mosaic-upgrade
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-upgrade
@@ -0,0 +1,218 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# mosaic-upgrade — Clean up stale per-project files after Mosaic centralization
+#
+# SOUL.md    → Now global at ~/.config/mosaic/SOUL.md (remove from projects)
+# CLAUDE.md  → Now a thin pointer or removable (replace with pointer or remove)
+# AGENTS.md  → Keep project-specific content, strip stale load-order directives
+#
+# Usage:
+#   mosaic-upgrade [path]          Upgrade a specific project (default: current dir)
+#   mosaic-upgrade --all           Scan ~/src/* for projects to upgrade
+#   mosaic-upgrade --dry-run       Show what would change without touching anything
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+
+# Colors (disabled if not a terminal)
+if [[ -t 1 ]]; then
+  GREEN='\033[0;32m' YELLOW='\033[0;33m' RED='\033[0;31m'
+  CYAN='\033[0;36m' BOLD='\033[1m' DIM='\033[2m' RESET='\033[0m'
+else
+  GREEN='' YELLOW='' RED='' CYAN='' BOLD='' DIM='' RESET=''
+fi
+
+ok()   { echo -e "  ${GREEN}✓${RESET} $1"; }
+skip() { echo -e "  ${DIM}–${RESET} $1"; }
+warn() { echo -e "  ${YELLOW}⚠${RESET} $1"; }
+act()  { echo -e "  ${CYAN}→${RESET} $1"; }
+
+DRY_RUN=false
+ALL=false
+TARGET=""
+SEARCH_ROOT="${HOME}/src"
+
+usage() {
+  cat <<USAGE
+mosaic-upgrade — Clean up stale per-project files
+
+Usage:
+  mosaic-upgrade [path]          Upgrade a specific project (default: cwd)
+  mosaic-upgrade --all           Scan ~/src/* for all git projects
+  mosaic-upgrade --dry-run       Preview changes without writing
+  mosaic-upgrade --all --dry-run Preview all projects
+
+After Mosaic centralization:
+  SOUL.md    → Removed (now global at ~/.config/mosaic/SOUL.md)
+  CLAUDE.md  → Replaced with thin pointer or removed
+  AGENTS.md  → Stale load-order sections stripped; project content preserved
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --dry-run)  DRY_RUN=true; shift ;;
+    --all)      ALL=true; shift ;;
+    --root)     SEARCH_ROOT="$2"; shift 2 ;;
+    -h|--help)  usage; exit 0 ;;
+    -*)         echo "Unknown flag: $1" >&2; usage >&2; exit 1 ;;
+    *)          TARGET="$1"; shift ;;
+  esac
+done
+
+# Generate the thin CLAUDE.md pointer
+CLAUDE_POINTER='# CLAUDE Compatibility Pointer
+
+This file exists so Claude Code sessions load Mosaic standards.
+
+## MANDATORY — Read Before Any Response
+
+BEFORE responding to any user message, READ `~/.config/mosaic/AGENTS.md`.
+
+That file is the universal agent configuration. Do NOT respond until you have loaded it.
+Then read the project-local `AGENTS.md` in this repository for project-specific guidance.'
+
+upgrade_project() {
+  local project_dir="$1"
+  local project_name
+  project_name="$(basename "$project_dir")"
+  local changed=false
+
+  echo -e "\n${BOLD}$project_name${RESET} ${DIM}($project_dir)${RESET}"
+
+  # ── SOUL.md ──────────────────────────────────────────────
+  local soul="$project_dir/SOUL.md"
+  if [[ -f "$soul" ]]; then
+    if [[ "$DRY_RUN" == "true" ]]; then
+      act "Would remove SOUL.md (now global at ~/.config/mosaic/SOUL.md)"
+    else
+      rm "$soul"
+      ok "Removed SOUL.md (now global)"
+    fi
+    changed=true
+  else
+    skip "No SOUL.md (already clean)"
+  fi
+
+  # ── CLAUDE.md ────────────────────────────────────────────
+  local claude_md="$project_dir/CLAUDE.md"
+  if [[ -f "$claude_md" ]]; then
+    local claude_content
+    claude_content="$(cat "$claude_md")"
+
+    # Check if it's already a thin pointer to AGENTS.md
+    if echo "$claude_content" | grep -q "READ.*~/.config/mosaic/AGENTS.md"; then
+      skip "CLAUDE.md already points to global AGENTS.md"
+    else
+      if [[ "$DRY_RUN" == "true" ]]; then
+        act "Would replace CLAUDE.md with thin pointer to global AGENTS.md"
+      else
+        # Back up the original
+        cp "$claude_md" "${claude_md}.mosaic-bak"
+        echo "$CLAUDE_POINTER" > "$claude_md"
+        ok "Replaced CLAUDE.md with pointer (backup: CLAUDE.md.mosaic-bak)"
+      fi
+      changed=true
+    fi
+  else
+    skip "No CLAUDE.md"
+  fi
+
+  # ── AGENTS.md (strip stale load-order, preserve project content) ─
+  local agents="$project_dir/AGENTS.md"
+  if [[ -f "$agents" ]]; then
+    # Detect stale load-order patterns
+    local has_stale=false
+
+    # Pattern 1: References to SOUL.md in load order
+    if grep -qE "(Read|READ|Load).*SOUL\.md" "$agents" 2>/dev/null; then
+      has_stale=true
+    fi
+
+    # Pattern 2: Old "## Load Order" section that references centralized files
+    if grep -q "## Load Order" "$agents" 2>/dev/null && \
+       grep -qE "STANDARDS\.md|SOUL\.md" "$agents" 2>/dev/null; then
+      has_stale=true
+    fi
+
+    # Pattern 3: Old ~/.mosaic/ path (pre-centralization)
+    if grep -q '~/.mosaic/' "$agents" 2>/dev/null; then
+      has_stale=true
+    fi
+
+    if [[ "$has_stale" == "true" ]]; then
+      if [[ "$DRY_RUN" == "true" ]]; then
+        act "Would strip stale load-order section from AGENTS.md"
+        # Show what we detect
+        if grep -qn "## Load Order" "$agents" 2>/dev/null; then
+          local line
+          line=$(grep -n "## Load Order" "$agents" | head -1 | cut -d: -f1)
+          echo -e "    ${DIM}Line $line: Found '## Load Order' section referencing SOUL.md/STANDARDS.md${RESET}"
+        fi
+        if grep -qn '~/.mosaic/' "$agents" 2>/dev/null; then
+          echo -e "    ${DIM}Found references to old ~/.mosaic/ path${RESET}"
+        fi
+      else
+        cp "$agents" "${agents}.mosaic-bak"
+
+        # Strip the Load Order section (from "## Load Order" to next "##" or "---")
+        if grep -q "## Load Order" "$agents"; then
+          awk '
+            /^## Load Order/ { skip=1; next }
+            skip && /^(## |---)/ { skip=0 }
+            skip { next }
+            { print }
+          ' "${agents}.mosaic-bak" > "$agents"
+        fi
+
+        # Fix old ~/.mosaic/ → ~/.config/mosaic/
+        if grep -q '~/.mosaic/' "$agents"; then
+          sed -i 's|~/.mosaic/|~/.config/mosaic/|g' "$agents"
+        fi
+
+        ok "Stripped stale load-order from AGENTS.md (backup: AGENTS.md.mosaic-bak)"
+      fi
+      changed=true
+    else
+      skip "AGENTS.md has no stale directives"
+    fi
+  else
+    skip "No AGENTS.md"
+  fi
+
+  # ── .claude/settings.json (leave alone) ──────────────────
+  # Project-specific settings are fine — don't touch them.
+
+  if [[ "$changed" == "false" ]]; then
+    echo -e "  ${GREEN}Already up to date.${RESET}"
+  fi
+}
+
+# ── Main ───────────────────────────────────────────────────
+
+if [[ "$DRY_RUN" == "true" ]]; then
+  echo -e "${BOLD}Mode: DRY RUN (no files will be changed)${RESET}"
+fi
+
+if [[ "$ALL" == "true" ]]; then
+  echo -e "${BOLD}Scanning $SEARCH_ROOT for projects...${RESET}"
+  count=0
+  for dir in "$SEARCH_ROOT"/*/; do
+    [[ -d "$dir/.git" ]] || continue
+    upgrade_project "$dir"
+    count=$((count + 1))
+  done
+  echo -e "\n${BOLD}Scanned $count projects.${RESET}"
+elif [[ -n "$TARGET" ]]; then
+  if [[ ! -d "$TARGET" ]]; then
+    echo "[mosaic-upgrade] ERROR: $TARGET is not a directory." >&2
+    exit 1
+  fi
+  upgrade_project "$TARGET"
+else
+  upgrade_project "$(pwd)"
+fi
+
+if [[ "$DRY_RUN" == "true" ]]; then
+  echo -e "\n${YELLOW}This was a dry run. Run without --dry-run to apply changes.${RESET}"
+fi
--- a/packages/mosaic/framework/tools/_scripts/mosaic-upgrade-slaves
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-upgrade-slaves
@@ -0,0 +1,116 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+BOOTSTRAP_CMD="$MOSAIC_HOME/tools/_scripts/mosaic-bootstrap-repo"
+
+roots=("$HOME/src")
+apply=0
+
+usage() {
+  cat <<USAGE
+Usage: $(basename "$0") [options]
+
+Upgrade all Mosaic-linked slave repositories by re-running repo bootstrap with --force.
+
+Options:
+  --root <path>   Add a search root (repeatable). Default: $HOME/src
+  --apply         Execute upgrades. Without this flag, script is dry-run.
+  -h, --help      Show this help
+USAGE
+}
+
+while [[ $# -gt 0 ]]; do
+  case "$1" in
+    --root)
+      [[ $# -lt 2 ]] && { echo "Missing value for --root" >&2; exit 1; }
+      roots+=("$2")
+      shift 2
+      ;;
+    --apply)
+      apply=1
+      shift
+      ;;
+    -h|--help)
+      usage
+      exit 0
+      ;;
+    *)
+      echo "Unknown argument: $1" >&2
+      usage >&2
+      exit 1
+      ;;
+  esac
+done
+
+if [[ ! -x "$BOOTSTRAP_CMD" ]]; then
+  echo "[mosaic-upgrade] Missing bootstrap command: $BOOTSTRAP_CMD" >&2
+  echo "[mosaic-upgrade] Install/refresh framework first: ~/.config/mosaic/install.sh" >&2
+  exit 1
+fi
+
+# De-duplicate roots while preserving order.
+uniq_roots=()
+for r in "${roots[@]}"; do
+  skip=0
+  for e in "${uniq_roots[@]}"; do
+    [[ "$r" == "$e" ]] && { skip=1; break; }
+  done
+  [[ $skip -eq 0 ]] && uniq_roots+=("$r")
+done
+
+candidates=()
+for root in "${uniq_roots[@]}"; do
+  [[ -d "$root" ]] || continue
+
+  while IFS= read -r marker; do
+    repo_dir="$(dirname "$(dirname "$marker")")"
+    if [[ -d "$repo_dir/.git" ]]; then
+      candidates+=("$repo_dir")
+    fi
+  done < <(find "$root" -type f -path '*/.mosaic/README.md' 2>/dev/null)
+done
+
+# De-duplicate repos while preserving order.
+repos=()
+for repo in "${candidates[@]}"; do
+  skip=0
+  for existing in "${repos[@]}"; do
+    [[ "$repo" == "$existing" ]] && { skip=1; break; }
+  done
+  [[ $skip -eq 0 ]] && repos+=("$repo")
+done
+
+count_total=${#repos[@]}
+count_ok=0
+count_fail=0
+
+mode="DRY-RUN"
+[[ $apply -eq 1 ]] && mode="APPLY"
+
+echo "[mosaic-upgrade] Mode: $mode"
+echo "[mosaic-upgrade] Roots: ${uniq_roots[*]}"
+echo "[mosaic-upgrade] Linked repos found: $count_total"
+
+if [[ $count_total -eq 0 ]]; then
+  exit 0
+fi
+
+for repo in "${repos[@]}"; do
+  if [[ $apply -eq 1 ]]; then
+    if "$BOOTSTRAP_CMD" "$repo" --force >/dev/null; then
+      echo "[mosaic-upgrade] upgraded: $repo"
+      count_ok=$((count_ok + 1))
+    else
+      echo "[mosaic-upgrade] FAILED: $repo" >&2
+      count_fail=$((count_fail + 1))
+    fi
+  else
+    echo "[mosaic-upgrade] would upgrade: $repo"
+  fi
+done
+
+if [[ $apply -eq 1 ]]; then
+  echo "[mosaic-upgrade] complete: ok=$count_ok failed=$count_fail total=$count_total"
+  [[ $count_fail -gt 0 ]] && exit 1
+fi
--- a/packages/mosaic/framework/tools/_scripts/mosaic-wizard
+++ b/packages/mosaic/framework/tools/_scripts/mosaic-wizard
@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# mosaic-wizard — Thin shell wrapper for the bundled TypeScript wizard
+MOSAIC_HOME="${MOSAIC_HOME:-$HOME/.config/mosaic}"
+
+# Look for the bundle in the installed location first, then the source repo
+WIZARD_BIN="$MOSAIC_HOME/dist/mosaic-wizard.mjs"
+if [[ ! -f "$WIZARD_BIN" ]]; then
+  WIZARD_BIN="$(cd "$(dirname "$0")/.." && pwd)/dist/mosaic-wizard.mjs"
+fi
+
+if [[ ! -f "$WIZARD_BIN" ]]; then
+  echo "[mosaic-wizard] ERROR: Wizard bundle not found." >&2
+  echo "[mosaic-wizard] Re-install with: npm install -g @mosaic/mosaic" >&2
+  exit 1
+fi
+
+if ! command -v node >/dev/null 2>&1; then
+  echo "[mosaic-wizard] ERROR: Node.js is required but not found." >&2
+  echo "[mosaic-wizard] Install Node.js 18+ from https://nodejs.org" >&2
+  exit 1
+fi
+
+exec node "$WIZARD_BIN" "$@"
--- a/packages/mosaic/framework/tools/orchestrator/session-run.sh
+++ b/packages/mosaic/framework/tools/orchestrator/session-run.sh
@@ -80,11 +80,11 @@ echo -e "${C_CYAN}Capsule:${C_RESET} $(next_task_capsule_path "$PROJECT")"

 cd "$PROJECT"
 if [[ "$YOLO" == true ]]; then
-  exec "$MOSAIC_HOME/bin/mosaic" yolo "$runtime" "$launch_prompt"
+  exec mosaic yolo "$runtime" "$launch_prompt"
 elif [[ "$runtime" == "claude" ]]; then
-  exec "$MOSAIC_HOME/bin/mosaic" claude "$launch_prompt"
+  exec mosaic claude "$launch_prompt"
 elif [[ "$runtime" == "codex" ]]; then
-  exec "$MOSAIC_HOME/bin/mosaic" codex "$launch_prompt"
+  exec mosaic codex "$launch_prompt"
 fi

 echo -e "${C_RED}Unsupported coord runtime: $runtime${C_RESET}" >&2