chore: bump @mosaic/mosaic and @mosaic/cli to 0.0.4

git pull --rebase fails with 'cannot pull with rebase: You have
unstaged changes' when the skills repo has local modifications.

Fix: detect dirty index/worktree, stash before pull, restore after.
Also gracefully handle pull failures (warn and continue with existing
checkout) and stash pop conflicts.

apps/gateway/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/gateway",
-  "version": "0.0.0",
+  "version": "0.0.2",
   "private": true,
   "type": "module",
   "main": "dist/main.js",

apps/web/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/web",
-  "version": "0.0.0",
+  "version": "0.0.2",
   "private": true,
   "scripts": {
     "build": "next build",

packages/agent/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/agent",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "exports": {

packages/auth/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/auth",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

packages/brain/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/brain",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "exports": {

packages/cli/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/cli",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.4",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

packages/cli/src/cli.ts

@@ -5,7 +5,7 @@ import { Command } from 'commander';
 import { createQualityRailsCli } from '@mosaic/quality-rails';
 import { registerAgentCommand } from './commands/agent.js';
 import { registerMissionCommand } from './commands/mission.js';
-import { registerPrdyCommand } from './commands/prdy.js';
+// prdy is registered via launch.ts
 import { registerLaunchCommands } from './commands/launch.js';
 
 const _require = createRequire(import.meta.url);
@@ -298,10 +298,6 @@ registerAgentCommand(program);
 
 registerMissionCommand(program);
 
-// ─── prdy ──────────────────────────────────────────────────────────────
-
-registerPrdyCommand(program);
-
 // ─── quality-rails ──────────────────────────────────────────────────────
 
 const qrWrapper = createQualityRailsCli();

packages/cli/src/commands/launch.ts

@@ -54,12 +54,24 @@ function checkRuntime(cmd: string): void {
 function checkSoul(): void {
   const soulPath = join(MOSAIC_HOME, 'SOUL.md');
   if (!existsSync(soulPath)) {
-    console.log('[mosaic] SOUL.md not found. Running mosaic init...');
+    console.log('[mosaic] SOUL.md not found. Running setup wizard...');
+
+    // Prefer the TypeScript wizard (idempotent, detects existing files)
+    try {
+      const result = spawnSync(process.execPath, [process.argv[1]!, 'wizard'], {
+        stdio: 'inherit',
+      });
+      if (result.status === 0 && existsSync(soulPath)) return;
+    } catch {
+      // Fall through to legacy init
+    }
+
+    // Fallback: legacy bash mosaic-init
     const initBin = join(MOSAIC_HOME, 'tools', '_scripts', 'mosaic-init');
     if (existsSync(initBin)) {
       spawnSync(initBin, [], { stdio: 'inherit' });
     } else {
-      console.error('[mosaic] mosaic-init not found. Run: mosaic wizard');
+      console.error('[mosaic] Setup failed. Run: mosaic wizard');
       process.exit(1);
     }
   }
@@ -461,23 +473,191 @@ function execRuntime(cmd: string, args: string[]): void {
   }
 }
 
-// ─── Framework script delegation (for tools that remain in bash) ─────────────
+// ─── Framework script/tool delegation ───────────────────────────────────────
 
-function delegateToFrameworkScript(script: string, args: string[]): never {
+function delegateToScript(scriptPath: string, args: string[], env?: Record<string, string>): never {
-  const scriptPath = join(MOSAIC_HOME, 'tools', '_scripts', script);
   if (!existsSync(scriptPath)) {
     console.error(`[mosaic] Script not found: ${scriptPath}`);
     process.exit(1);
   }
   try {
-    execFileSync(scriptPath, args, { stdio: 'inherit' });
+    execFileSync('bash', [scriptPath, ...args], {
+      stdio: 'inherit',
+      env: { ...process.env, ...env },
+    });
     process.exit(0);
   } catch (err) {
     process.exit((err as { status?: number }).status ?? 1);
   }
 }
 
-// ─── Commander registration ──────────────────────────────────────────────────
+function fwScript(name: string): string {
+  return join(MOSAIC_HOME, 'tools', '_scripts', name);
+}
+
+function toolScript(toolDir: string, name: string): string {
+  return join(MOSAIC_HOME, 'tools', toolDir, name);
+}
+
+// ─── Coord (mission orchestrator) ───────────────────────────────────────────
+
+const COORD_SUBCMDS: Record<string, string> = {
+  status: 'session-status.sh',
+  session: 'session-status.sh',
+  init: 'mission-init.sh',
+  mission: 'mission-status.sh',
+  progress: 'mission-status.sh',
+  continue: 'continue-prompt.sh',
+  next: 'continue-prompt.sh',
+  run: 'session-run.sh',
+  start: 'session-run.sh',
+  smoke: 'smoke-test.sh',
+  test: 'smoke-test.sh',
+  resume: 'session-resume.sh',
+  recover: 'session-resume.sh',
+};
+
+function runCoord(args: string[]): never {
+  checkMosaicHome();
+  let runtime = 'claude';
+  let yoloFlag = '';
+  const coordArgs: string[] = [];
+
+  for (const arg of args) {
+    if (arg === '--claude' || arg === '--codex' || arg === '--pi') {
+      runtime = arg.slice(2);
+    } else if (arg === '--yolo') {
+      yoloFlag = '--yolo';
+    } else {
+      coordArgs.push(arg);
+    }
+  }
+
+  const subcmd = coordArgs[0] ?? 'help';
+  const subArgs = coordArgs.slice(1);
+  const script = COORD_SUBCMDS[subcmd];
+
+  if (!script) {
+    console.log(`mosaic coord — mission coordinator tools
+
+Commands:
+  init --name <name> [opts]   Initialize a new mission
+  mission [--project <path>]  Show mission progress dashboard
+  status [--project <path>]   Check agent session health
+  continue [--project <path>] Generate continuation prompt
+  run [--project <path>]      Launch runtime with mission context
+  smoke                       Run orchestration smoke checks
+  resume [--project <path>]   Crash recovery
+
+Runtime: --claude (default) | --codex | --pi | --yolo`);
+    process.exit(subcmd === 'help' ? 0 : 1);
+  }
+
+  if (yoloFlag) subArgs.unshift(yoloFlag);
+  delegateToScript(toolScript('orchestrator', script), subArgs, {
+    MOSAIC_COORD_RUNTIME: runtime,
+  });
+}
+
+// ─── Prdy (PRD tools via framework scripts) ─────────────────────────────────
+
+const PRDY_SUBCMDS: Record<string, string> = {
+  init: 'prdy-init.sh',
+  update: 'prdy-update.sh',
+  validate: 'prdy-validate.sh',
+  check: 'prdy-validate.sh',
+  status: 'prdy-status.sh',
+};
+
+function runPrdyLocal(args: string[]): never {
+  checkMosaicHome();
+  let runtime = 'claude';
+  const prdyArgs: string[] = [];
+
+  for (const arg of args) {
+    if (arg === '--claude' || arg === '--codex' || arg === '--pi') {
+      runtime = arg.slice(2);
+    } else {
+      prdyArgs.push(arg);
+    }
+  }
+
+  const subcmd = prdyArgs[0] ?? 'help';
+  const subArgs = prdyArgs.slice(1);
+  const script = PRDY_SUBCMDS[subcmd];
+
+  if (!script) {
+    console.log(`mosaic prdy — PRD creation and validation
+
+Commands:
+  init [--project <path>] [--name <feature>]   Create docs/PRD.md
+  update [--project <path>]                    Update existing PRD
+  validate [--project <path>]                  Check PRD completeness
+  status [--project <path>]                    Quick PRD health check
+
+Runtime: --claude (default) | --codex | --pi`);
+    process.exit(subcmd === 'help' ? 0 : 1);
+  }
+
+  delegateToScript(toolScript('prdy', script), subArgs, {
+    MOSAIC_PRDY_RUNTIME: runtime,
+  });
+}
+
+// ─── Seq (sequential-thinking MCP) ──────────────────────────────────────────
+
+function runSeq(args: string[]): never {
+  checkMosaicHome();
+  const action = args[0] ?? 'check';
+  const rest = args.slice(1);
+  const checker = fwScript('mosaic-ensure-sequential-thinking');
+
+  switch (action) {
+    case 'check':
+      delegateToScript(checker, ['--check', ...rest]);
+      break; // unreachable
+    case 'fix':
+    case 'apply':
+      delegateToScript(checker, rest);
+      break;
+    case 'start': {
+      console.log('[mosaic] Starting sequential-thinking MCP server...');
+      try {
+        execFileSync('npx', ['-y', '@modelcontextprotocol/server-sequential-thinking', ...rest], {
+          stdio: 'inherit',
+        });
+        process.exit(0);
+      } catch (err) {
+        process.exit((err as { status?: number }).status ?? 1);
+      }
+      break;
+    }
+    default:
+      console.error(`[mosaic] Unknown seq subcommand '${action}'. Use: check|fix|start`);
+      process.exit(1);
+  }
+}
+
+// ─── Upgrade ────────────────────────────────────────────────────────────────
+
+function runUpgrade(args: string[]): never {
+  checkMosaicHome();
+  const subcmd = args[0];
+
+  if (!subcmd || subcmd === 'release') {
+    delegateToScript(fwScript('mosaic-release-upgrade'), args.slice(subcmd === 'release' ? 1 : 0));
+  } else if (subcmd === 'check') {
+    delegateToScript(fwScript('mosaic-release-upgrade'), ['--dry-run', ...args.slice(1)]);
+  } else if (subcmd === 'project') {
+    delegateToScript(fwScript('mosaic-upgrade'), args.slice(1));
+  } else if (subcmd.startsWith('-')) {
+    delegateToScript(fwScript('mosaic-release-upgrade'), args);
+  } else {
+    delegateToScript(fwScript('mosaic-upgrade'), args);
+  }
+}
+
+// ─── Commander registration ─────────────────────────────────────────────────
 
 export function registerLaunchCommands(program: Command): void {
   // Runtime launchers
@@ -509,15 +689,58 @@ export function registerLaunchCommands(program: Command): void {
       launchRuntime(runtime as RuntimeName, cmd.args, true);
     });
 
-  // Framework management commands (delegate to bash scripts)
+  // Coord (mission orchestrator)
-  const frameworkCommands: Record<string, { desc: string; script: string }> = {
+  program
+    .command('coord')
+    .description('Mission coordinator tools (init, status, run, continue, resume)')
+    .allowUnknownOption(true)
+    .allowExcessArguments(true)
+    .action((_opts: unknown, cmd: Command) => {
+      runCoord(cmd.args);
+    });
+
+  // Prdy (PRD tools via local framework scripts)
+  program
+    .command('prdy')
+    .description('PRD creation and validation (init, update, validate, status)')
+    .allowUnknownOption(true)
+    .allowExcessArguments(true)
+    .action((_opts: unknown, cmd: Command) => {
+      runPrdyLocal(cmd.args);
+    });
+
+  // Seq (sequential-thinking MCP management)
+  program
+    .command('seq')
+    .description('sequential-thinking MCP management (check/fix/start)')
+    .allowUnknownOption(true)
+    .allowExcessArguments(true)
+    .action((_opts: unknown, cmd: Command) => {
+      runSeq(cmd.args);
+    });
+
+  // Upgrade (release + project)
+  program
+    .command('upgrade')
+    .description('Upgrade Mosaic release or project files')
+    .allowUnknownOption(true)
+    .allowExcessArguments(true)
+    .action((_opts: unknown, cmd: Command) => {
+      runUpgrade(cmd.args);
+    });
+
+  // Direct framework script delegates
+  const directCommands: Record<string, { desc: string; script: string }> = {
     init: { desc: 'Generate SOUL.md (agent identity contract)', script: 'mosaic-init' },
     doctor: { desc: 'Health audit — detect drift and missing files', script: 'mosaic-doctor' },
     sync: { desc: 'Sync skills from canonical source', script: 'mosaic-sync-skills' },
-    bootstrap: { desc: 'Bootstrap a repo with Mosaic standards', script: 'mosaic-bootstrap-repo' },
+    bootstrap: {
+      desc: 'Bootstrap a repo with Mosaic standards',
+      script: 'mosaic-bootstrap-repo',
+    },
   };
 
-  for (const [name, { desc, script }] of Object.entries(frameworkCommands)) {
+  for (const [name, { desc, script }] of Object.entries(directCommands)) {
     program
       .command(name)
       .description(desc)
@@ -525,7 +748,7 @@ export function registerLaunchCommands(program: Command): void {
       .allowExcessArguments(true)
       .action((_opts: unknown, cmd: Command) => {
         checkMosaicHome();
-        delegateToFrameworkScript(script, cmd.args);
+        delegateToScript(fwScript(script), cmd.args);
       });
   }
 }

packages/coord/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/coord",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "exports": {

packages/db/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/db",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

packages/design-tokens/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/design-tokens",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

packages/forge/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/forge",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

packages/log/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/log",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

packages/macp/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/macp",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

packages/memory/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/memory",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

packages/mosaic/__tests__/platform/file-ops.test.ts

@@ -0,0 +1,88 @@
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import {
+  mkdtempSync,
+  mkdirSync,
+  writeFileSync,
+  readFileSync,
+  existsSync,
+  chmodSync,
+  rmSync,
+} from 'node:fs';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+import { syncDirectory } from '../../src/platform/file-ops.js';
+
+describe('syncDirectory', () => {
+  let tmpDir: string;
+
+  beforeEach(() => {
+    tmpDir = mkdtempSync(join(tmpdir(), 'mosaic-file-ops-'));
+  });
+
+  afterEach(() => {
+    rmSync(tmpDir, { recursive: true, force: true });
+  });
+
+  it('is a no-op when source and target are the same path', () => {
+    const dir = join(tmpDir, 'same');
+    mkdirSync(dir, { recursive: true });
+    writeFileSync(join(dir, 'file.txt'), 'hello');
+    // Should not throw even with read-only files
+    const gitDir = join(dir, '.git', 'objects', 'pack');
+    mkdirSync(gitDir, { recursive: true });
+    const packFile = join(gitDir, 'pack-abc.idx');
+    writeFileSync(packFile, 'data');
+    chmodSync(packFile, 0o444);
+
+    expect(() => syncDirectory(dir, dir)).not.toThrow();
+  });
+
+  it('skips nested .git directories when excludeGit is true', () => {
+    const src = join(tmpDir, 'src');
+    const dest = join(tmpDir, 'dest');
+
+    // Create source with a nested .git
+    mkdirSync(join(src, 'sources', 'skills', '.git', 'objects'), { recursive: true });
+    writeFileSync(join(src, 'sources', 'skills', '.git', 'objects', 'pack.idx'), 'git-data');
+    writeFileSync(join(src, 'sources', 'skills', 'SKILL.md'), 'skill content');
+    writeFileSync(join(src, 'README.md'), 'readme');
+
+    syncDirectory(src, dest, { excludeGit: true });
+
+    // .git contents should NOT be copied
+    expect(existsSync(join(dest, 'sources', 'skills', '.git'))).toBe(false);
+    // Normal files should be copied
+    expect(readFileSync(join(dest, 'sources', 'skills', 'SKILL.md'), 'utf-8')).toBe(
+      'skill content',
+    );
+    expect(readFileSync(join(dest, 'README.md'), 'utf-8')).toBe('readme');
+  });
+
+  it('copies nested .git directories when excludeGit is false', () => {
+    const src = join(tmpDir, 'src');
+    const dest = join(tmpDir, 'dest');
+
+    mkdirSync(join(src, 'sub', '.git'), { recursive: true });
+    writeFileSync(join(src, 'sub', '.git', 'HEAD'), 'ref: refs/heads/main');
+
+    syncDirectory(src, dest, { excludeGit: false });
+
+    expect(readFileSync(join(dest, 'sub', '.git', 'HEAD'), 'utf-8')).toBe('ref: refs/heads/main');
+  });
+
+  it('respects preserve option', () => {
+    const src = join(tmpDir, 'src');
+    const dest = join(tmpDir, 'dest');
+
+    mkdirSync(src, { recursive: true });
+    mkdirSync(dest, { recursive: true });
+    writeFileSync(join(src, 'SOUL.md'), 'new soul');
+    writeFileSync(join(dest, 'SOUL.md'), 'old soul');
+    writeFileSync(join(src, 'README.md'), 'new readme');
+
+    syncDirectory(src, dest, { preserve: ['SOUL.md'] });
+
+    expect(readFileSync(join(dest, 'SOUL.md'), 'utf-8')).toBe('old soul');
+    expect(readFileSync(join(dest, 'README.md'), 'utf-8')).toBe('new readme');
+  });
+});

packages/mosaic/__tests__/stages/detect-install.test.ts

@@ -65,4 +65,36 @@ describe('detectInstallStage', () => {
     expect(state.installAction).toBe('keep');
     expect(state.soul.agentName).toBe('TestAgent');
   });
+
+  it('pre-populates state when reconfiguring', async () => {
+    mkdirSync(join(tmpDir, 'bin'), { recursive: true });
+    writeFileSync(join(tmpDir, 'SOUL.md'), 'You are **Jarvis** in this session.');
+    writeFileSync(join(tmpDir, 'USER.md'), '**Name:** TestUser');
+
+    const p = new HeadlessPrompter({
+      'What would you like to do?': 'reconfigure',
+    });
+    const state = createState(tmpDir);
+    await detectInstallStage(p, state, mockConfig);
+
+    expect(state.installAction).toBe('reconfigure');
+    // Existing values loaded as defaults for reconfiguration
+    expect(state.soul.agentName).toBe('TestAgent');
+    expect(state.user.userName).toBe('TestUser');
+  });
+
+  it('does not pre-populate state on fresh reset', async () => {
+    mkdirSync(join(tmpDir, 'bin'), { recursive: true });
+    writeFileSync(join(tmpDir, 'SOUL.md'), 'You are **Jarvis** in this session.');
+
+    const p = new HeadlessPrompter({
+      'What would you like to do?': 'reset',
+    });
+    const state = createState(tmpDir);
+    await detectInstallStage(p, state, mockConfig);
+
+    expect(state.installAction).toBe('reset');
+    // Reset should NOT load existing values
+    expect(state.soul.agentName).toBeUndefined();
+  });
 });

packages/mosaic/framework/tools/_scripts/mosaic-init

@@ -60,12 +60,14 @@ Options:
   --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
+  --force                  Overwrite existing files without prompting
   -h, --help               Show help
 USAGE
 }
 
 NON_INTERACTIVE=0
 SOUL_ONLY=0
+FORCE=0
 
 while [[ $# -gt 0 ]]; do
   case "$1" in
@@ -79,6 +81,7 @@ while [[ $# -gt 0 ]]; do
     --timezone) TIMEZONE="$2"; shift 2 ;;
     --non-interactive) NON_INTERACTIVE=1; shift ;;
     --soul-only) SOUL_ONLY=1; shift ;;
+    --force) FORCE=1; shift ;;
     -h|--help) usage; exit 0 ;;
     *) echo "Unknown argument: $1" >&2; usage >&2; exit 1 ;;
   esac
@@ -139,6 +142,134 @@ prompt_multiline() {
   eval "$var_name=\"$value\""
 }
 
+# ── Existing file detection ────────────────────────────────────
+
+detect_existing_config() {
+  local found=0
+  local existing_files=()
+
+  [[ -f "$SOUL_OUTPUT" ]] && { found=1; existing_files+=("SOUL.md"); }
+  [[ -f "$USER_OUTPUT" ]] && { found=1; existing_files+=("USER.md"); }
+  [[ -f "$TOOLS_OUTPUT" ]] && { found=1; existing_files+=("TOOLS.md"); }
+
+  if [[ $found -eq 0 || $FORCE -eq 1 ]]; then
+    return 0  # No existing files or --force: proceed with fresh install
+  fi
+
+  echo "[mosaic-init] Existing configuration detected:"
+  for f in "${existing_files[@]}"; do
+    echo "  ✓ $f"
+  done
+
+  # Show current agent name if SOUL.md exists
+  if [[ -f "$SOUL_OUTPUT" ]]; then
+    local current_name
+    current_name=$(grep -oP 'You are \*\*\K[^*]+' "$SOUL_OUTPUT" 2>/dev/null || true)
+    if [[ -n "$current_name" ]]; then
+      echo "  Agent: $current_name"
+    fi
+  fi
+  echo ""
+
+  if [[ $NON_INTERACTIVE -eq 1 ]]; then
+    echo "[mosaic-init] Existing config found. Use --force to overwrite in non-interactive mode."
+    exit 0
+  fi
+
+  echo "What would you like to do?"
+  echo "  1) keep       — Keep existing files, skip init (default)"
+  echo "  2) import     — Import values from existing files as defaults, then regenerate"
+  echo "  3) overwrite  — Start fresh, overwrite all files"
+  printf "Choose [1/2/3]: "
+  read -r choice
+
+  case "${choice:-1}" in
+    1|keep)
+      echo "[mosaic-init] Keeping existing configuration."
+      # Still push to runtime adapters in case framework was updated
+      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
+      ;;
+    2|import)
+      echo "[mosaic-init] Importing values from existing files as defaults..."
+      import_existing_values
+      ;;
+    3|overwrite)
+      echo "[mosaic-init] Starting fresh install..."
+      # Back up existing files
+      local ts
+      ts=$(date +%Y%m%d%H%M%S)
+      for f in "${existing_files[@]}"; do
+        local src="$MOSAIC_HOME/$f"
+        if [[ -f "$src" ]]; then
+          cp "$src" "${src}.bak.${ts}"
+          echo "  Backed up $f → ${f}.bak.${ts}"
+        fi
+      done
+      ;;
+    *)
+      echo "[mosaic-init] Invalid choice. Keeping existing configuration."
+      exit 0
+      ;;
+  esac
+}
+
+import_existing_values() {
+  # Import SOUL.md values
+  if [[ -f "$SOUL_OUTPUT" ]]; then
+    local content
+    content=$(cat "$SOUL_OUTPUT")
+
+    if [[ -z "$AGENT_NAME" ]]; then
+      AGENT_NAME=$(echo "$content" | grep -oP 'You are \*\*\K[^*]+' 2>/dev/null || true)
+    fi
+    if [[ -z "$ROLE_DESCRIPTION" ]]; then
+      ROLE_DESCRIPTION=$(echo "$content" | grep -oP 'Role identity: \K.+' 2>/dev/null || true)
+    fi
+    if [[ -z "$STYLE" ]]; then
+      if echo "$content" | grep -q 'Be direct, concise'; then
+        STYLE="direct"
+      elif echo "$content" | grep -q 'Be warm and conversational'; then
+        STYLE="friendly"
+      elif echo "$content" | grep -q 'Use professional, structured'; then
+        STYLE="formal"
+      fi
+    fi
+  fi
+
+  # Import USER.md values
+  if [[ -f "$USER_OUTPUT" ]]; then
+    local content
+    content=$(cat "$USER_OUTPUT")
+
+    if [[ -z "$USER_NAME" ]]; then
+      USER_NAME=$(echo "$content" | grep -oP '\*\*Name:\*\* \K.+' 2>/dev/null || true)
+    fi
+    if [[ -z "$PRONOUNS" ]]; then
+      PRONOUNS=$(echo "$content" | grep -oP '\*\*Pronouns:\*\* \K.+' 2>/dev/null || true)
+    fi
+    if [[ -z "$TIMEZONE" ]]; then
+      TIMEZONE=$(echo "$content" | grep -oP '\*\*Timezone:\*\* \K.+' 2>/dev/null || true)
+    fi
+  fi
+
+  # Import TOOLS.md values
+  if [[ -f "$TOOLS_OUTPUT" ]]; then
+    local content
+    content=$(cat "$TOOLS_OUTPUT")
+
+    if [[ -z "$CREDENTIALS_LOCATION" ]]; then
+      CREDENTIALS_LOCATION=$(echo "$content" | grep -oP '\*\*Location:\*\* \K.+' 2>/dev/null || true)
+    fi
+  fi
+}
+
+detect_existing_config
+
 # ── SOUL.md Generation ────────────────────────────────────────
 echo "[mosaic-init] Generating SOUL.md — agent identity contract"
 echo ""

packages/mosaic/framework/tools/_scripts/mosaic-sync-skills

@@ -55,7 +55,26 @@ 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
+
+    # Stash any local changes (dirty index or worktree) before pulling
+    local_changes=0
+    if ! git -C "$SKILLS_REPO_DIR" diff --quiet 2>/dev/null || \
+       ! git -C "$SKILLS_REPO_DIR" diff --cached --quiet 2>/dev/null; then
+      local_changes=1
+      echo "[mosaic-skills] Stashing local changes..."
+      git -C "$SKILLS_REPO_DIR" stash push -q -m "mosaic-sync-skills auto-stash"
+    fi
+
+    if ! git -C "$SKILLS_REPO_DIR" pull --rebase; then
+      echo "[mosaic-skills] WARN: pull failed — continuing with existing checkout" >&2
+    fi
+
+    # Restore stashed changes
+    if [[ $local_changes -eq 1 ]]; then
+      echo "[mosaic-skills] Restoring local changes..."
+      git -C "$SKILLS_REPO_DIR" stash pop -q 2>/dev/null || \
+        echo "[mosaic-skills] WARN: stash pop had conflicts — check $SKILLS_REPO_DIR" >&2
+    fi
   else
     echo "[mosaic-skills] Cloning skills source to: $SKILLS_REPO_DIR"
     mkdir -p "$(dirname "$SKILLS_REPO_DIR")"

packages/mosaic/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/mosaic",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.4",
   "description": "Mosaic agent framework — installation wizard and meta package",
   "type": "module",
   "main": "dist/index.js",

packages/mosaic/src/constants.ts

@@ -1,7 +1,7 @@
 import { homedir } from 'node:os';
 import { join } from 'node:path';
 
-export const VERSION = '0.1.0';
+export const VERSION = '0.0.2';
 
 export const DEFAULT_MOSAIC_HOME = join(homedir(), '.config', 'mosaic');
 

packages/mosaic/src/platform/file-ops.ts

@@ -9,7 +9,7 @@ import {
   unlinkSync,
   statSync,
 } from 'node:fs';
-import { dirname, join, relative } from 'node:path';
+import { dirname, join, relative, resolve } from 'node:path';
 
 const MAX_BACKUPS = 3;
 
@@ -68,6 +68,9 @@ export function syncDirectory(
   target: string,
   options: { preserve?: string[]; excludeGit?: boolean } = {},
 ): void {
+  // Guard: source and target are the same directory — nothing to sync
+  if (resolve(source) === resolve(target)) return;
+
   const preserveSet = new Set(options.preserve ?? []);
 
   // Collect files from source
@@ -77,9 +80,10 @@ export function syncDirectory(
     const stat = statSync(src);
     if (stat.isDirectory()) {
       const relPath = relative(relBase, src);
+      const dirName = relPath.split('/').pop() ?? '';
 
-      // Skip .git
+      // Skip any .git directory (top-level or nested, e.g. sources/agent-skills/.git)
-      if (options.excludeGit && relPath === '.git') return;
+      if (options.excludeGit && (dirName === '.git' || relPath.includes('/.git'))) return;
 
       // Skip preserved paths at top level
       if (preserveSet.has(relPath) && existsSync(dest)) return;
@@ -91,6 +95,9 @@ export function syncDirectory(
     } else {
       const relPath = relative(relBase, src);
 
+      // Skip files inside .git directories
+      if (options.excludeGit && relPath.includes('/.git/')) return;
+
       // Skip preserved files at top level
       if (preserveSet.has(relPath) && existsSync(dest)) return;
 

packages/mosaic/src/stages/detect-install.ts

@@ -87,7 +87,9 @@ export async function detectInstallStage(
     ],
   });
 
-  if (state.installAction === 'keep') {
+  if (state.installAction === 'keep' || state.installAction === 'reconfigure') {
+    // Load existing values — for 'keep' they're final, for 'reconfigure'
+    // they become pre-populated defaults so the user can tweak them.
     state.soul = await config.readSoul();
     state.user = await config.readUser();
     state.tools = await config.readTools();

packages/mosaic/src/stages/soul-setup.ts

@@ -24,6 +24,18 @@ export async function soulSetupStage(p: WizardPrompter, state: WizardState): Pro
         return undefined;
       },
     });
+  } else if (state.installAction === 'reconfigure') {
+    // Show existing value as default so the user can accept or change it
+    state.soul.agentName = await p.text({
+      message: 'What name should agents use?',
+      placeholder: state.soul.agentName,
+      defaultValue: state.soul.agentName,
+      validate: (v) => {
+        if (v.length === 0) return 'Name cannot be empty';
+        if (v.length > 50) return 'Name must be under 50 characters';
+        return undefined;
+      },
+    });
   }
 
   if (state.mode === 'advanced') {
@@ -38,7 +50,7 @@ export async function soulSetupStage(p: WizardPrompter, state: WizardState): Pro
     state.soul.roleDescription ??= DEFAULTS.roleDescription;
   }
 
-  if (!state.soul.communicationStyle) {
+  if (!state.soul.communicationStyle || state.installAction === 'reconfigure') {
     state.soul.communicationStyle = await p.select<CommunicationStyle>({
       message: 'Communication style',
       options: [
@@ -46,7 +58,7 @@ export async function soulSetupStage(p: WizardPrompter, state: WizardState): Pro
         { value: 'friendly', label: 'Friendly', hint: 'Warm but efficient, conversational' },
         { value: 'formal', label: 'Formal', hint: 'Professional, structured, thorough' },
       ],
-      initialValue: 'direct',
+      initialValue: state.soul.communicationStyle ?? 'direct',
     });
   }
 

packages/prdy/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/prdy",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "exports": {

packages/quality-rails/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/quality-rails",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "type": "module",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",

packages/queue/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/queue",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "exports": {

packages/types/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/types",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "exports": {

plugins/discord/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/discord-plugin",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "exports": {

plugins/macp/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/oc-macp-plugin",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "type": "module",
   "main": "src/index.ts",
   "description": "OpenClaw ACP runtime backend that routes sessions_spawn(runtime:\"macp\") to the Pi MACP runner.",

plugins/mosaic-framework/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/oc-framework-plugin",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "type": "module",
   "main": "src/index.ts",
   "description": "Injects Mosaic framework rails, runtime contract, and active mission context into all OpenClaw agent sessions and ACP subagent spawns.",

plugins/telegram/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@mosaic/telegram-plugin",
-  "version": "0.0.1-alpha.2",
+  "version": "0.0.2",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
   "exports": {