fix(mosaic): seed TOOLS.md from defaults on install (#458)

Co-authored-by: Jason Woltje <jason@diversecanvas.com>
Co-committed-by: Jason Woltje <jason@diversecanvas.com>

packages/mosaic/framework/install.sh

@@ -222,12 +222,17 @@ sync_framework
 mkdir -p "$TARGET_DIR/memory"
 mkdir -p "$TARGET_DIR/credentials"
 
-# Seed defaults — copy from defaults/ to framework root if not already present.
-# These are user-editable files that ship with sensible defaults but should
+# Seed defaults — copy framework contract files from defaults/ to framework
+# root if not already present. These ship with sensible defaults but must
 # never be overwritten once the user has customized them.
+#
+# This list must match the framework-contract whitelist in
+# packages/mosaic/src/config/file-adapter.ts (FileConfigAdapter.syncFramework).
+# SOUL.md and USER.md are intentionally NOT seeded here — they are generated
+# by `mosaic init` from templates with user-supplied values.
 DEFAULTS_DIR="$TARGET_DIR/defaults"
 if [[ -d "$DEFAULTS_DIR" ]]; then
-  for default_file in AGENTS.md STANDARDS.md; do
+  for default_file in AGENTS.md STANDARDS.md TOOLS.md; do
     if [[ -f "$DEFAULTS_DIR/$default_file" ]] && [[ ! -f "$TARGET_DIR/$default_file" ]]; then
       cp "$DEFAULTS_DIR/$default_file" "$TARGET_DIR/$default_file"
       ok "Seeded $default_file from defaults"

packages/mosaic/framework/templates/TOOLS.md.template

@@ -5,32 +5,32 @@ Project-specific tooling belongs in the project's `AGENTS.md`, not here.
 
 ## Mosaic Git Wrappers (Use First)
 
-Mosaic wrappers at `~/.config/mosaic/rails/git/*.sh` handle platform detection and edge cases. Always use these before raw CLI commands.
+Mosaic wrappers at `~/.config/mosaic/tools/git/*.sh` handle platform detection and edge cases. Always use these before raw CLI commands.
 
 ```bash
 # Issues
-~/.config/mosaic/rails/git/issue-create.sh
-~/.config/mosaic/rails/git/issue-close.sh
+~/.config/mosaic/tools/git/issue-create.sh
+~/.config/mosaic/tools/git/issue-close.sh
 
 # PRs
-~/.config/mosaic/rails/git/pr-create.sh
-~/.config/mosaic/rails/git/pr-merge.sh
+~/.config/mosaic/tools/git/pr-create.sh
+~/.config/mosaic/tools/git/pr-merge.sh
 
 # Milestones
-~/.config/mosaic/rails/git/milestone-create.sh
+~/.config/mosaic/tools/git/milestone-create.sh
 
 # CI queue guard (required before push/merge)
-~/.config/mosaic/rails/git/ci-queue-wait.sh --purpose push|merge
+~/.config/mosaic/tools/git/ci-queue-wait.sh --purpose push|merge
 ```
 
 ## Code Review (Codex)
 
 ```bash
 # Code quality review
-~/.config/mosaic/rails/codex/codex-code-review.sh --uncommitted
+~/.config/mosaic/tools/codex/codex-code-review.sh --uncommitted
 
 # Security review
-~/.config/mosaic/rails/codex/codex-security-review.sh --uncommitted
+~/.config/mosaic/tools/codex/codex-security-review.sh --uncommitted
 ```
 
 ## Git Providers

packages/mosaic/src/config/file-adapter.test.ts

@@ -0,0 +1,134 @@
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { mkdtempSync, mkdirSync, writeFileSync, rmSync, readFileSync, existsSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
+import { FileConfigAdapter, DEFAULT_SEED_FILES } from './file-adapter.js';
+
+/**
+ * Regression tests for the `FileConfigAdapter.syncFramework` seed behavior.
+ *
+ * Background: the bash installer (`framework/install.sh`) and this TS wizard
+ * path both seed framework-contract files from `framework/defaults/` into the
+ * user's mosaic home on first install. Before this fix:
+ *
+ *   - The bash installer only seeded `AGENTS.md` and `STANDARDS.md`, leaving
+ *     `TOOLS.md` missing despite it being listed as mandatory in the
+ *     AGENTS.md load order (position 5).
+ *   - The TS wizard iterated every file in `defaults/` and copied it to the
+ *     mosaic home root — including `defaults/SOUL.md` (hardcoded "Jarvis"),
+ *     `defaults/USER.md` (placeholder), and internal framework files like
+ *     `README.md` and `AUDIT-*.md`. That clobbered the identity flow on
+ *     fresh installs and leaked framework-internal clutter into the user's
+ *     home directory.
+ *
+ * This suite pins the whitelist and the preservation semantics so both
+ * regressions stay fixed.
+ */
+
+function makeFixture(): { sourceDir: string; mosaicHome: string; defaultsDir: string } {
+  const root = mkdtempSync(join(tmpdir(), 'mosaic-file-adapter-'));
+  const sourceDir = join(root, 'source');
+  const mosaicHome = join(root, 'mosaic-home');
+  const defaultsDir = join(sourceDir, 'defaults');
+
+  mkdirSync(defaultsDir, { recursive: true });
+  mkdirSync(mosaicHome, { recursive: true });
+
+  // Framework-contract defaults we expect the wizard to seed.
+  writeFileSync(join(defaultsDir, 'AGENTS.md'), '# AGENTS default\n');
+  writeFileSync(join(defaultsDir, 'STANDARDS.md'), '# STANDARDS default\n');
+  writeFileSync(join(defaultsDir, 'TOOLS.md'), '# TOOLS default\n');
+
+  // Non-contract files we must NOT seed on first install.
+  writeFileSync(join(defaultsDir, 'SOUL.md'), '# SOUL default (should not be seeded)\n');
+  writeFileSync(join(defaultsDir, 'USER.md'), '# USER default (should not be seeded)\n');
+  writeFileSync(join(defaultsDir, 'README.md'), '# README (framework-internal)\n');
+  writeFileSync(
+    join(defaultsDir, 'AUDIT-2026-02-17-framework-consistency.md'),
+    '# Audit snapshot\n',
+  );
+
+  return { sourceDir, mosaicHome, defaultsDir };
+}
+
+describe('FileConfigAdapter.syncFramework — defaults seeding', () => {
+  let fixture: ReturnType<typeof makeFixture>;
+
+  beforeEach(() => {
+    fixture = makeFixture();
+  });
+
+  afterEach(() => {
+    rmSync(join(fixture.sourceDir, '..'), { recursive: true, force: true });
+  });
+
+  it('seeds the three framework-contract files on a fresh mosaic home', async () => {
+    const adapter = new FileConfigAdapter(fixture.mosaicHome, fixture.sourceDir);
+
+    await adapter.syncFramework('fresh');
+
+    for (const name of DEFAULT_SEED_FILES) {
+      expect(existsSync(join(fixture.mosaicHome, name))).toBe(true);
+    }
+    expect(readFileSync(join(fixture.mosaicHome, 'TOOLS.md'), 'utf-8')).toContain(
+      '# TOOLS default',
+    );
+  });
+
+  it('does NOT seed SOUL.md or USER.md from defaults/ (wizard stages own those)', async () => {
+    const adapter = new FileConfigAdapter(fixture.mosaicHome, fixture.sourceDir);
+
+    await adapter.syncFramework('fresh');
+
+    // SOUL.md and USER.md live in defaults/ for historical reasons, but they
+    // are template-rendered per-user by the wizard stages. Seeding them here
+    // would clobber the identity flow and leak placeholder content.
+    expect(existsSync(join(fixture.mosaicHome, 'SOUL.md'))).toBe(false);
+    expect(existsSync(join(fixture.mosaicHome, 'USER.md'))).toBe(false);
+  });
+
+  it('does NOT seed README.md or AUDIT-*.md from defaults/', async () => {
+    const adapter = new FileConfigAdapter(fixture.mosaicHome, fixture.sourceDir);
+
+    await adapter.syncFramework('fresh');
+
+    expect(existsSync(join(fixture.mosaicHome, 'README.md'))).toBe(false);
+    expect(existsSync(join(fixture.mosaicHome, 'AUDIT-2026-02-17-framework-consistency.md'))).toBe(
+      false,
+    );
+  });
+
+  it('preserves existing contract files — never overwrites user customization', async () => {
+    // Also plant a root-level AGENTS.md in sourceDir so that `syncDirectory`
+    // itself (not just the seed loop) has something to try to overwrite.
+    // Without this, the test would silently pass even if preserve semantics
+    // were broken in syncDirectory.
+    writeFileSync(join(fixture.sourceDir, 'AGENTS.md'), '# shipped AGENTS from source root\n');
+
+    writeFileSync(join(fixture.mosaicHome, 'TOOLS.md'), '# user-customized TOOLS\n');
+    writeFileSync(join(fixture.mosaicHome, 'AGENTS.md'), '# user-customized AGENTS\n');
+
+    const adapter = new FileConfigAdapter(fixture.mosaicHome, fixture.sourceDir);
+    await adapter.syncFramework('keep');
+
+    expect(readFileSync(join(fixture.mosaicHome, 'TOOLS.md'), 'utf-8')).toBe(
+      '# user-customized TOOLS\n',
+    );
+    expect(readFileSync(join(fixture.mosaicHome, 'AGENTS.md'), 'utf-8')).toBe(
+      '# user-customized AGENTS\n',
+    );
+    // And the missing contract file still gets seeded.
+    expect(readFileSync(join(fixture.mosaicHome, 'STANDARDS.md'), 'utf-8')).toContain(
+      '# STANDARDS default',
+    );
+  });
+
+  it('is a no-op for seeding when defaults/ dir does not exist', async () => {
+    rmSync(fixture.defaultsDir, { recursive: true });
+
+    const adapter = new FileConfigAdapter(fixture.mosaicHome, fixture.sourceDir);
+    await expect(adapter.syncFramework('fresh')).resolves.toBeUndefined();
+
+    expect(existsSync(join(fixture.mosaicHome, 'TOOLS.md'))).toBe(false);
+  });
+});

packages/mosaic/src/config/file-adapter.ts

@@ -1,5 +1,19 @@
-import { readFileSync, existsSync, readdirSync, statSync, copyFileSync } from 'node:fs';
+import { readFileSync, existsSync, statSync, copyFileSync } from 'node:fs';
 import { join } from 'node:path';
+
+/**
+ * Framework-contract files that `syncFramework` seeds from `framework/defaults/`
+ * into the mosaic home root on first install. These are the only files the
+ * wizard is allowed to touch as a one-time seed — SOUL.md and USER.md are
+ * generated from templates by their respective wizard stages with
+ * user-supplied values, and anything else under `defaults/` (README.md,
+ * audit snapshots, etc.) is framework-internal and must not leak into the
+ * user's mosaic home.
+ *
+ * This list must match the explicit seed loop in
+ * packages/mosaic/framework/install.sh.
+ */
+export const DEFAULT_SEED_FILES = ['AGENTS.md', 'STANDARDS.md', 'TOOLS.md'] as const;
 import type { ConfigService, ConfigSection, ResolvedConfig } from './config-service.js';
 import type { SoulConfig, UserConfig, ToolsConfig, InstallAction } from '../types.js';
 import { soulSchema, userSchema, toolsSchema } from './schemas.js';
@@ -131,9 +145,24 @@ export class FileConfigAdapter implements ConfigService {
   }
 
   async syncFramework(action: InstallAction): Promise<void> {
+    // Must match PRESERVE_PATHS in packages/mosaic/framework/install.sh so
+    // the bash and TS install paths have the same upgrade-preservation
+    // semantics. Contract files (AGENTS.md, STANDARDS.md, TOOLS.md) are
+    // seeded from defaults/ on first install and preserved thereafter;
+    // identity files (SOUL.md, USER.md) are generated by wizard stages and
+    // must never be touched by the framework sync.
     const preservePaths =
       action === 'keep' || action === 'reconfigure'
-        ? ['SOUL.md', 'USER.md', 'TOOLS.md', 'memory']
+        ? [
+            'AGENTS.md',
+            'SOUL.md',
+            'USER.md',
+            'TOOLS.md',
+            'STANDARDS.md',
+            'memory',
+            'sources',
+            'credentials',
+          ]
         : [];
 
     syncDirectory(this.sourceDir, this.mosaicHome, {
@@ -141,20 +170,23 @@ export class FileConfigAdapter implements ConfigService {
       excludeGit: true,
     });
 
-    // Copy default root-level .md files (AGENTS.md, STANDARDS.md, etc.)
-    // from framework/defaults/ into mosaicHome root if they don't exist yet.
-    // These are framework contracts — only written on first install, never
-    // overwritten (user may have customized them).
+    // Copy framework-contract files (AGENTS.md, STANDARDS.md, TOOLS.md)
+    // from framework/defaults/ into the mosaic home root if they don't
+    // exist yet. These are written on first install only and are never
+    // overwritten afterwards — the user may have customized them.
+    //
+    // SOUL.md and USER.md are deliberately NOT seeded here. They are
+    // generated from templates by the soul/user wizard stages with
+    // user-supplied values; seeding them from defaults would clobber the
+    // identity flow and leak placeholder content into the mosaic home.
     const defaultsDir = join(this.sourceDir, 'defaults');
     if (existsSync(defaultsDir)) {
-      for (const entry of readdirSync(defaultsDir)) {
+      for (const entry of DEFAULT_SEED_FILES) {
+        const src = join(defaultsDir, entry);
         const dest = join(this.mosaicHome, entry);
-        if (!existsSync(dest)) {
-          const src = join(defaultsDir, entry);
-          if (statSync(src).isFile()) {
-            copyFileSync(src, dest);
-          }
-        }
+        if (existsSync(dest)) continue;
+        if (!existsSync(src) || !statSync(src).isFile()) continue;
+        copyFileSync(src, dest);
       }
     }
   }