takomi 2.1.34 → 2.1.35

package/assets/.agent/skills/photo-book-builder/SKILL.md

@@ -1,7 +1,7 @@
 ---
 name: photo-book-builder
 description: >
-  Automates high-resolution photo book creation, including chronological sorting, orientation balancing (landscape vs. portrait), print-ready full-bleed masonry layout generation, and cover art upscaling. Use this skill when asked to: (1) Organize a set of photos into chronological pages, (2) Generate 12" x 30" open spreads (9000 x 3600 px at 300 DPI) with exact gutter margins (150 px vertical center gutter) and custom margins, (3) Create or assemble full-bleed masonry grid layouts, (4) Upscale front, back, or briefcase box covers using high-quality LANCZOS interpolation.
+  Automates high-resolution photo book creation and correction passes, including chronological sorting, orientation balancing, print-ready full-bleed masonry layout generation, existing layout crop corrections, contact-sheet/cell mapping, and cover art upscaling. Use this skill when asked to: (1) Organize photos into page folders, (2) Generate or regenerate 12" x 30" open spreads (9000 x 3600 px at 300 DPI) with gutter margins, (3) Create or adapt full-bleed masonry grid layouts with project-specific photo counts, (4) Correct existing exports by raising/lowering images or adjusting per-image crop framing without overwriting originals, (5) Upscale front, back, or briefcase box covers using high-quality LANCZOS interpolation.
 ---
 
 # Photo Book Builder
@@ -10,7 +10,7 @@ This skill provides a complete system for organizing, structuring, and generatin
 
 ## Core Capabilities
 
-The photo book builder relies on four main stages:
+The photo book builder supports five main stages:
 
 ```mermaid
 graph TD
@@ -18,6 +18,8 @@ graph TD
     B --> C[Stage 2 & 3: Layout Generation]
     C -->|create_full_bleed_layouts.py| D[9000x3600 px Print Spreads]
     E[Stage 4: Cover Upscaling] -->|upscale_covers.py| F[Print-Ready Cover JPEGs]
+    D --> G[Stage 5: Correction Pass]
+    G -->|custom renderer or patched generator| H[New Corrected Export Folder]
 ```
 
 ---
@@ -50,6 +52,8 @@ Layout configurations are determined dynamically based on photo counts and orien
 *   **Template 6A (6 Photos: 5L, 1P)**: Two landscape rows (4 total), one portrait + landscape col.
 *   **Template 6B (6 Photos: 4L, 2P)**: Two large landscape rows (2 total), one double-portrait + double-landscape col.
 
+These templates are defaults, not hard limits. When a project already has a custom generator, page folders, or spreads with a different number of photos (for example 23-24 images per spread), preserve that project's generator and layout rules. Do not force the default 5/6-photo half-page templates onto an existing custom book.
+
 For a complete coordinate reference and details on column configurations, see [layout_templates.md](references/layout_templates.md).
 
 ---
@@ -58,6 +62,8 @@ For a complete coordinate reference and details on column configurations, see [l
 The layout compiler reads the page directories, detects photo orientations on the fly, applies the coordinate grids, crops photos to fill cells (using centered LANCZOS fit-scale), and merges them into $9000 \times 3600$ px JPEG spreads.
 *   **Page Swapping**: Alternating layout orientation avoids monotonous designs. Left page columns swap if `page_num % 2 == 0`, and right page columns swap if `page_num % 3 == 0`.
 
+When regenerating an existing project, first inspect local scripts in the delivery/project folder. If a project-specific script exists, prefer adapting it over the bundled default scripts. Avoid rerunning any organizer/reorganizer that flattens or moves page folders unless the user explicitly asks for a new organization pass.
+
 **Execution**:
 Compile the print-ready layouts:
 ```bash
@@ -79,6 +85,44 @@ python scripts/upscale_covers.py --src "path/to/cover.png" --out "path/to/upscal
 
 ---
 
+### Stage 5: Existing Layout Correction Pass
+Use this when the user provides screenshots or notes such as "blue means raise the image" and "red means take it down" for already-exported spreads.
+
+**Correction workflow**:
+1. Identify the current source workspace, existing export folder, and correction screenshots.
+2. Inspect the local layout generator and `photo_organization_map.json` if present.
+3. Create a contact sheet or map preview that overlays each cell with its source filename and rectangle. This prevents guessing from screenshots.
+4. Translate annotations into per-image corrections:
+    * Blue / "raise image up": move the visible subject up in the cell. In crop-ratio terms this usually means increasing vertical crop offset when there is extra source height below the crop.
+    * Red / "take it down": move the visible subject down in the cell. In crop-ratio terms this usually means decreasing vertical crop offset when there is extra source height above the crop.
+    * If the crop is already pinned at the top or bottom, use a small top-anchored or bottom-anchored overscale instead of adding filler or painting pixels. Start tiny, e.g. `1.006` to `1.012`; larger values can overshoot.
+5. Render to a new export folder. Never overwrite the original export unless the user explicitly asks.
+6. Verify file count, output dimensions, and a reduced review sheet of corrected spreads.
+
+**Per-image correction patterns**:
+```python
+CROP_OVERRIDES = {
+    "DSC01234.jpg": {"y_ratio": 0.30},  # raise visible subject
+    "DSC05678.jpg": {"y_ratio": 0.00},  # lower visible subject
+}
+```
+
+For edge-pinned images where ratio changes cannot move the frame:
+```python
+TOP_ANCHORED_OVERSCALE = {
+    "DSC01234.jpg": 1.010,  # tiny downward nudge without filler
+}
+```
+
+Keep corrections local to filenames/cells. Avoid global crop changes unless every affected image needs the same behavior.
+
+**Safety rules for correction passes**:
+* Preserve existing page folders and mapping files.
+* Prefer a renderer that reads existing pages and writes new spreads over a script that reorganizes files.
+* Use output folder names like `10 - layouts - crop-corrections-YYYYMMDD`.
+* Keep a short correction log with source filenames, correction type, output folder, and verification result.
+* On Windows, avoid giant one-shot patches or command lines; keep scripts and path lists small.
+
 ## Revert Option
 If you need to restart the process or undo the page folder classification, run the revert tool to move photos back to the root workspace directory and remove empty page folders:
 ```bash
@@ -88,9 +132,9 @@ python scripts/revert_organization.py --workspace-dir "path/to/workspace"
 ## Bundled Resources
 
 *   **Scripts**:
-    *   [organize_photos.py](file:///C:/Users/johno/.gemini/config/skills/photo-book-builder/scripts/organize_photos.py) - Groups and balances photo directories.
-    *   [create_full_bleed_layouts.py](file:///C:/Users/johno/.gemini/config/skills/photo-book-builder/scripts/create_full_bleed_layouts.py) - Assembles masonry grid pages into print-ready spreads.
-    *   [upscale_covers.py](file:///C:/Users/johno/.gemini/config/skills/photo-book-builder/scripts/upscale_covers.py) - General-purpose upscaling script.
-    *   [revert_organization.py](file:///C:/Users/johno/.gemini/config/skills/photo-book-builder/scripts/revert_organization.py) - Restores files back to flat source directories.
+    *   [organize_photos.py](scripts/organize_photos.py) - Groups and balances photo directories.
+    *   [create_full_bleed_layouts.py](scripts/create_full_bleed_layouts.py) - Assembles masonry grid pages into print-ready spreads.
+    *   [upscale_covers.py](scripts/upscale_covers.py) - General-purpose upscaling script.
+    *   [revert_organization.py](scripts/revert_organization.py) - Restores files back to flat source directories.
 *   **References**:
-    *   [layout_templates.md](file:///C:/Users/johno/.gemini/config/skills/photo-book-builder/references/layout_templates.md) - Exact coordinates, dimensions, and grid cells.
+    *   [layout_templates.md](references/layout_templates.md) - Exact coordinates, dimensions, and grid cells.

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "takomi",
-  "version": "2.1.34",
+  "version": "2.1.35",
   "description": "🎯 Stop wrestling with AI. Start building with purpose. The artisan's toolkit for agent workflows, Codex skills, and original Takomi capabilities like 21st.dev integration.",
   "type": "module",
   "bin": {
@@ -23,7 +23,9 @@
   ],
   "scripts": {
     "postinstall": "node src/postinstall.js",
-    "test": "node scripts/test-skill-selection.js",
+    "test": "npm run test:typecheck && npm run test:regressions && npm run test:skills",
+    "test:typecheck": "tsc --noEmit",
+    "test:regressions": "node scripts/test-regressions.js",
     "test:skills": "node scripts/test-skill-selection.js"
   },
   "repository": {
@@ -52,6 +54,20 @@
     "picocolors": "^1.1.1",
     "prompts": "^2.4.2"
   },
+  "overrides": {
+    "protobufjs": "7.6.3",
+    "@protobufjs/utf8": "1.1.1",
+    "ws": "8.21.0",
+    "brace-expansion": "5.0.6"
+  },
+  "pnpm": {
+    "overrides": {
+      "protobufjs": "7.6.3",
+      "@protobufjs/utf8": "1.1.1",
+      "ws": "8.21.0",
+      "brace-expansion": "5.0.6"
+    }
+  },
   "bugs": {
     "url": "https://github.com/JStaRFilms/VibeCode-Protocol-Suite/issues"
   },

package/src/cli.js

@@ -928,11 +928,14 @@ async function add(url) {
   console.log(pc.cyan('📡 Fetching from GitHub...\n'));
 
   // Try assets/.agent/skills/ first (Takomi structure)
+  const githubOptions = { repo: repoSlug };
+
   let skillCount = await downloadDirectoryFromGitHub(
     'assets/.agent/skills',
     skillsDest,
     null,
-    250
+    250,
+    githubOptions
   );
 
   // Fallback: try .agent/skills/
@@ -941,7 +944,8 @@ async function add(url) {
       '.agent/skills',
       skillsDest,
       null,
-      250
+      250,
+      githubOptions
     );
   }
 
@@ -950,7 +954,8 @@ async function add(url) {
     'assets/.agent/workflows',
     workflowsDest,
     (item) => item.name.endsWith('.md'),
-    250
+    250,
+    githubOptions
   );
 
   if (workflowCount === 0) {
@@ -958,7 +963,8 @@ async function add(url) {
       '.agent/workflows',
       workflowsDest,
       (item) => item.name.endsWith('.md'),
-      250
+      250,
+      githubOptions
     );
   }
 
@@ -1050,19 +1056,30 @@ async function updateProjectResources() {
   if (!response.components || response.components.length === 0) return;
 
   const destRoot = process.cwd();
+  let remoteDownloadCount = 0;
+  let remoteUpdateRequested = false;
+  const remoteFailures = [];
+  const runRemoteUpdate = async (label, updater) => {
+    remoteUpdateRequested = true;
+    try {
+      remoteDownloadCount += await updater();
+    } catch (error) {
+      remoteFailures.push(`${label}: ${error.message}`);
+    }
+  };
 
   if (response.components.includes('agent')) {
     const agentDest = path.join(destRoot, '.agent');
-    await updateWorkflows(path.join(agentDest, 'workflows'));
-    await updateSkills(path.join(agentDest, 'skills'));
+    await runRemoteUpdate('workflows', () => updateWorkflows(path.join(agentDest, 'workflows')));
+    await runRemoteUpdate('skills', () => updateSkills(path.join(agentDest, 'skills')));
   }
 
   if (response.components.includes('yamls')) {
-    await updateAgentYamls(path.join(destRoot, 'Takomi-Agents'));
+    await runRemoteUpdate('agent YAMLs', () => updateAgentYamls(path.join(destRoot, 'Takomi-Agents')));
   }
 
   if (response.components.includes('legacy')) {
-    await updateLegacyManual(path.join(destRoot, 'Legacy-Protocols'));
+    await runRemoteUpdate('legacy protocols', () => updateLegacyManual(path.join(destRoot, 'Legacy-Protocols')));
   }
 
   // Update global store if selected
@@ -1089,6 +1106,19 @@ async function updateProjectResources() {
     await writeManifest(manifest);
   }
 
+  if (remoteFailures.length) {
+    console.log(pc.red('\nSome project resources failed to download from GitHub:'));
+    for (const failure of remoteFailures) console.log(pc.dim(`  - ${failure}`));
+    process.exitCode = 1;
+    return;
+  }
+
+  if (remoteUpdateRequested && remoteDownloadCount === 0) {
+    console.log(pc.red('\nNo project resources were downloaded from GitHub. Check the network or repository paths.'));
+    process.exitCode = 1;
+    return;
+  }
+
   console.log(pc.magenta('\n✨ Your toolkit is fresh and ready to ship.'));
 }
 
@@ -1116,7 +1146,7 @@ Examples:
   takomi refresh pi   Refresh only Pi-related pieces
 
 Legacy aliases still work:
-  install -> setup, sync/upgrade -> refresh, init -> setup project,
+  install -> setup, sync -> sync, upgrade -> refresh, init -> setup project,
   harnesses -> status, update -> refresh project
 `);
 
@@ -1171,8 +1201,8 @@ program
 // Re-sync (legacy alias)
 program
   .command('sync [target]', { hidden: true })
-  .description('Legacy alias: use "takomi refresh [target]"')
-  .action(refresh);
+  .description('Legacy alias for global store sync')
+  .action(sync);
 
 // Add remote skills (NEW)
 program

package/src/harness.js

@@ -1,8 +1,8 @@
 import fs from 'fs-extra';
 import path from 'path';
 import os from 'os';
-import crypto from 'crypto';
 import pc from 'picocolors';
+import { hashPath, normalizeOwnedMap, copyOwnedTree } from './owned-tree.js';
 
 // ─── Cross-Platform Home Directory ───────────────────────────────────────────
 const HOME = os.homedir();
@@ -170,44 +170,6 @@ export function printHarnessStatus(detected) {
  * @param {string} label       - Human-readable label for logging
  * @returns {Promise<number>}  - Number of items copied
  */
-function sha256(value) {
-  return crypto.createHash('sha256').update(value).digest('hex');
-}
-
-async function hashPath(targetPath) {
-  if (!await fs.pathExists(targetPath)) return null;
-  const stat = await fs.stat(targetPath);
-  if (stat.isFile()) return sha256(await fs.readFile(targetPath));
-
-  const entries = [];
-  async function walk(current, prefix = '') {
-    const names = (await fs.readdir(current)).sort();
-    for (const name of names) {
-      const full = path.join(current, name);
-      const rel = path.join(prefix, name).replace(/\\/g, '/');
-      const st = await fs.stat(full);
-      if (st.isDirectory()) {
-        entries.push(`dir:${rel}`);
-        await walk(full, rel);
-      } else {
-        entries.push(`file:${rel}:${sha256(await fs.readFile(full))}`);
-      }
-    }
-  }
-  await walk(targetPath);
-  return sha256(entries.join('\n'));
-}
-
-function normalizeOwnedMap(value) {
-  if (!value || typeof value !== 'object') return {};
-  const normalized = {};
-  for (const [name, entry] of Object.entries(value)) {
-    if (typeof entry === 'string') normalized[name] = { hash: entry };
-    else if (entry?.hash) normalized[name] = entry;
-  }
-  return normalized;
-}
-
 /**
  * Syncs a directory to a target path. When ownership is supplied, it also
  * prunes previous Takomi-owned items that are no longer in the source while
@@ -263,7 +225,7 @@ export async function syncDirectory(sourcePath, targetPath, label = '', options
         await fs.remove(dest);
       }
 
-      await fs.copy(src, dest, { overwrite: true });
+      await copyOwnedTree(src, dest);
       nextOwned[item] = {
         hash: await hashPath(dest),
         targetPath: dest,
@@ -285,7 +247,7 @@ export async function syncDirectory(sourcePath, targetPath, label = '', options
     if (label) {
       console.log(pc.red(`  ✗ ${label}: ${error.message}`));
     }
-    return options.returnDetails ? { copied: 0, pruned: 0, preservedManual: [], preservedModified: [], owned: {} } : 0;
+    return options.returnDetails ? { copied: 0, pruned: 0, preservedManual: [], preservedModified: [], owned: normalizeOwnedMap(options.owned), ok: false, error: error.message } : 0;
   }
 }
 
@@ -329,8 +291,8 @@ export async function syncFile(sourceFile, targetPaths, label = '') {
  * @returns {Promise<{skills: number, workflows: number, yamls: number}>}
  */
 export async function syncToHarness(harness, storePath, options = {}) {
-  const results = { skills: 0, workflows: 0, yamls: 0, owned: { skills: {}, workflows: {} } };
   const harnessOwned = options.owned?.[harness.id] || {};
+  const results = { skills: 0, workflows: 0, yamls: 0, owned: { skills: normalizeOwnedMap(harnessOwned.skills), workflows: normalizeOwnedMap(harnessOwned.workflows) }, ok: true, errors: [] };
   const useOwnership = Boolean(options.useOwnership);
 
   console.log(pc.cyan(`\n  📡 Syncing to ${harness.name}...`));
@@ -352,6 +314,10 @@ export async function syncToHarness(harness, storePath, options = {}) {
     if (useOwnership) {
       results.skills = skillResult.copied;
       results.owned.skills = skillResult.owned;
+      if (skillResult.ok === false) {
+        results.ok = false;
+        results.errors.push(skillResult.error);
+      }
     } else {
       results.skills = skillResult;
     }
@@ -374,6 +340,10 @@ export async function syncToHarness(harness, storePath, options = {}) {
     if (useOwnership) {
       results.workflows = workflowResult.copied;
       results.owned.workflows = workflowResult.owned;
+      if (workflowResult.ok === false) {
+        results.ok = false;
+        results.errors.push(workflowResult.error);
+      }
     } else {
       results.workflows = workflowResult;
     }

package/src/owned-tree.js

@@ -0,0 +1,86 @@
+import fs from 'fs-extra';
+import path from 'path';
+import crypto from 'crypto';
+import { createReadStream } from 'fs';
+
+export function sha256(value) {
+  return crypto.createHash('sha256').update(value).digest('hex');
+}
+
+async function hashFile(filePath) {
+  return new Promise((resolve, reject) => {
+    const hash = crypto.createHash('sha256');
+    const stream = createReadStream(filePath);
+    stream.on('data', (chunk) => hash.update(chunk));
+    stream.on('error', reject);
+    stream.on('end', () => resolve(hash.digest('hex')));
+  });
+}
+
+/**
+ * Hash a file tree without following symlinks.
+ *
+ * Symlinks are represented by their link target string instead of the linked
+ * file contents. This prevents store/harness reconciliation from recursively
+ * reading outside the intended tree or looping through symlink cycles.
+ */
+export async function hashPath(targetPath) {
+  if (!await fs.pathExists(targetPath)) return null;
+
+  const rootStat = await fs.lstat(targetPath);
+  if (rootStat.isSymbolicLink()) return sha256(`symlink:${await fs.readlink(targetPath).catch(() => '')}`);
+  if (rootStat.isFile()) return hashFile(targetPath);
+  if (!rootStat.isDirectory()) return sha256(`other:${rootStat.mode}:${rootStat.size}`);
+
+  const entries = [];
+  async function walk(current, prefix = '') {
+    const names = (await fs.readdir(current)).sort();
+    for (const name of names) {
+      const full = path.join(current, name);
+      const rel = path.join(prefix, name).replace(/\\/g, '/');
+      const stat = await fs.lstat(full);
+      if (stat.isSymbolicLink()) {
+        const linkTarget = await fs.readlink(full).catch(() => '');
+        entries.push(`symlink:${rel}:${linkTarget}`);
+      } else if (stat.isDirectory()) {
+        entries.push(`dir:${rel}`);
+        await walk(full, rel);
+      } else if (stat.isFile()) {
+        entries.push(`file:${rel}:${await hashFile(full)}`);
+      } else {
+        entries.push(`other:${rel}:${stat.mode}:${stat.size}`);
+      }
+    }
+  }
+  await walk(targetPath);
+  return sha256(entries.join('\n'));
+}
+
+export function normalizeOwnedMap(value) {
+  if (!value || typeof value !== 'object') return {};
+  const normalized = {};
+  for (const [name, entry] of Object.entries(value)) {
+    if (typeof entry === 'string') normalized[name] = { hash: entry };
+    else if (entry?.hash) normalized[name] = entry;
+  }
+  return normalized;
+}
+
+export async function copyOwnedTree(src, dest, options = {}) {
+  const { allowSymlinks = false, filter, ...copyOptions } = options;
+  await fs.copy(src, dest, {
+    overwrite: true,
+    errorOnExist: false,
+    dereference: false,
+    ...copyOptions,
+    filter: async (candidate) => {
+      if (filter && !await filter(candidate)) return false;
+      if (allowSymlinks) return true;
+      const stat = await fs.lstat(candidate).catch(() => null);
+      if (stat?.isSymbolicLink()) {
+        throw new Error(`Refusing to copy symlink in managed tree: ${candidate}`);
+      }
+      return true;
+    },
+  });
+}

package/src/pi-installer.js

@@ -1,47 +1,15 @@
 import fs from 'fs-extra';
 import os from 'os';
 import path from 'path';
-import crypto from 'crypto';
 import pc from 'picocolors';
 import { PATHS } from './utils.js';
 import { getPiGlobalTargets } from './pi-harness.js';
+import { hashPath, copyOwnedTree } from './owned-tree.js';
 
 const HOME = os.homedir();
 const TAKOMI_HOME = path.join(HOME, '.takomi');
 export const PI_MANIFEST_PATH = path.join(TAKOMI_HOME, 'pi-manifest.json');
 
-function sha256(value) {
-  return crypto.createHash('sha256').update(value).digest('hex');
-}
-
-async function hashPath(targetPath) {
-  if (!await fs.pathExists(targetPath)) return null;
-  const stat = await fs.stat(targetPath);
-  if (stat.isFile()) {
-    const buf = await fs.readFile(targetPath);
-    return sha256(buf);
-  }
-
-  const entries = [];
-  async function walk(dir, prefix = '') {
-    const names = (await fs.readdir(dir)).sort();
-    for (const name of names) {
-      const full = path.join(dir, name);
-      const rel = path.join(prefix, name).replace(/\\/g, '/');
-      const st = await fs.stat(full);
-      if (st.isDirectory()) {
-        entries.push(`dir:${rel}`);
-        await walk(full, rel);
-      } else {
-        const buf = await fs.readFile(full);
-        entries.push(`file:${rel}:${sha256(buf)}`);
-      }
-    }
-  }
-  await walk(targetPath);
-  return sha256(entries.join('\n'));
-}
-
 async function pathIsSameSymlink(dest, src) {
   try {
     const stat = await fs.lstat(dest);
@@ -69,7 +37,7 @@ async function copyOwnedDirectory(src, dest) {
   await fs.ensureDir(path.dirname(dest));
   const mode = await prepareOwnedTarget(src, dest);
   if (mode === 'symlink') return hashPath(src);
-  await fs.copy(src, dest, { overwrite: true });
+  await copyOwnedTree(src, dest);
   return hashPath(dest);
 }
 
@@ -77,7 +45,7 @@ async function copyOwnedFile(src, dest) {
   await fs.ensureDir(path.dirname(dest));
   const mode = await prepareOwnedTarget(src, dest);
   if (mode === 'symlink') return hashPath(src);
-  await fs.copy(src, dest, { overwrite: true });
+  await copyOwnedTree(src, dest);
   return hashPath(dest);
 }
 
@@ -96,6 +64,8 @@ export async function writePiInstallManifest(manifest) {
 export async function installPiHarnessAssets(version = 'unknown') {
   const srcRoot = PATHS.pi;
   const targets = getPiGlobalTargets();
+  const previousSettingsHash = await hashPath(targets.settings);
+  const previousRoutingPolicyHash = await hashPath(targets.routingPolicy);
 
   const copied = {};
 
@@ -153,7 +123,9 @@ export async function installPiHarnessAssets(version = 'unknown') {
     owned: copied,
     preserved: {
       settings: targets.settings,
+      settingsHash: previousSettingsHash,
       routingPolicy: targets.routingPolicy,
+      routingPolicyHash: previousRoutingPolicyHash,
       userStateDir: targets.takomi,
     },
   };
@@ -168,6 +140,9 @@ export async function syncPiHarnessAssets(version = 'unknown') {
 
 export async function validatePiHarnessInstall() {
   const targets = getPiGlobalTargets();
+  const manifest = await readPiInstallManifest();
+  const currentSettingsHash = await hashPath(targets.settings);
+  const currentRoutingPolicyHash = await hashPath(targets.routingPolicy);
   return {
     runtime: await fs.pathExists(path.join(targets.extensions, 'takomi-runtime')),
     subagents: await fs.pathExists(path.join(targets.extensions, 'takomi-subagents')),
@@ -180,7 +155,8 @@ export async function validatePiHarnessInstall() {
     readme: await fs.pathExists(path.join(targets.root, 'README.md')),
     core: await fs.pathExists(path.join(path.dirname(targets.root), 'src', 'pi-takomi-core')),
     piSubagentsModule: await fs.pathExists(path.join(targets.root, 'node_modules', 'pi-subagents')),
-    settingsPreserved: !await fs.pathExists(path.join(PATHS.pi, 'settings.json')) || true,
+    settingsPreserved: !manifest || manifest.preserved?.settingsHash === currentSettingsHash,
+    routingPolicyPreserved: !manifest || manifest.preserved?.routingPolicyHash === currentRoutingPolicyHash,
   };
 }
 

package/src/store.js

@@ -1,53 +1,16 @@
 import fs from 'fs-extra';
 import path from 'path';
 import os from 'os';
-import crypto from 'crypto';
 import pc from 'picocolors';
 import { PATHS } from './utils.js';
 import { CORE_SKILLS } from './skills-catalog.js';
+import { hashPath as hashDirectory, normalizeOwnedMap, copyOwnedTree } from './owned-tree.js';
 
 // ─── Global Store Path ───────────────────────────────────────────────────────
 const HOME = os.homedir();
 export const STORE_PATH = process.env.TAKOMI_STORE_PATH || process.env.TAKOMI_HOME_DIR || path.join(HOME, '.takomi');
 export const MANIFEST_PATH = path.join(STORE_PATH, 'manifest.json');
 
-function sha256(value) {
-    return crypto.createHash('sha256').update(value).digest('hex');
-}
-
-async function hashDirectory(dir) {
-    if (!await fs.pathExists(dir)) return null;
-    const rootStat = await fs.stat(dir);
-    if (rootStat.isFile()) return sha256(await fs.readFile(dir));
-    const entries = [];
-    async function walk(current, prefix = '') {
-        const names = (await fs.readdir(current)).sort();
-        for (const name of names) {
-            const full = path.join(current, name);
-            const rel = path.join(prefix, name).replace(/\\/g, '/');
-            const stat = await fs.stat(full);
-            if (stat.isDirectory()) {
-                entries.push(`dir:${rel}`);
-                await walk(full, rel);
-            } else {
-                entries.push(`file:${rel}:${sha256(await fs.readFile(full))}`);
-            }
-        }
-    }
-    await walk(dir);
-    return sha256(entries.join('\n'));
-}
-
-function normalizeOwnedMap(value) {
-    if (!value || typeof value !== 'object') return {};
-    const normalized = {};
-    for (const [name, entry] of Object.entries(value)) {
-        if (typeof entry === 'string') normalized[name] = { hash: entry };
-        else if (entry?.hash) normalized[name] = entry;
-    }
-    return normalized;
-}
-
 function createDefaultManifest() {
     return {
         version: '2.0.0',
@@ -250,7 +213,7 @@ export async function populateSkills(mode) {
                 await fs.remove(dest);
             }
 
-            await fs.copy(src, dest, { overwrite: true });
+            await copyOwnedTree(src, dest);
             nextOwned[skill] = {
                 hash: await hashDirectory(dest),
                 targetPath: dest,
@@ -327,7 +290,7 @@ export async function populateWorkflows(mode) {
                 await fs.remove(dest);
             }
 
-            await fs.copy(src, dest, { overwrite: true });
+            await copyOwnedTree(src, dest);
             nextOwned[workflow] = {
                 hash: await hashDirectory(dest),
                 targetPath: dest,

package/src/takomi-stats.js

@@ -1,4 +1,5 @@
-import { promises as fs } from 'node:fs';
+import { createReadStream, promises as fs } from 'node:fs';
+import readline from 'node:readline';
 import os from 'os';
 import path from 'path';
 
@@ -167,9 +168,16 @@ async function scanPiSessions(root, source, events, sessionRows = [], taskRows =
     const row = { key: session, session, source, file, project: projectKey(file), cwd, start: '', end: '', turns: 0, messages: 0, toolCalls: 0, subagentCalls: 0, roles: new Map(), stages: new Map(), workflows: new Map(), activeMs: 0, activityIntervals: [] };
     const rowTracker = createActivityTracker();
     const toolCalls = new Map();
-    const text = await fs.readFile(file, 'utf8').catch(() => '');
 
-    for (const line of text.split(/\r?\n/)) {
+    let lines;
+    try {
+      lines = readline.createInterface({ input: createReadStream(file, { encoding: 'utf8' }), crlfDelay: Infinity });
+    } catch {
+      continue;
+    }
+
+    try {
+      for await (const line of lines) {
       const obj = safeJson(line); if (!obj) continue;
       if (obj.timestamp) { row.start ||= obj.timestamp; row.end = obj.timestamp; }
       if (obj.type === 'session') { session = obj.id || session; cwd = obj.cwd || cwd; row.key = session; row.session = session; row.cwd = cwd; }
@@ -254,6 +262,9 @@ async function scanPiSessions(root, source, events, sessionRows = [], taskRows =
         if (currentTask) currentTask.end = ts;
       }
 
+      }
+    } catch {
+      continue;
     }
     pushTask(taskRows, currentTask);
     if (currentTaskTracker && currentTask) {