@notis_ai/cli 0.2.0-beta.165.1 → 0.2.0-beta.167.1

package/dist/agent-hooks/notis-agent-hook.mjs

@@ -3669,10 +3669,34 @@ async function extractZipToDirectory(zipPath, destinationDir) {
     await fs2.rm(destinationDir, { recursive: true, force: true });
     await fs2.mkdir(path2.dirname(destinationDir), { recursive: true });
     await fs2.cp(sourceDir, destinationDir, { recursive: true });
+    return await listRelativeFiles(destinationDir);
   } finally {
     await fs2.rm(extractRoot, { recursive: true, force: true });
   }
 }
+async function listRelativeFiles(dirPath) {
+  try {
+    const files = await listFilesRecursive2(dirPath);
+    return files.map((filePath) => toPosixRelativePath(dirPath, filePath)).sort();
+  } catch (error) {
+    if (error?.code === "ENOENT") return [];
+    throw error;
+  }
+}
+function toPosixRelativePath(rootDir, filePath) {
+  return path2.relative(rootDir, filePath).split(path2.sep).join("/");
+}
+async function preserveUnmanagedFiles(existingDir, stagingDir, previouslyApplied) {
+  const managed = previouslyApplied ? new Set(previouslyApplied) : null;
+  for (const existingFile of await listFilesRecursive2(existingDir)) {
+    const relativePath = toPosixRelativePath(existingDir, existingFile);
+    if (managed?.has(relativePath)) continue;
+    const stagedPath = path2.join(stagingDir, ...relativePath.split("/"));
+    if (await pathExists(stagedPath)) continue;
+    await fs2.mkdir(path2.dirname(stagedPath), { recursive: true });
+    await fs2.copyFile(existingFile, stagedPath);
+  }
+}
 async function pathExists(targetPath) {
   try {
     await fs2.access(targetPath);
@@ -3681,7 +3705,7 @@ async function pathExists(targetPath) {
     return false;
   }
 }
-async function replaceSkillDirectoryAtomically(skillDir, populateDir) {
+async function replaceSkillDirectoryAtomically(skillDir, populateDir, preserve) {
   const parentDir = path2.dirname(skillDir);
   const skillName = path2.basename(skillDir);
   await fs2.mkdir(parentDir, { recursive: true });
@@ -3697,6 +3721,9 @@ async function replaceSkillDirectoryAtomically(skillDir, populateDir) {
   let cleanupError = null;
   try {
     await populateDir(stagingDir);
+    if (preserve && await pathExists(skillDir)) {
+      await preserveUnmanagedFiles(skillDir, stagingDir, preserve.previouslyApplied);
+    }
     if (await pathExists(skillDir)) {
       await fs2.rename(skillDir, backupDir);
       movedExisting = true;
@@ -3744,11 +3771,12 @@ async function createSkillBundleBase64(skill) {
     await fs2.rm(zipPath, { force: true });
   }
 }
-async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PATHS) {
+async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PATHS, options = {}) {
   const skillDir = path2.join(
     paths.skillsDir,
     safeName(skill.name, paths.skillsDir)
   );
+  const preserve = { previouslyApplied: options.previouslyApplied };
   if (bundleBytes?.length) {
     const bundlePath2 = path2.join(
       os.tmpdir(),
@@ -3756,8 +3784,11 @@ async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PA
     );
     try {
       await fs2.writeFile(bundlePath2, bundleBytes);
-      await extractZipToDirectory(bundlePath2, skillDir);
-      return true;
+      let appliedFiles = [];
+      await replaceSkillDirectoryAtomically(skillDir, async (stagingDir) => {
+        appliedFiles = await extractZipToDirectory(bundlePath2, stagingDir);
+      }, preserve);
+      return { written: true, appliedFiles };
     } finally {
       await fs2.rm(bundlePath2, { force: true });
     }
@@ -3771,6 +3802,7 @@ async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PA
         `Synced bundle for "${skill.name}" is missing SKILL.md or SKILLS.md`
       );
     }
+    const appliedFiles = [];
     await replaceSkillDirectoryAtomically(skillDir, async (stagingDir) => {
       for (const bundleFile of skill.bundle_files || []) {
         const filePath = resolveSkillBundleFilePath(
@@ -3782,9 +3814,10 @@ async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PA
           filePath,
           Buffer.from(bundleFile.content_b64, "base64")
         );
+        appliedFiles.push(toPosixRelativePath(stagingDir, filePath));
       }
-    });
-    return true;
+    }, preserve);
+    return { written: true, appliedFiles: appliedFiles.sort() };
   }
   await replaceSkillDirectoryAtomically(skillDir, async (stagingDir) => {
     await fs2.writeFile(
@@ -3792,8 +3825,8 @@ async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PA
       skill.skill_md ?? "",
       "utf8"
     );
-  });
-  return true;
+  }, preserve);
+  return { written: true, appliedFiles: ["SKILL.md"] };
 }
 async function requestJson(url, jwt, options = {}) {
   const response = await fetch(url, {
@@ -4174,7 +4207,7 @@ async function writeCloudSkillWithBundleFallback(skill, dependencies) {
       const bundleBytes = await dependencies.downloadSkillBundle(skill.skill_source_url);
       const wroteBundleToDisk = await dependencies.writeCloudSkillToDisk(skill, bundleBytes);
       if (wroteBundleToDisk) {
-        return true;
+        return wroteBundleToDisk;
       }
       dependencies.onWarning?.(
         `Bundle sync for "${skill.name}" produced no local changes, falling back to SKILL.md payload.`,
@@ -4267,12 +4300,20 @@ function collectAppliedCloudRevisions(pullResponse, previousState, writtenSkillN
   }
   return applied;
 }
-function buildSyncState(pullResponse, localSkills, lastSyncedAt, verifiedAgentLinks = {}, failedContentNames = /* @__PURE__ */ new Set(), appliedRevisions = {}) {
+function collectAppliedFiles(pullResponse, previousState, appliedFilesByName) {
+  const applied = {};
+  for (const skill of selectCloudSkillsToApply(pullResponse.skills)) {
+    applied[skill.name] = appliedFilesByName[skill.name] ?? previousState.skills[skill.name]?.appliedFiles;
+  }
+  return applied;
+}
+function buildSyncState(pullResponse, localSkills, lastSyncedAt, verifiedAgentLinks = {}, failedContentNames = /* @__PURE__ */ new Set(), appliedRevisions = {}, appliedFiles = {}) {
   const localSkillMap = toSkillMap(localSkills);
   const skills = Object.fromEntries(
     selectCloudSkillsToApply(pullResponse.skills).map((skill) => {
       const localSkill = localSkillMap.get(skill.name);
       const appliedCloudFolderHash = appliedRevisions[skill.name];
+      const appliedFileList = appliedFiles[skill.name];
       return [
         skill.name,
         {
@@ -4283,6 +4324,7 @@ function buildSyncState(pullResponse, localSkills, lastSyncedAt, verifiedAgentLi
           cloudUpdatedAt: skill.updated_at,
           ...!failedContentNames.has(skill.name) && !skill.skill_source_url ? { cloudContentHash: cloudContentHash(skill) } : {},
           ...appliedCloudFolderHash !== void 0 ? { appliedCloudFolderHash } : {},
+          ...appliedFileList !== void 0 ? { appliedFiles: appliedFileList } : {},
           syncedAt: lastSyncedAt || (/* @__PURE__ */ new Date()).toISOString()
         }
       ];
@@ -4338,7 +4380,7 @@ function applyLegacyFirstRunState(localSkills, scopedState, legacyState) {
     skills: migratedSkills
   };
 }
-async function writePulledSkillsToScopedMirror(pullResponse, localSkills, previousState, syncPaths, deps, failures = [], writtenSkillNames = /* @__PURE__ */ new Set()) {
+async function writePulledSkillsToScopedMirror(pullResponse, localSkills, previousState, syncPaths, deps, failures = [], writtenSkillNames = /* @__PURE__ */ new Set(), appliedFilesByName = {}) {
   const localSkillMap = toSkillMap(localSkills);
   const warnSkillSync = (message, error) => {
     console.warn(`[Notis] ${message}`, error);
@@ -4348,13 +4390,21 @@ async function writePulledSkillsToScopedMirror(pullResponse, localSkills, previo
     if (!shouldWriteCloudSkill(cloudSkill, localSkillMap, previousState)) {
       continue;
     }
-    if (await writeCloudSkillWithBundleFallback(cloudSkill, {
+    const outcome = await writeCloudSkillWithBundleFallback(cloudSkill, {
       downloadSkillBundle: deps.downloadSkillBundle,
-      writeCloudSkillToDisk: (skill, bundleBytes) => deps.writeCloudSkillToDisk(skill, bundleBytes, syncPaths),
+      writeCloudSkillToDisk: (skill, bundleBytes) => deps.writeCloudSkillToDisk(skill, bundleBytes, syncPaths, {
+        // What the last write put there. Everything else in the folder was
+        // produced locally and survives this one.
+        previouslyApplied: previousState.skills[skill.name]?.appliedFiles
+      }),
       onWarning: warnSkillSync
-    })) {
+    });
+    if (outcome) {
       downloaded += 1;
       writtenSkillNames.add(cloudSkill.name);
+      if (typeof outcome === "object" && Array.isArray(outcome.appliedFiles)) {
+        appliedFilesByName[cloudSkill.name] = outcome.appliedFiles;
+      }
     } else {
       failures.push({ name: cloudSkill.name, error: "Skill content could not be downloaded or written; sync will retry" });
     }
@@ -4386,6 +4436,7 @@ async function materializeCloudSkillsForLocalShell(serverUrl, jwt, dependencies
   const localSkills = await deps.scanLocalSkills(syncPaths);
   const failedDownloads = [];
   const writtenSkillNames = /* @__PURE__ */ new Set();
+  const appliedFilesByName = {};
   const downloaded = await writePulledSkillsToScopedMirror(
     pullResponse,
     localSkills,
@@ -4393,7 +4444,8 @@ async function materializeCloudSkillsForLocalShell(serverUrl, jwt, dependencies
     syncPaths,
     deps,
     failedDownloads,
-    writtenSkillNames
+    writtenSkillNames,
+    appliedFilesByName
   );
   const finalLocalSkills = await deps.scanLocalSkills(syncPaths);
   const lastSyncedAt = pullResponse.last_synced_at || (/* @__PURE__ */ new Date()).toISOString();
@@ -4426,7 +4478,8 @@ async function materializeCloudSkillsForLocalShell(serverUrl, jwt, dependencies
     lastSyncedAt,
     verifiedLinks,
     new Set(failedDownloads.map((item) => item.name)),
-    collectAppliedCloudRevisions(pullResponse, previousState, writtenSkillNames)
+    collectAppliedCloudRevisions(pullResponse, previousState, writtenSkillNames),
+    collectAppliedFiles(pullResponse, previousState, appliedFilesByName)
   );
   for (const [name, entry] of Object.entries(materializedState.skills)) {
     if (writtenSkillNames.has(name)) continue;
@@ -4607,6 +4660,7 @@ async function runSkillSync(serverUrl, jwt, dependencies = {}, options = {}) {
   }
   const failedDownloads = [];
   const writtenSkillNames = /* @__PURE__ */ new Set();
+  const appliedFilesByName = {};
   const downloaded = await writePulledSkillsToScopedMirror(
     pullResponse,
     localSkills,
@@ -4614,7 +4668,8 @@ async function runSkillSync(serverUrl, jwt, dependencies = {}, options = {}) {
     syncPaths,
     deps,
     failedDownloads,
-    writtenSkillNames
+    writtenSkillNames,
+    appliedFilesByName
   );
   const finalLocalSkills = (await deps.scanLocalSkills(syncPaths)).filter((skill) => !BASE_SKILL_NAMES2.has(skill.name));
   const symlinkResult = await deps.syncSymlinks(
@@ -4631,7 +4686,8 @@ async function runSkillSync(serverUrl, jwt, dependencies = {}, options = {}) {
       lastSyncedAt,
       verifiedLinks,
       new Set(failedDownloads.map((item) => item.name)),
-      collectAppliedCloudRevisions(pullResponse, previousState, writtenSkillNames)
+      collectAppliedCloudRevisions(pullResponse, previousState, writtenSkillNames),
+      collectAppliedFiles(pullResponse, previousState, appliedFilesByName)
     ),
     syncPaths
   );

package/dist/skill-sync/index.js

@@ -625,10 +625,34 @@ async function extractZipToDirectory(zipPath, destinationDir) {
     await fs.rm(destinationDir, { recursive: true, force: true });
     await fs.mkdir(path.dirname(destinationDir), { recursive: true });
     await fs.cp(sourceDir, destinationDir, { recursive: true });
+    return await listRelativeFiles(destinationDir);
   } finally {
     await fs.rm(extractRoot, { recursive: true, force: true });
   }
 }
+async function listRelativeFiles(dirPath) {
+  try {
+    const files = await listFilesRecursive(dirPath);
+    return files.map((filePath) => toPosixRelativePath(dirPath, filePath)).sort();
+  } catch (error) {
+    if (error?.code === "ENOENT") return [];
+    throw error;
+  }
+}
+function toPosixRelativePath(rootDir, filePath) {
+  return path.relative(rootDir, filePath).split(path.sep).join("/");
+}
+async function preserveUnmanagedFiles(existingDir, stagingDir, previouslyApplied) {
+  const managed = previouslyApplied ? new Set(previouslyApplied) : null;
+  for (const existingFile of await listFilesRecursive(existingDir)) {
+    const relativePath = toPosixRelativePath(existingDir, existingFile);
+    if (managed?.has(relativePath)) continue;
+    const stagedPath = path.join(stagingDir, ...relativePath.split("/"));
+    if (await pathExists(stagedPath)) continue;
+    await fs.mkdir(path.dirname(stagedPath), { recursive: true });
+    await fs.copyFile(existingFile, stagedPath);
+  }
+}
 async function pathExists(targetPath) {
   try {
     await fs.access(targetPath);
@@ -637,7 +661,7 @@ async function pathExists(targetPath) {
     return false;
   }
 }
-async function replaceSkillDirectoryAtomically(skillDir, populateDir) {
+async function replaceSkillDirectoryAtomically(skillDir, populateDir, preserve) {
   const parentDir = path.dirname(skillDir);
   const skillName = path.basename(skillDir);
   await fs.mkdir(parentDir, { recursive: true });
@@ -653,6 +677,9 @@ async function replaceSkillDirectoryAtomically(skillDir, populateDir) {
   let cleanupError = null;
   try {
     await populateDir(stagingDir);
+    if (preserve && await pathExists(skillDir)) {
+      await preserveUnmanagedFiles(skillDir, stagingDir, preserve.previouslyApplied);
+    }
     if (await pathExists(skillDir)) {
       await fs.rename(skillDir, backupDir);
       movedExisting = true;
@@ -700,11 +727,12 @@ async function createSkillBundleBase64(skill) {
     await fs.rm(zipPath, { force: true });
   }
 }
-async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PATHS) {
+async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PATHS, options = {}) {
   const skillDir = path.join(
     paths.skillsDir,
     safeName(skill.name, paths.skillsDir)
   );
+  const preserve = { previouslyApplied: options.previouslyApplied };
   if (bundleBytes?.length) {
     const bundlePath = path.join(
       os.tmpdir(),
@@ -712,8 +740,11 @@ async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PA
     );
     try {
       await fs.writeFile(bundlePath, bundleBytes);
-      await extractZipToDirectory(bundlePath, skillDir);
-      return true;
+      let appliedFiles = [];
+      await replaceSkillDirectoryAtomically(skillDir, async (stagingDir) => {
+        appliedFiles = await extractZipToDirectory(bundlePath, stagingDir);
+      }, preserve);
+      return { written: true, appliedFiles };
     } finally {
       await fs.rm(bundlePath, { force: true });
     }
@@ -727,6 +758,7 @@ async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PA
         `Synced bundle for "${skill.name}" is missing SKILL.md or SKILLS.md`
       );
     }
+    const appliedFiles = [];
     await replaceSkillDirectoryAtomically(skillDir, async (stagingDir) => {
       for (const bundleFile of skill.bundle_files || []) {
         const filePath = resolveSkillBundleFilePath(
@@ -738,9 +770,10 @@ async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PA
           filePath,
           Buffer.from(bundleFile.content_b64, "base64")
         );
+        appliedFiles.push(toPosixRelativePath(stagingDir, filePath));
       }
-    });
-    return true;
+    }, preserve);
+    return { written: true, appliedFiles: appliedFiles.sort() };
   }
   await replaceSkillDirectoryAtomically(skillDir, async (stagingDir) => {
     await fs.writeFile(
@@ -748,8 +781,8 @@ async function writeCloudSkillToDisk(skill, bundleBytes, paths = DEFAULT_SYNC_PA
       skill.skill_md ?? "",
       "utf8"
     );
-  });
-  return true;
+  }, preserve);
+  return { written: true, appliedFiles: ["SKILL.md"] };
 }
 
 // src/runtime/skill-sync/cloud-client.ts
@@ -1154,7 +1187,7 @@ async function writeCloudSkillWithBundleFallback(skill, dependencies) {
       const bundleBytes = await dependencies.downloadSkillBundle(skill.skill_source_url);
       const wroteBundleToDisk = await dependencies.writeCloudSkillToDisk(skill, bundleBytes);
       if (wroteBundleToDisk) {
-        return true;
+        return wroteBundleToDisk;
       }
       dependencies.onWarning?.(
         `Bundle sync for "${skill.name}" produced no local changes, falling back to SKILL.md payload.`,
@@ -1268,12 +1301,20 @@ function collectAppliedCloudRevisions(pullResponse, previousState, writtenSkillN
   }
   return applied;
 }
-function buildSyncState(pullResponse, localSkills, lastSyncedAt, verifiedAgentLinks = {}, failedContentNames = /* @__PURE__ */ new Set(), appliedRevisions = {}) {
+function collectAppliedFiles(pullResponse, previousState, appliedFilesByName) {
+  const applied = {};
+  for (const skill of selectCloudSkillsToApply(pullResponse.skills)) {
+    applied[skill.name] = appliedFilesByName[skill.name] ?? previousState.skills[skill.name]?.appliedFiles;
+  }
+  return applied;
+}
+function buildSyncState(pullResponse, localSkills, lastSyncedAt, verifiedAgentLinks = {}, failedContentNames = /* @__PURE__ */ new Set(), appliedRevisions = {}, appliedFiles = {}) {
   const localSkillMap = toSkillMap(localSkills);
   const skills = Object.fromEntries(
     selectCloudSkillsToApply(pullResponse.skills).map((skill) => {
       const localSkill = localSkillMap.get(skill.name);
       const appliedCloudFolderHash = appliedRevisions[skill.name];
+      const appliedFileList = appliedFiles[skill.name];
       return [
         skill.name,
         {
@@ -1284,6 +1325,7 @@ function buildSyncState(pullResponse, localSkills, lastSyncedAt, verifiedAgentLi
           cloudUpdatedAt: skill.updated_at,
           ...!failedContentNames.has(skill.name) && !skill.skill_source_url ? { cloudContentHash: cloudContentHash(skill) } : {},
           ...appliedCloudFolderHash !== void 0 ? { appliedCloudFolderHash } : {},
+          ...appliedFileList !== void 0 ? { appliedFiles: appliedFileList } : {},
           syncedAt: lastSyncedAt || (/* @__PURE__ */ new Date()).toISOString()
         }
       ];
@@ -1339,7 +1381,7 @@ function applyLegacyFirstRunState(localSkills, scopedState, legacyState) {
     skills: migratedSkills
   };
 }
-async function writePulledSkillsToScopedMirror(pullResponse, localSkills, previousState, syncPaths, deps, failures = [], writtenSkillNames = /* @__PURE__ */ new Set()) {
+async function writePulledSkillsToScopedMirror(pullResponse, localSkills, previousState, syncPaths, deps, failures = [], writtenSkillNames = /* @__PURE__ */ new Set(), appliedFilesByName = {}) {
   const localSkillMap = toSkillMap(localSkills);
   const warnSkillSync = (message, error) => {
     console.warn(`[Notis] ${message}`, error);
@@ -1349,13 +1391,21 @@ async function writePulledSkillsToScopedMirror(pullResponse, localSkills, previo
     if (!shouldWriteCloudSkill(cloudSkill, localSkillMap, previousState)) {
       continue;
     }
-    if (await writeCloudSkillWithBundleFallback(cloudSkill, {
+    const outcome = await writeCloudSkillWithBundleFallback(cloudSkill, {
       downloadSkillBundle: deps.downloadSkillBundle,
-      writeCloudSkillToDisk: (skill, bundleBytes) => deps.writeCloudSkillToDisk(skill, bundleBytes, syncPaths),
+      writeCloudSkillToDisk: (skill, bundleBytes) => deps.writeCloudSkillToDisk(skill, bundleBytes, syncPaths, {
+        // What the last write put there. Everything else in the folder was
+        // produced locally and survives this one.
+        previouslyApplied: previousState.skills[skill.name]?.appliedFiles
+      }),
       onWarning: warnSkillSync
-    })) {
+    });
+    if (outcome) {
       downloaded += 1;
       writtenSkillNames.add(cloudSkill.name);
+      if (typeof outcome === "object" && Array.isArray(outcome.appliedFiles)) {
+        appliedFilesByName[cloudSkill.name] = outcome.appliedFiles;
+      }
     } else {
       failures.push({ name: cloudSkill.name, error: "Skill content could not be downloaded or written; sync will retry" });
     }
@@ -1387,6 +1437,7 @@ async function materializeCloudSkillsForLocalShell(serverUrl, jwt, dependencies
   const localSkills = await deps.scanLocalSkills(syncPaths);
   const failedDownloads = [];
   const writtenSkillNames = /* @__PURE__ */ new Set();
+  const appliedFilesByName = {};
   const downloaded = await writePulledSkillsToScopedMirror(
     pullResponse,
     localSkills,
@@ -1394,7 +1445,8 @@ async function materializeCloudSkillsForLocalShell(serverUrl, jwt, dependencies
     syncPaths,
     deps,
     failedDownloads,
-    writtenSkillNames
+    writtenSkillNames,
+    appliedFilesByName
   );
   const finalLocalSkills = await deps.scanLocalSkills(syncPaths);
   const lastSyncedAt = pullResponse.last_synced_at || (/* @__PURE__ */ new Date()).toISOString();
@@ -1427,7 +1479,8 @@ async function materializeCloudSkillsForLocalShell(serverUrl, jwt, dependencies
     lastSyncedAt,
     verifiedLinks,
     new Set(failedDownloads.map((item) => item.name)),
-    collectAppliedCloudRevisions(pullResponse, previousState, writtenSkillNames)
+    collectAppliedCloudRevisions(pullResponse, previousState, writtenSkillNames),
+    collectAppliedFiles(pullResponse, previousState, appliedFilesByName)
   );
   for (const [name, entry] of Object.entries(materializedState.skills)) {
     if (writtenSkillNames.has(name)) continue;
@@ -1608,6 +1661,7 @@ async function runSkillSync(serverUrl, jwt, dependencies = {}, options = {}) {
   }
   const failedDownloads = [];
   const writtenSkillNames = /* @__PURE__ */ new Set();
+  const appliedFilesByName = {};
   const downloaded = await writePulledSkillsToScopedMirror(
     pullResponse,
     localSkills,
@@ -1615,7 +1669,8 @@ async function runSkillSync(serverUrl, jwt, dependencies = {}, options = {}) {
     syncPaths,
     deps,
     failedDownloads,
-    writtenSkillNames
+    writtenSkillNames,
+    appliedFilesByName
   );
   const finalLocalSkills = (await deps.scanLocalSkills(syncPaths)).filter((skill) => !BASE_SKILL_NAMES.has(skill.name));
   const symlinkResult = await deps.syncSymlinks(
@@ -1632,7 +1687,8 @@ async function runSkillSync(serverUrl, jwt, dependencies = {}, options = {}) {
       lastSyncedAt,
       verifiedLinks,
       new Set(failedDownloads.map((item) => item.name)),
-      collectAppliedCloudRevisions(pullResponse, previousState, writtenSkillNames)
+      collectAppliedCloudRevisions(pullResponse, previousState, writtenSkillNames),
+      collectAppliedFiles(pullResponse, previousState, appliedFilesByName)
     ),
     syncPaths
   );