@flydocs/cli 0.6.0-alpha.31 → 0.6.0-alpha.33

package/dist/cli.js

@@ -15,7 +15,7 @@ var CLI_VERSION, CLI_NAME, PACKAGE_NAME, POSTHOG_API_KEY;
 var init_constants = __esm({
   "src/lib/constants.ts"() {
     "use strict";
-    CLI_VERSION = "0.6.0-alpha.31";
+    CLI_VERSION = "0.6.0-alpha.33";
     CLI_NAME = "flydocs";
     PACKAGE_NAME = "@flydocs/cli";
     POSTHOG_API_KEY = "phc_v1MSJTQDFkMS90CBh3mxIz3v8bYCCnKU6v1ir6bz0Xn";
@@ -281,7 +281,7 @@ var init_types = __esm({
 // src/lib/config-integrity.ts
 import { createHash } from "crypto";
 function computeConfigHash(config) {
-  const { configHash: _, ...rest } = config;
+  const { configHash: _, artifactOverrides: _overrides, ...rest } = config;
   const serialized = JSON.stringify(rest, Object.keys(rest).sort());
   return `sha256:${createHash("sha256").update(serialized, "utf-8").digest("hex")}`;
 }
@@ -423,7 +423,7 @@ async function installOwnedSkills(templateDir, targetDir, _tier) {
 async function replaceOwnedSkills(templateDir, targetDir, _tier) {
   const skillsDir = join4(targetDir, ".claude", "skills");
   const templateSkillsDir = join4(templateDir, ".claude", "skills");
-  const { rm: rm7 } = await import("fs/promises");
+  const { rm: rm9 } = await import("fs/promises");
   await replaceDirectory(
     join4(templateSkillsDir, OWNED_SKILL),
     join4(skillsDir, OWNED_SKILL)
@@ -431,7 +431,7 @@ async function replaceOwnedSkills(templateDir, targetDir, _tier) {
   for (const legacy of LEGACY_SKILLS) {
     const legacyPath = join4(skillsDir, legacy);
     if (await pathExists(legacyPath)) {
-      await rm7(legacyPath, { recursive: true, force: true });
+      await rm9(legacyPath, { recursive: true, force: true });
     }
   }
   const readmeSrc = join4(templateSkillsDir, "README.md");
@@ -440,9 +440,9 @@ async function replaceOwnedSkills(templateDir, targetDir, _tier) {
   }
 }
 async function copyCursorRules(targetDir) {
-  const { mkdir: mkdir12 } = await import("fs/promises");
+  const { mkdir: mkdir16 } = await import("fs/promises");
   const rulesDir = join4(targetDir, ".cursor", "rules");
-  await mkdir12(rulesDir, { recursive: true });
+  await mkdir16(rulesDir, { recursive: true });
   const workflowRule = join4(
     targetDir,
     ".claude",
@@ -453,11 +453,11 @@ async function copyCursorRules(targetDir) {
   if (await pathExists(workflowRule)) {
     await copyFile(workflowRule, join4(rulesDir, "flydocs-workflow.mdc"));
   }
-  const { rm: rm7 } = await import("fs/promises");
+  const { rm: rm9 } = await import("fs/promises");
   for (const legacy of ["flydocs-mechanism.mdc", "flydocs-context7.mdc"]) {
     const legacyRule = join4(rulesDir, legacy);
     if (await pathExists(legacyRule)) {
-      await rm7(legacyRule, { force: true });
+      await rm9(legacyRule, { force: true });
     }
   }
 }
@@ -1492,10 +1492,20 @@ import { join as join11 } from "path";
 async function ensureGitignore(targetDir) {
   const gitignorePath = join11(targetDir, ".gitignore");
   if (await pathExists(gitignorePath)) {
-    const content = await readFile6(gitignorePath, "utf-8");
+    let content = await readFile6(gitignorePath, "utf-8");
+    let modified = false;
     if (!content.includes("# FlyDocs")) {
-      const section = "\n# FlyDocs\n" + FLYDOCS_GITIGNORE_ENTRIES.join("\n") + "\n";
-      await appendFile(gitignorePath, section, "utf-8");
+      const section = "\n# FlyDocs \u2014 local state\n" + FLYDOCS_GITIGNORE_ENTRIES.join("\n") + "\n";
+      content += section;
+      modified = true;
+    }
+    if (!content.includes("# FlyDocs \u2014 server-managed")) {
+      const section = "\n# FlyDocs \u2014 server-managed (rebuilt by flydocs sync)\n" + SERVER_MANAGED_GITIGNORE_ENTRIES.join("\n") + "\n";
+      content += section;
+      modified = true;
+    }
+    if (modified) {
+      await writeFile4(gitignorePath, content, "utf-8");
       printStatus("Added FlyDocs entries to .gitignore");
     }
   } else {
@@ -1507,33 +1517,55 @@ async function migrateGitignore(targetDir) {
   const gitignorePath = join11(targetDir, ".gitignore");
   if (!await pathExists(gitignorePath)) return;
   let content = await readFile6(gitignorePath, "utf-8");
-  for (const entry of FLYDOCS_GITIGNORE_ENTRIES) {
+  let modified = false;
+  content = migrateEntriesToSection(
+    content,
+    FLYDOCS_GITIGNORE_ENTRIES,
+    "# FlyDocs"
+  );
+  if (!content.includes("# FlyDocs \u2014 server-managed")) {
+    const section = "\n# FlyDocs \u2014 server-managed (rebuilt by flydocs sync)\n" + SERVER_MANAGED_GITIGNORE_ENTRIES.join("\n") + "\n";
+    content += section;
+    modified = true;
+  } else {
+    const before = content;
+    content = migrateEntriesToSection(
+      content,
+      SERVER_MANAGED_GITIGNORE_ENTRIES,
+      "# FlyDocs \u2014 server-managed"
+    );
+    if (content !== before) modified = true;
+  }
+  if (!modified) {
+    const original = await readFile6(gitignorePath, "utf-8");
+    if (content !== original) modified = true;
+  }
+  if (modified) {
+    await writeFile4(gitignorePath, content, "utf-8");
+    printStatus("Updated .gitignore with new FlyDocs entries");
+  }
+}
+function migrateEntriesToSection(content, entries, sectionMarker) {
+  for (const entry of entries) {
     if (content.includes(entry)) continue;
-    if (content.includes("# FlyDocs")) {
-      const lines = content.split("\n");
-      const flyDocsIdx = lines.findIndex((l) => l.trim() === "# FlyDocs");
-      if (flyDocsIdx !== -1) {
-        let insertIdx = flyDocsIdx + 1;
-        while (insertIdx < lines.length && lines[insertIdx].trim() !== "" && !lines[insertIdx].startsWith("#")) {
-          insertIdx++;
-        }
-        lines.splice(insertIdx, 0, entry);
-        content = lines.join("\n");
-        await writeFile4(gitignorePath, content, "utf-8");
-      } else {
-        content += `
-${entry}
-`;
-        await writeFile4(gitignorePath, content, "utf-8");
+    const lines = content.split("\n");
+    const sectionIdx = lines.findIndex(
+      (l) => l.trim().startsWith(sectionMarker)
+    );
+    if (sectionIdx !== -1) {
+      let insertIdx = sectionIdx + 1;
+      while (insertIdx < lines.length && lines[insertIdx].trim() !== "" && !lines[insertIdx].startsWith("#")) {
+        insertIdx++;
       }
+      lines.splice(insertIdx, 0, entry);
+      content = lines.join("\n");
     } else {
       content += `
 ${entry}
 `;
-      await writeFile4(gitignorePath, content, "utf-8");
     }
-    printStatus(`Added ${entry} to .gitignore`);
   }
+  return content;
 }
 async function ensurePlatformIgnores(targetDir) {
   for (const filename of PLATFORM_IGNORE_FILES) {
@@ -1546,7 +1578,7 @@ async function ensurePlatformIgnores(targetDir) {
     printStatus(`Added FlyDocs exclusions to ${filename}`);
   }
 }
-var PLATFORM_IGNORE_FILES, FLYDOCS_DEPLOY_EXCLUSIONS, FLYDOCS_GITIGNORE_ENTRIES, FULL_GITIGNORE_TEMPLATE;
+var PLATFORM_IGNORE_FILES, FLYDOCS_DEPLOY_EXCLUSIONS, FLYDOCS_GITIGNORE_ENTRIES, SERVER_MANAGED_GITIGNORE_ENTRIES, FULL_GITIGNORE_TEMPLATE;
 var init_gitignore = __esm({
   "src/lib/gitignore.ts"() {
     "use strict";
@@ -1582,12 +1614,23 @@ var init_gitignore = __esm({
       ".flydocs/session/",
       "flydocs/context/graph.json"
     ];
+    SERVER_MANAGED_GITIGNORE_ENTRIES = [
+      ".claude/skills/",
+      ".claude/commands/",
+      ".claude/hooks/",
+      ".claude/agents/",
+      ".claude/settings.json",
+      ".claude/CLAUDE.md",
+      ".cursor/rules/",
+      ".cursor/commands/",
+      "AGENTS.md"
+    ];
     FULL_GITIGNORE_TEMPLATE = `# Environment
 .env
 .env.local
 .env.*.local
 
-# FlyDocs
+# FlyDocs \u2014 local state
 .flydocs/session.json
 .flydocs/logs/
 .flydocs/backup-*/
@@ -1597,6 +1640,17 @@ var init_gitignore = __esm({
 .flydocs/session/
 flydocs/context/graph.json
 
+# FlyDocs \u2014 server-managed (rebuilt by flydocs sync)
+.claude/skills/
+.claude/commands/
+.claude/hooks/
+.claude/agents/
+.claude/settings.json
+.claude/CLAUDE.md
+.cursor/rules/
+.cursor/commands/
+AGENTS.md
+
 # Dependencies
 node_modules/
 
@@ -2973,6 +3027,65 @@ async function fetchTemplates(apiKey, sinceVersion, workspaceId) {
   }
   return await response.json();
 }
+async function fetchArtifacts(apiKey, sinceVersion) {
+  const baseUrl = resolveRelayUrl();
+  const response = await fetch(`${baseUrl}/artifacts?since=${sinceVersion}`, {
+    method: "GET",
+    headers: headers(apiKey),
+    signal: AbortSignal.timeout(3e4)
+  });
+  if (!response.ok) {
+    const body = await response.text().catch(() => "");
+    throw new RelayError(
+      `artifacts fetch failed (${response.status})`,
+      response.status,
+      body
+    );
+  }
+  return await response.json();
+}
+async function fetchAgentConfigs(apiKey, workspaceId) {
+  const baseUrl = resolveRelayUrl();
+  const response = await fetch(`${baseUrl}/artifacts/agent-configs`, {
+    method: "GET",
+    headers: headers(apiKey, workspaceId),
+    signal: AbortSignal.timeout(15e3)
+  });
+  if (!response.ok) {
+    const body = await response.text().catch(() => "");
+    throw new RelayError(
+      `agent-configs fetch failed (${response.status})`,
+      response.status,
+      body
+    );
+  }
+  return await response.json();
+}
+async function triggerScan(apiKey, repoName, options) {
+  const baseUrl = resolveRelayUrl();
+  const body = {
+    repoName,
+    options: {
+      regenerate: options.regenerate ?? false,
+      includeIdeConfigs: options.includeIdeConfigs ?? false
+    }
+  };
+  const response = await fetch(`${baseUrl}/ai/generate-context`, {
+    method: "POST",
+    headers: headers(apiKey, options.workspaceId),
+    body: JSON.stringify(body),
+    signal: AbortSignal.timeout(6e4)
+  });
+  if (!response.ok) {
+    const responseBody = await response.text().catch(() => "");
+    throw new RelayError(
+      `ai/generate-context failed (${response.status})`,
+      response.status,
+      responseBody
+    );
+  }
+  return await response.json();
+}
 var DEFAULT_RELAY_URL, RelayError;
 var init_relay_client = __esm({
   "src/lib/relay-client.ts"() {
@@ -2989,6 +3102,205 @@ var init_relay_client = __esm({
   }
 });
 
+// src/lib/managed-paths.ts
+import { join as join18 } from "path";
+import { readdir as readdir4, rm as rm4, unlink } from "fs/promises";
+function isSkipped(path, skipPaths) {
+  return skipPaths.some((skip) => path === skip || path.startsWith(skip));
+}
+async function wipeManagedPaths(targetDir, skipPaths = []) {
+  let deleted = 0;
+  let skipped = 0;
+  for (const dir of MANAGED_DIRECTORIES) {
+    const fullPath = join18(targetDir, dir);
+    if (isSkipped(dir + "/", skipPaths) || isSkipped(dir, skipPaths)) {
+      if (await pathExists(fullPath)) {
+        skipped++;
+      }
+      continue;
+    }
+    if (await pathExists(fullPath)) {
+      await rm4(fullPath, { recursive: true, force: true });
+      deleted++;
+    }
+  }
+  for (const file of MANAGED_FILES) {
+    if (isSkipped(file, skipPaths)) {
+      skipped++;
+      continue;
+    }
+    const fullPath = join18(targetDir, file);
+    if (await pathExists(fullPath)) {
+      await unlink(fullPath);
+      deleted++;
+    }
+  }
+  const skillsDir = join18(targetDir, ".claude", "skills");
+  if (await pathExists(skillsDir)) {
+    const entries = await readdir4(skillsDir, { withFileTypes: true });
+    for (const entry of entries) {
+      if (!entry.isDirectory()) continue;
+      if (!entry.name.startsWith(CORE_SKILL_PREFIX)) continue;
+      const skillPath = `.claude/skills/${entry.name}/`;
+      if (isSkipped(skillPath, skipPaths)) {
+        skipped++;
+        continue;
+      }
+      await rm4(join18(skillsDir, entry.name), { recursive: true, force: true });
+      deleted++;
+    }
+  }
+  if (deleted > 0) {
+    printStatus(`Wiped ${deleted} managed path(s)`);
+  }
+  if (skipped > 0) {
+    printInfo(`Preserved ${skipped} path(s) via skipPaths override`);
+  }
+  return { deleted, skipped };
+}
+var MANAGED_DIRECTORIES, MANAGED_FILES, CORE_SKILL_PREFIX;
+var init_managed_paths = __esm({
+  "src/lib/managed-paths.ts"() {
+    "use strict";
+    init_fs_ops();
+    init_ui();
+    MANAGED_DIRECTORIES = [
+      ".claude/hooks",
+      ".claude/commands",
+      ".claude/agents",
+      ".cursor/rules",
+      ".cursor/commands",
+      ".cursor/agents"
+    ];
+    MANAGED_FILES = [
+      ".claude/settings.json",
+      ".claude/CLAUDE.md",
+      ".cursor/hooks.json",
+      "AGENTS.md"
+    ];
+    CORE_SKILL_PREFIX = "flydocs-";
+  }
+});
+
+// src/lib/artifacts.ts
+import { mkdir as mkdir9, writeFile as writeFile11 } from "fs/promises";
+import { join as join19, dirname as dirname3 } from "path";
+function isPathSkipped(artifactPath, skipPaths) {
+  return skipPaths.some(
+    (skip) => artifactPath === skip || artifactPath.startsWith(skip)
+  );
+}
+async function syncArtifacts(targetDir, apiKey, workspaceId, currentVersion, skipPaths = []) {
+  const response = await fetchArtifacts(apiKey, currentVersion);
+  if (response.artifacts.length === 0) {
+    return { written: 0, skipped: 0, version: currentVersion };
+  }
+  let written = 0;
+  let skipped = 0;
+  for (const artifact of response.artifacts) {
+    if (skipPaths.length > 0 && isPathSkipped(artifact.path, skipPaths)) {
+      skipped++;
+      continue;
+    }
+    await writeArtifact(targetDir, artifact);
+    written++;
+  }
+  printStatus(
+    `Synced ${written} artifact(s) (v${currentVersion} \u2192 v${response.version})`
+  );
+  if (skipped > 0) {
+    printInfo(`Skipped ${skipped} artifact(s) via artifactOverrides.skipPaths`);
+  }
+  return { written, skipped, version: response.version };
+}
+async function syncAgentConfigs(targetDir, apiKey, workspaceId, skipPaths = []) {
+  const response = await fetchAgentConfigs(apiKey, workspaceId);
+  let written = 0;
+  for (const file of response.files) {
+    if (skipPaths.length > 0 && isPathSkipped(file.path, skipPaths)) {
+      continue;
+    }
+    const filePath = join19(targetDir, file.path);
+    await mkdir9(dirname3(filePath), { recursive: true });
+    await writeFile11(filePath, file.content, "utf-8");
+    written++;
+  }
+  if (written > 0) {
+    printStatus(`Wrote ${written} agent config(s) (CLAUDE.md, AGENTS.md)`);
+  }
+  return written;
+}
+async function writeArtifact(targetDir, artifact) {
+  const filePath = join19(targetDir, artifact.path);
+  await mkdir9(dirname3(filePath), { recursive: true });
+  await writeFile11(filePath, artifact.content, "utf-8");
+}
+async function syncAllArtifacts(targetDir, apiKey, workspaceId, currentArtifactVersion, skipPaths = []) {
+  const changes = [];
+  let artifactVersion = currentArtifactVersion;
+  const { deleted, skipped } = await wipeManagedPaths(targetDir, skipPaths);
+  if (deleted > 0) {
+    changes.push(`Wiped ${deleted} managed path(s)`);
+  }
+  if (skipped > 0) {
+    changes.push(`Preserved ${skipped} path(s) (skipPaths override)`);
+  }
+  try {
+    const result = await syncArtifacts(
+      targetDir,
+      apiKey,
+      workspaceId,
+      currentArtifactVersion,
+      skipPaths
+    );
+    if (result.written > 0) {
+      changes.push(`Synced ${result.written} artifact(s)`);
+      artifactVersion = result.version;
+    }
+    if (result.skipped > 0) {
+      changes.push(
+        `Skipped ${result.skipped} artifact(s) (skipPaths override)`
+      );
+    }
+  } catch (err) {
+    if (err instanceof RelayError) {
+      printWarning(
+        `Could not fetch artifacts (${err.status}). Will retry on next sync.`
+      );
+    } else {
+      printWarning("Artifact sync failed. Will retry on next sync.");
+    }
+  }
+  try {
+    const configCount = await syncAgentConfigs(
+      targetDir,
+      apiKey,
+      workspaceId,
+      skipPaths
+    );
+    if (configCount > 0) {
+      changes.push(`Wrote ${configCount} agent config(s)`);
+    }
+  } catch (err) {
+    if (err instanceof RelayError) {
+      printWarning(
+        `Could not fetch agent configs (${err.status}). Will retry on next sync.`
+      );
+    } else {
+      printWarning("Agent config sync failed. Will retry on next sync.");
+    }
+  }
+  return { artifactVersion, changes };
+}
+var init_artifacts = __esm({
+  "src/lib/artifacts.ts"() {
+    "use strict";
+    init_ui();
+    init_relay_client();
+    init_managed_paths();
+  }
+});
+
 // src/commands/cleanup.ts
 var cleanup_exports = {};
 __export(cleanup_exports, {
@@ -2998,11 +3310,11 @@ __export(cleanup_exports, {
 });
 import { defineCommand as defineCommand2 } from "citty";
 import pc7 from "picocolors";
-import { join as join18 } from "path";
-import { readFile as readFile13, writeFile as writeFile11, rm as rm4 } from "fs/promises";
+import { join as join20 } from "path";
+import { readFile as readFile13, writeFile as writeFile12, rm as rm5 } from "fs/promises";
 async function scanArtifacts(targetDir) {
   const actions = [];
-  const localMePath = join18(targetDir, ".flydocs", "me.json");
+  const localMePath = join20(targetDir, ".flydocs", "me.json");
   if (await pathExists(localMePath) && await pathExists(globalMePath())) {
     actions.push({
       description: "Remove .flydocs/me.json (migrated to ~/.flydocs/me.json)",
@@ -3010,7 +3322,7 @@ async function scanArtifacts(targetDir) {
       type: "file"
     });
   }
-  const validationCachePath = join18(
+  const validationCachePath = join20(
     targetDir,
     ".flydocs",
     "validation-cache.json"
@@ -3024,7 +3336,7 @@ async function scanArtifacts(targetDir) {
   }
   const hasGlobalCreds = await pathExists(credentialsPath());
   for (const envFile of [".env", ".env.local"]) {
-    const envPath = join18(targetDir, envFile);
+    const envPath = join20(targetDir, envFile);
     if (!await pathExists(envPath)) continue;
     const content = await readFile13(envPath, "utf-8");
     const lines = content.split("\n");
@@ -3049,7 +3361,7 @@ async function scanArtifacts(targetDir) {
   try {
     const config = await readAnyConfig(targetDir);
     const rawContent = await readFile13(
-      join18(targetDir, ".flydocs", "config.json"),
+      join20(targetDir, ".flydocs", "config.json"),
       "utf-8"
     );
     const raw = JSON.parse(rawContent);
@@ -3058,7 +3370,7 @@ async function scanArtifacts(targetDir) {
       if (field in raw) {
         actions.push({
           description: `Remove ghost field "${field}" from config.json`,
-          path: join18(targetDir, ".flydocs", "config.json"),
+          path: join20(targetDir, ".flydocs", "config.json"),
           type: "field"
         });
       }
@@ -3077,7 +3389,7 @@ async function scanArtifacts(targetDir) {
         if (field in raw) {
           actions.push({
             description: `Remove v1 field "${field}" from config.json (server-owned in v2)`,
-            path: join18(targetDir, ".flydocs", "config.json"),
+            path: join20(targetDir, ".flydocs", "config.json"),
             type: "field"
           });
         }
@@ -3092,7 +3404,7 @@ async function executeCleanup(targetDir, actions) {
   const lineRemovals = actions.filter((a) => a.type === "line");
   const fieldRemovals = actions.filter((a) => a.type === "field");
   for (const action of fileRemovals) {
-    await rm4(action.path, { force: true });
+    await rm5(action.path, { force: true });
   }
   const envFiles = /* @__PURE__ */ new Map();
   for (const action of lineRemovals) {
@@ -3110,13 +3422,13 @@ async function executeCleanup(targetDir, actions) {
       (l) => l.trim().length > 0 && !l.trim().startsWith("#")
     );
     if (!hasContent) {
-      await rm4(envPath, { force: true });
+      await rm5(envPath, { force: true });
     } else {
-      await writeFile11(envPath, filtered.join("\n"), "utf-8");
+      await writeFile12(envPath, filtered.join("\n"), "utf-8");
     }
   }
   if (fieldRemovals.length > 0) {
-    const configPath = join18(targetDir, ".flydocs", "config.json");
+    const configPath = join20(targetDir, ".flydocs", "config.json");
     const content = await readFile13(configPath, "utf-8");
     const config = JSON.parse(content);
     for (const action of fieldRemovals) {
@@ -3125,7 +3437,7 @@ async function executeCleanup(targetDir, actions) {
         delete config[match[1]];
       }
     }
-    await writeFile11(
+    await writeFile12(
       configPath,
       JSON.stringify(config, null, 2) + "\n",
       "utf-8"
@@ -3163,7 +3475,7 @@ var init_cleanup = __esm({
         console.log(`  ${pc7.bold("FlyDocs Cleanup")}`);
         console.log();
         const hasConfig = await pathExists(
-          join18(targetDir, ".flydocs", "config.json")
+          join20(targetDir, ".flydocs", "config.json")
         );
         if (!hasConfig) {
           printError("No .flydocs/config.json found. Run flydocs init first.");
@@ -3206,33 +3518,106 @@ var init_cleanup = __esm({
   }
 });
 
+// src/lib/ide-archive.ts
+import { readFile as readFile14, writeFile as writeFile13, mkdir as mkdir10, readdir as readdir5 } from "fs/promises";
+import { join as join21, basename } from "path";
+async function archiveIdeConfigs(targetDir) {
+  const archived = [];
+  for (const cfg of SINGLE_FILE_CONFIGS) {
+    const absSource = join21(targetDir, cfg.source);
+    if (!await pathExists(absSource)) continue;
+    const content = await readFile14(absSource, "utf-8");
+    const absDest = join21(targetDir, cfg.archive);
+    await mkdir10(join21(absDest, ".."), { recursive: true });
+    await writeFile13(absDest, content, "utf-8");
+    archived.push({
+      sourcePath: cfg.source,
+      archivePath: cfg.archive,
+      content
+    });
+    printStatus(`Archived ${cfg.source}`);
+  }
+  const cursorRulesDir = join21(targetDir, ".cursor", "rules");
+  if (await pathExists(cursorRulesDir)) {
+    let entries;
+    try {
+      entries = await readdir5(cursorRulesDir);
+    } catch {
+      entries = [];
+    }
+    const mdFiles = entries.filter((f) => f.endsWith(".md"));
+    if (mdFiles.length > 0) {
+      const archiveSubdir = join21(
+        targetDir,
+        "flydocs",
+        "knowledge",
+        "archived",
+        "cursor-rules"
+      );
+      await mkdir10(archiveSubdir, { recursive: true });
+      for (const file of mdFiles) {
+        const absSource = join21(cursorRulesDir, file);
+        const content = await readFile14(absSource, "utf-8");
+        const archivePath = `flydocs/knowledge/archived/cursor-rules/${basename(file)}`;
+        const absDest = join21(targetDir, archivePath);
+        await writeFile13(absDest, content, "utf-8");
+        archived.push({
+          sourcePath: `.cursor/rules/${file}`,
+          archivePath,
+          content
+        });
+        printStatus(`Archived .cursor/rules/${file}`);
+      }
+    }
+  }
+  return archived;
+}
+var SINGLE_FILE_CONFIGS;
+var init_ide_archive = __esm({
+  "src/lib/ide-archive.ts"() {
+    "use strict";
+    init_fs_ops();
+    init_ui();
+    SINGLE_FILE_CONFIGS = [
+      {
+        source: ".cursorrules",
+        archive: "flydocs/knowledge/archived/cursorrules.md"
+      },
+      {
+        source: ".claude/CLAUDE.md",
+        archive: "flydocs/knowledge/archived/claude-md.md"
+      }
+    ];
+  }
+});
+
 // src/lib/workspace.ts
-import { readFile as readFile14, writeFile as writeFile12, readdir as readdir4, stat as stat2 } from "fs/promises";
-import { join as join19, dirname as dirname3, relative, resolve as resolve3 } from "path";
+import { readFile as readFile15, writeFile as writeFile14, readdir as readdir6, stat as stat2 } from "fs/promises";
+import { join as join22, dirname as dirname4, relative, resolve as resolve3 } from "path";
 async function readWorkspaceFile(dir) {
-  const filePath = join19(dir, WORKSPACE_FILENAME);
+  const filePath = join22(dir, WORKSPACE_FILENAME);
   if (!await pathExists(filePath)) return null;
-  const content = await readFile14(filePath, "utf-8");
+  const content = await readFile15(filePath, "utf-8");
   const parsed = JSON.parse(content);
   validateWorkspaceFile(parsed);
   return parsed;
 }
 async function writeWorkspaceFile(dir, workspace) {
-  const filePath = join19(dir, WORKSPACE_FILENAME);
+  const filePath = join22(dir, WORKSPACE_FILENAME);
   const content = JSON.stringify(workspace, null, 2) + "\n";
-  await writeFile12(filePath, content, "utf-8");
+  await writeFile14(filePath, content, "utf-8");
 }
 async function detectSiblingRepos(parentDir) {
   const repos = {};
-  const entries = await readdir4(parentDir);
+  const entries = await readdir6(parentDir);
   for (const entry of entries) {
     if (entry.startsWith(".")) continue;
-    const entryPath = join19(parentDir, entry);
+    const entryPath = join22(parentDir, entry);
     const entryStat = await stat2(entryPath).catch(() => null);
     if (!entryStat?.isDirectory()) continue;
-    const hasGit = await pathExists(join19(entryPath, ".git"));
+    const hasGit = await pathExists(join22(entryPath, ".git"));
     const hasFlydocs = await pathExists(
-      join19(entryPath, ".flydocs", "config.json")
+      join22(entryPath, ".flydocs", "config.json")
     );
     if (hasGit || hasFlydocs) {
       repos[entry] = { path: `./${entry}` };
@@ -3247,10 +3632,10 @@ async function readSiblingDescriptors(workspaceDir, repos) {
   const descriptors = [];
   for (const [name, entry] of Object.entries(repos)) {
     const repoDir = resolve3(workspaceDir, entry.path);
-    const serviceJsonPath = join19(repoDir, "flydocs", "context", "service.json");
+    const serviceJsonPath = join22(repoDir, "flydocs", "context", "service.json");
     if (!await pathExists(serviceJsonPath)) continue;
     try {
-      const content = await readFile14(serviceJsonPath, "utf-8");
+      const content = await readFile15(serviceJsonPath, "utf-8");
       const descriptor = JSON.parse(content);
       descriptors.push({ name, path: entry.path, descriptor });
     } catch {
@@ -3353,96 +3738,290 @@ var init_workspace = __esm({
   }
 });
 
-// src/commands/init.ts
-var init_exports = {};
-__export(init_exports, {
-  default: () => init_default
+// src/commands/scan.ts
+var scan_exports = {};
+__export(scan_exports, {
+  default: () => scan_default,
+  runScan: () => runScan
 });
 import { defineCommand as defineCommand3 } from "citty";
-import { text as text2, confirm as confirm3, select as select2, isCancel as isCancel4, cancel as cancel3 } from "@clack/prompts";
+import { spinner } from "@clack/prompts";
 import pc8 from "picocolors";
-import { join as join20 } from "path";
-import { mkdir as mkdir9, writeFile as writeFile13 } from "fs/promises";
-import { execFile } from "child_process";
-import { promisify } from "util";
-async function resolveAndValidateKey(keyArg, targetDir) {
-  let resolved = await resolveApiKey(keyArg, targetDir);
-  if (!resolved) {
-    console.log(
-      `  ${pc8.dim("Get your API key (fdk_...) from your FlyDocs dashboard")}`
-    );
-    console.log();
-    const keyInput = await text2({
-      message: "Enter your API key",
-      placeholder: "fdk_...",
-      validate(value) {
-        if (!value.trim()) return "API key is required";
-        if (detectKeyType(value.trim()) !== "relay") {
-          return "Key must start with fdk_ (FlyDocs API key)";
-        }
-        return void 0;
-      }
-    });
-    if (isCancel4(keyInput)) {
-      cancel3("Init cancelled.");
-      process.exit(0);
-    }
-    resolved = { key: keyInput.trim(), source: "prompt" };
-  } else {
-    printInfo(`Using key from ${resolved.source}`);
-  }
-  const apiKey = resolved.key;
-  printInfo("Validating API key...");
+import { join as join23 } from "path";
+import { mkdir as mkdir11, writeFile as writeFile15 } from "fs/promises";
+async function resolveRepoName(targetDir, repoArg) {
+  if (repoArg) return repoArg;
   try {
-    const result = await validateRelayKey(apiKey);
-    if (!result.valid) {
-      printError("Invalid API key. Check your key and try again.");
-      process.exit(1);
+    const config = await readAnyConfig(targetDir);
+    if (!isConfigV2(config) && config.sourceRepo) {
+      return config.sourceRepo;
     }
-    printStatus(`Authenticated with ${pc8.bold(result.org)}`);
   } catch {
-    printError(
-      "Could not reach FlyDocs API. Check your network and try again."
+  }
+  try {
+    const { execFile: execFile2 } = await import("child_process");
+    const { promisify: promisify2 } = await import("util");
+    const execFileAsync2 = promisify2(execFile2);
+    const { stdout } = await execFileAsync2(
+      "git",
+      ["-C", targetDir, "remote", "get-url", "origin"],
+      { timeout: 5e3 }
     );
-    console.log(
-      `  ${pc8.dim("flydocs init requires server access. For offline use, run flydocs install instead.")}`
+    const url = stdout.trim();
+    const match = url.match(/[/:]([\w.-]+\/[\w.-]+?)(?:\.git)?$/);
+    if (match) return match[1];
+  } catch {
+  }
+  return null;
+}
+async function writeScanResults(targetDir, response) {
+  const written = [];
+  const contextDir = join23(targetDir, "flydocs", "context");
+  await mkdir11(contextDir, { recursive: true });
+  if (response.projectMd) {
+    const projectMdPath = join23(contextDir, "project.md");
+    await writeFile15(projectMdPath, response.projectMd, "utf-8");
+    written.push("flydocs/context/project.md");
+  }
+  if (response.serviceJson) {
+    const serviceJsonPath = join23(contextDir, "service.json");
+    await writeFile15(
+      serviceJsonPath,
+      JSON.stringify(response.serviceJson, null, 2) + "\n",
+      "utf-8"
     );
-    process.exit(1);
+    written.push("flydocs/context/service.json");
   }
-  const workspaces = await fetchWorkspaces(apiKey);
-  let workspaceId;
-  if (workspaces.length === 0) {
-    printError("No workspaces found. Create one at app.flydocs.ai first.");
-    process.exit(1);
-  } else if (workspaces.length === 1) {
-    workspaceId = workspaces[0].id;
-    printStatus(`Workspace: ${pc8.bold(workspaces[0].name)}`);
-  } else {
-    const choice = await select2({
-      message: "Select workspace",
-      options: workspaces.map((ws) => ({
-        value: ws.id,
-        label: ws.name
-      }))
+  return written;
+}
+async function runScan(apiKey, workspaceId, targetDir, repoName, regenerate) {
+  const s = spinner();
+  s.start("Running AI scan (this may take 5-20 seconds)...");
+  try {
+    const response = await triggerScan(apiKey, repoName, {
+      workspaceId,
+      regenerate
     });
-    if (isCancel4(choice)) {
-      cancel3("Init cancelled.");
-      process.exit(0);
+    if (!response.success) {
+      s.stop("Scan returned unsuccessful", 1);
+      return { success: false, written: [] };
     }
-    workspaceId = choice;
+    s.stop("Scan complete");
+    const written = await writeScanResults(targetDir, response);
+    return { success: true, written };
+  } catch (err) {
+    if (err instanceof RelayError) {
+      if (err.status === 403) {
+        s.stop("Permission denied", 1);
+        printError(
+          "Admin role required. Only workspace admins can trigger AI scans."
+        );
+      } else {
+        s.stop("Scan failed", 1);
+        printError(`Server error: ${err.message}`);
+      }
+    } else {
+      s.stop("Scan failed", 1);
+      printError("Could not reach server. Check your network and try again.");
+    }
+    return { success: false, written: [] };
   }
-  await writeGlobalCredential({
-    apiKey,
-    workspaceId,
-    createdAt: (/* @__PURE__ */ new Date()).toISOString(),
-    lastValidated: (/* @__PURE__ */ new Date()).toISOString()
+}
+var scan_default;
+var init_scan = __esm({
+  "src/commands/scan.ts"() {
+    "use strict";
+    init_ui();
+    init_global_config();
+    init_config();
+    init_types();
+    init_relay_client();
+    scan_default = defineCommand3({
+      meta: {
+        name: "scan",
+        description: "Trigger server-side AI scan to generate project context"
+      },
+      args: {
+        force: {
+          type: "boolean",
+          description: "Regenerate context even if it already exists",
+          default: false
+        },
+        path: {
+          type: "string",
+          description: "Path to project directory"
+        },
+        repo: {
+          type: "string",
+          description: "Override repo name (owner/repo format)"
+        }
+      },
+      async run({ args }) {
+        const targetDir = args.path ?? process.cwd();
+        console.log();
+        printInfo("FlyDocs AI Scan");
+        console.log();
+        const resolved = await resolveApiKey(void 0, targetDir);
+        if (!resolved) {
+          printError(
+            "No API key found. Run `flydocs auth` or `flydocs init` first."
+          );
+          process.exit(1);
+        }
+        const apiKey = resolved.key;
+        const cred = await readGlobalCredential();
+        const workspaceId = cred?.workspaceId;
+        if (!workspaceId) {
+          printError(
+            "No workspace ID found. Run `flydocs init` to set up your workspace."
+          );
+          process.exit(1);
+        }
+        printInfo("Checking permissions...");
+        try {
+          const configResponse = await fetchConfigV2(apiKey, { workspaceId });
+          if (configResponse.identity?.role !== "admin") {
+            printError(
+              "Admin role required. Only workspace admins can trigger AI scans."
+            );
+            console.log(
+              `  ${pc8.dim("Your role: " + (configResponse.identity?.role ?? "unknown"))}`
+            );
+            console.log(
+              `  ${pc8.dim("Ask a workspace admin to run this command or promote your role.")}`
+            );
+            process.exit(1);
+          }
+        } catch (err) {
+          if (err instanceof RelayError) {
+            printError(`Could not verify permissions: ${err.message}`);
+          } else {
+            printError("Could not reach server. Check your network.");
+          }
+          process.exit(1);
+        }
+        const repoName = await resolveRepoName(targetDir, args.repo);
+        if (!repoName) {
+          printError(
+            "Could not determine repo name. Use --repo owner/name to specify it."
+          );
+          process.exit(1);
+        }
+        printInfo(`Repo: ${pc8.bold(repoName)}`);
+        const { success, written } = await runScan(
+          apiKey,
+          workspaceId,
+          targetDir,
+          repoName,
+          args.force
+        );
+        if (success) {
+          console.log();
+          for (const file of written) {
+            printStatus(`Wrote ${file}`);
+          }
+          if (written.length === 0) {
+            printWarning("Scan completed but no context files were returned.");
+          }
+          console.log();
+        } else {
+          process.exit(1);
+        }
+      }
+    });
+  }
+});
+
+// src/commands/init.ts
+var init_exports = {};
+__export(init_exports, {
+  default: () => init_default
+});
+import { defineCommand as defineCommand4 } from "citty";
+import { text as text2, confirm as confirm3, select as select2, isCancel as isCancel4, cancel as cancel3 } from "@clack/prompts";
+import pc9 from "picocolors";
+import { join as join24 } from "path";
+import { mkdir as mkdir12, writeFile as writeFile16 } from "fs/promises";
+import { execFile } from "child_process";
+import { promisify } from "util";
+async function resolveAndValidateKey(keyArg, targetDir) {
+  let resolved = await resolveApiKey(keyArg, targetDir);
+  if (!resolved) {
+    console.log(
+      `  ${pc9.dim("Get your API key (fdk_...) from your FlyDocs dashboard")}`
+    );
+    console.log();
+    const keyInput = await text2({
+      message: "Enter your API key",
+      placeholder: "fdk_...",
+      validate(value) {
+        if (!value.trim()) return "API key is required";
+        if (detectKeyType(value.trim()) !== "relay") {
+          return "Key must start with fdk_ (FlyDocs API key)";
+        }
+        return void 0;
+      }
+    });
+    if (isCancel4(keyInput)) {
+      cancel3("Init cancelled.");
+      process.exit(0);
+    }
+    resolved = { key: keyInput.trim(), source: "prompt" };
+  } else {
+    printInfo(`Using key from ${resolved.source}`);
+  }
+  const apiKey = resolved.key;
+  printInfo("Validating API key...");
+  try {
+    const result = await validateRelayKey(apiKey);
+    if (!result.valid) {
+      printError("Invalid API key. Check your key and try again.");
+      process.exit(1);
+    }
+    printStatus(`Authenticated with ${pc9.bold(result.org)}`);
+  } catch {
+    printError(
+      "Could not reach FlyDocs API. Check your network and try again."
+    );
+    console.log(
+      `  ${pc9.dim("flydocs init requires server access. For offline use, run flydocs install instead.")}`
+    );
+    process.exit(1);
+  }
+  const workspaces = await fetchWorkspaces(apiKey);
+  let workspaceId;
+  if (workspaces.length === 0) {
+    printError("No workspaces found. Create one at app.flydocs.ai first.");
+    process.exit(1);
+  } else if (workspaces.length === 1) {
+    workspaceId = workspaces[0].id;
+    printStatus(`Workspace: ${pc9.bold(workspaces[0].name)}`);
+  } else {
+    const choice = await select2({
+      message: "Select workspace",
+      options: workspaces.map((ws) => ({
+        value: ws.id,
+        label: ws.name
+      }))
+    });
+    if (isCancel4(choice)) {
+      cancel3("Init cancelled.");
+      process.exit(0);
+    }
+    workspaceId = choice;
+  }
+  await writeGlobalCredential({
+    apiKey,
+    workspaceId,
+    createdAt: (/* @__PURE__ */ new Date()).toISOString(),
+    lastValidated: (/* @__PURE__ */ new Date()).toISOString()
   });
   await checkCredentialPermissions();
   return { apiKey, workspaceId };
 }
 async function pullServerConfig(apiKey, targetDir, workspaceId, forceIncludeContext = false) {
   printInfo("Pulling config from server...");
-  const isFirstInit = forceIncludeContext || !await pathExists(join20(targetDir, ".flydocs", "config.json"));
+  const isFirstInit = forceIncludeContext || !await pathExists(join24(targetDir, ".flydocs", "config.json"));
   try {
     const response = await fetchConfigV2(apiKey, {
       includeContext: isFirstInit,
@@ -3458,7 +4037,7 @@ async function pullServerConfig(apiKey, targetDir, workspaceId, forceIncludeCont
       printError(`Server error: ${err.message}`);
       if (err.status === 401) {
         console.log(
-          `  ${pc8.dim("Your API key may be revoked. Run flydocs auth with a new key.")}`
+          `  ${pc9.dim("Your API key may be revoked. Run flydocs auth with a new key.")}`
         );
       }
     } else {
@@ -3467,10 +4046,11 @@ async function pullServerConfig(apiKey, targetDir, workspaceId, forceIncludeCont
     process.exit(1);
   }
 }
-async function initSingleRepo(targetDir, apiKey, serverResponse) {
+async function initSingleRepo(targetDir, apiKey, serverResponse, options = {}) {
   const actions = [];
   const skipped = [];
-  await mkdir9(join20(targetDir, ".flydocs"), { recursive: true });
+  const { childRepoMode = false } = options;
+  await mkdir12(join24(targetDir, ".flydocs"), { recursive: true });
   const configWithHash = applyConfigHash(serverResponse.config);
   await writeConfig(targetDir, configWithHash);
   actions.push("Wrote .flydocs/config.json (from server)");
@@ -3483,18 +4063,18 @@ async function initSingleRepo(targetDir, apiKey, serverResponse) {
     actions.push("Wrote ~/.flydocs/me.json");
   }
   if (serverResponse.context) {
-    const contextDir = join20(targetDir, "flydocs", "context");
-    await mkdir9(contextDir, { recursive: true });
-    const projectMdPath = join20(contextDir, "project.md");
+    const contextDir = join24(targetDir, "flydocs", "context");
+    await mkdir12(contextDir, { recursive: true });
+    const projectMdPath = join24(contextDir, "project.md");
     if (!await pathExists(projectMdPath)) {
-      await writeFile13(projectMdPath, serverResponse.context.projectMd, "utf-8");
+      await writeFile16(projectMdPath, serverResponse.context.projectMd, "utf-8");
       actions.push("Wrote flydocs/context/project.md");
     } else {
       skipped.push("flydocs/context/project.md (already exists)");
     }
-    const serviceJsonPath = join20(contextDir, "service.json");
+    const serviceJsonPath = join24(contextDir, "service.json");
     if (serverResponse.context.serviceJson && !await pathExists(serviceJsonPath)) {
-      await writeFile13(
+      await writeFile16(
         serviceJsonPath,
         JSON.stringify(serverResponse.context.serviceJson, null, 2) + "\n",
         "utf-8"
@@ -3504,6 +4084,27 @@ async function initSingleRepo(targetDir, apiKey, serverResponse) {
       skipped.push("flydocs/context/service.json (already exists)");
     }
   }
+  if (childRepoMode) {
+    const cleaned = await cleanServerManagedFiles(targetDir);
+    if (cleaned > 0) {
+      actions.push(
+        `Removed ${cleaned} server-managed file(s) (moved to workspace root)`
+      );
+    }
+  } else {
+    const archivedConfigs = await archiveIdeConfigs(targetDir);
+    if (archivedConfigs.length > 0) {
+      actions.push(`Archived ${archivedConfigs.length} existing IDE config(s)`);
+    }
+    const { changes: artifactChanges } = await syncAllArtifacts(
+      targetDir,
+      apiKey,
+      serverResponse.workspaceId,
+      0
+      // fresh init — fetch all artifacts
+    );
+    actions.push(...artifactChanges);
+  }
   await ensureGitignore(targetDir);
   await ensurePlatformIgnores(targetDir);
   actions.push("Updated ignore files");
@@ -3512,10 +4113,32 @@ async function initSingleRepo(targetDir, apiKey, serverResponse) {
     await executeCleanup(targetDir, artifacts);
     actions.push(`Cleaned ${artifacts.length} legacy artifact(s)`);
   }
-  return { actions, skipped };
+  return {
+    actions,
+    skipped
+  };
+}
+async function cleanServerManagedFiles(targetDir) {
+  const { rm: rm9 } = await import("fs/promises");
+  let cleaned = 0;
+  for (const dir of SERVER_MANAGED_DIRS) {
+    const fullPath = join24(targetDir, dir);
+    if (await pathExists(fullPath)) {
+      await rm9(fullPath, { recursive: true, force: true });
+      cleaned++;
+    }
+  }
+  for (const file of SERVER_MANAGED_FILES) {
+    const fullPath = join24(targetDir, file);
+    if (await pathExists(fullPath)) {
+      await rm9(fullPath, { force: true });
+      cleaned++;
+    }
+  }
+  return cleaned;
 }
 async function checkGitFreshness(repoDir) {
-  const hasGit = await pathExists(join20(repoDir, ".git"));
+  const hasGit = await pathExists(join24(repoDir, ".git"));
   if (!hasGit) return;
   try {
     await execFileAsync("git", ["-C", repoDir, "fetch", "--quiet"], {
@@ -3544,7 +4167,7 @@ async function checkGitFreshness(repoDir) {
   }
 }
 async function isEmptyOrNonRepo(dir) {
-  const hasGit = await pathExists(join20(dir, ".git"));
+  const hasGit = await pathExists(join24(dir, ".git"));
   if (hasGit) return false;
   const siblings = await detectSiblingRepos(dir);
   if (Object.keys(siblings).length >= 2) return false;
@@ -3557,7 +4180,7 @@ async function runCloneAndInit(targetDir, keyArg, repos, apiKey, workspaceId) {
   if (repos.length === 1) {
     const repo = repos[0];
     const shortName = repoShortName(repo.name);
-    printInfo(`Workspace has 1 repo: ${pc8.bold(shortName)}`);
+    printInfo(`Workspace has 1 repo: ${pc9.bold(shortName)}`);
     const shouldClone = await confirm3({
       message: `Clone ${shortName} into this directory and initialize?`
     });
@@ -3595,7 +4218,7 @@ async function runCloneAndInit(targetDir, keyArg, repos, apiKey, workspaceId) {
     const repoNames = repos.map((r) => repoShortName(r.name));
     printInfo(`Workspace has ${repos.length} repos:`);
     for (const name of repoNames) {
-      console.log(`    ${pc8.cyan(name)}`);
+      console.log(`    ${pc9.cyan(name)}`);
     }
     console.log();
     const shouldClone = await confirm3({
@@ -3614,13 +4237,13 @@ async function runCloneAndInit(targetDir, keyArg, repos, apiKey, workspaceId) {
     for (let i = 0; i < repos.length; i++) {
       const repo = repos[i];
       const shortName = repoNames[i];
-      const cloneDir = join20(targetDir, shortName);
+      const cloneDir = join24(targetDir, shortName);
       console.log();
-      if (await pathExists(join20(cloneDir, ".git"))) {
-        printInfo(`${pc8.bold(shortName)} already cloned, initializing...`);
+      if (await pathExists(join24(cloneDir, ".git"))) {
+        printInfo(`${pc9.bold(shortName)} already cloned, initializing...`);
         await checkGitFreshness(cloneDir);
       } else {
-        printInfo(`Cloning ${pc8.bold(shortName)}...`);
+        printInfo(`Cloning ${pc9.bold(shortName)}...`);
         await execFileAsync("git", ["clone", repo.cloneUrl, cloneDir], {
           timeout: 6e4
         });
@@ -3659,12 +4282,12 @@ async function runCloneAndInit(targetDir, keyArg, repos, apiKey, workspaceId) {
       );
       await writeWorkspaceFile(targetDir, workspaceFile);
       allActions.push(`.flydocs-workspace.json (${repos.length} repos)`);
-      const contextDir = join20(targetDir, "flydocs", "context");
-      const workspaceMdPath = join20(contextDir, "workspace.md");
+      const contextDir = join24(targetDir, "flydocs", "context");
+      const workspaceMdPath = join24(contextDir, "workspace.md");
       if (!await pathExists(workspaceMdPath)) {
-        await mkdir9(contextDir, { recursive: true });
+        await mkdir12(contextDir, { recursive: true });
         const content = firstResponse.context?.workspaceMd ?? await generateWorkspaceMd(targetDir, workspaceFile);
-        await writeFile13(workspaceMdPath, content, "utf-8");
+        await writeFile16(workspaceMdPath, content, "utf-8");
         const source = firstResponse.context?.workspaceMd ? "from server" : "generated locally";
         allActions.push(`Wrote flydocs/context/workspace.md (${source})`);
       }
@@ -3679,7 +4302,7 @@ async function runCloneAndInit(targetDir, keyArg, repos, apiKey, workspaceId) {
   }
 }
 async function isParentDirectory(dir) {
-  const hasGit = await pathExists(join20(dir, ".git"));
+  const hasGit = await pathExists(join24(dir, ".git"));
   if (hasGit) return false;
   const repos = await detectSiblingRepos(dir);
   return Object.keys(repos).length >= 2;
@@ -3689,7 +4312,7 @@ async function runMultiRepoInit(parentDir, keyArg) {
   const repoNames = Object.keys(repos).sort();
   printInfo(`Detected ${repoNames.length} repos:`);
   for (const name of repoNames) {
-    console.log(`    ${pc8.cyan(name)}`);
+    console.log(`    ${pc9.cyan(name)}`);
   }
   console.log();
   const shouldContinue = await confirm3({
@@ -3699,7 +4322,7 @@ async function runMultiRepoInit(parentDir, keyArg) {
     cancel3("Init cancelled.");
     process.exit(0);
   }
-  const firstRepoDir = join20(parentDir, repoNames[0]);
+  const firstRepoDir = join24(parentDir, repoNames[0]);
   const { apiKey, workspaceId } = await resolveAndValidateKey(
     keyArg,
     firstRepoDir
@@ -3710,17 +4333,38 @@ async function runMultiRepoInit(parentDir, keyArg) {
   const allSkipped = [];
   let allWarnings = [];
   let firstResponse;
+  const workspaceResponse = await pullServerConfig(
+    apiKey,
+    firstRepoDir,
+    workspaceId
+  );
+  firstResponse = workspaceResponse;
+  const archivedConfigs = await archiveIdeConfigs(parentDir);
+  if (archivedConfigs.length > 0) {
+    allActions.push(
+      `Archived ${archivedConfigs.length} existing IDE config(s) at workspace root`
+    );
+  }
+  const { changes: artifactChanges } = await syncAllArtifacts(
+    parentDir,
+    apiKey,
+    workspaceId,
+    0
+  );
+  allActions.push(...artifactChanges);
+  await ensureGitignore(parentDir);
+  allActions.push("Updated workspace root .gitignore");
   for (const repoName of repoNames) {
-    const repoDir = join20(parentDir, repoName);
+    const repoDir = join24(parentDir, repoName);
     console.log();
-    printInfo(`Initializing ${pc8.bold(repoName)}...`);
+    printInfo(`Initializing ${pc9.bold(repoName)}...`);
     await checkGitFreshness(repoDir);
     const serverResponse = await pullServerConfig(apiKey, repoDir, workspaceId);
-    if (!firstResponse) firstResponse = serverResponse;
     const { actions, skipped } = await initSingleRepo(
       repoDir,
       apiKey,
-      serverResponse
+      serverResponse,
+      { childRepoMode: true }
     );
     for (const action of actions) {
       allActions.push(`[${repoName}] ${action}`);
@@ -3743,15 +4387,15 @@ async function runMultiRepoInit(parentDir, keyArg) {
       await writeWorkspaceFile(parentDir, workspaceFile);
       allActions.push(`.flydocs-workspace.json (${repoNames.length} repos)`);
     }
-    const contextDir = join20(parentDir, "flydocs", "context");
-    const workspaceMdPath = join20(contextDir, "workspace.md");
+    const contextDir = join24(parentDir, "flydocs", "context");
+    const workspaceMdPath = join24(contextDir, "workspace.md");
     if (await pathExists(workspaceMdPath)) {
       allSkipped.push("flydocs/context/workspace.md (already exists)");
     } else {
-      await mkdir9(contextDir, { recursive: true });
+      await mkdir12(contextDir, { recursive: true });
       const workspaceJson = await readWorkspaceFile(parentDir) ?? buildWorkspaceFile(firstResponse.workspaceId, repos);
       const content = firstResponse.context?.workspaceMd ?? await generateWorkspaceMd(parentDir, workspaceJson);
-      await writeFile13(workspaceMdPath, content, "utf-8");
+      await writeFile16(workspaceMdPath, content, "utf-8");
       const source = firstResponse.context?.workspaceMd ? "from server" : "generated locally";
       allActions.push(`Wrote flydocs/context/workspace.md (${source})`);
     }
@@ -3768,35 +4412,35 @@ function printInitReport(actions, skipped, warnings, hasContext) {
   console.log();
   const lines = [];
   for (const action of actions) {
-    lines.push(`${pc8.green("+")} ${action}`);
+    lines.push(`${pc9.green("+")} ${action}`);
   }
   for (const skip of skipped) {
-    lines.push(`${pc8.dim("-")} ${skip}`);
+    lines.push(`${pc9.dim("-")} ${skip}`);
   }
   if (!hasContext) {
     lines.push("");
     lines.push(
-      `${pc8.yellow("!")} No generated context yet. An admin can generate it from the portal.`
+      `${pc9.yellow("!")} No generated context yet. An admin can generate it from the portal.`
     );
   }
   if (warnings.length > 0) {
     lines.push("");
     for (const warning of warnings) {
-      lines.push(`${pc8.yellow("!")} ${warning}`);
+      lines.push(`${pc9.yellow("!")} ${warning}`);
     }
   }
   printCompletionBox("FlyDocs Initialized", lines);
   console.log();
   console.log(`  Next steps:`);
   console.log(
-    `    ${pc8.cyan("flydocs sync")}       Pull latest config and templates`
+    `    ${pc9.cyan("flydocs sync")}       Pull latest config and templates`
   );
   console.log(
-    `    ${pc8.cyan("cursor .")} ${pc8.dim("or")} ${pc8.cyan("code .")}   Open your IDE, then use ${pc8.bold("/start-session")}`
+    `    ${pc9.cyan("cursor .")} ${pc9.dim("or")} ${pc9.cyan("code .")}   Open your IDE, then use ${pc9.bold("/start-session")}`
   );
   console.log();
 }
-var execFileAsync, init_default;
+var SERVER_MANAGED_DIRS, SERVER_MANAGED_FILES, execFileAsync, init_default;
 var init_init = __esm({
   "src/commands/init.ts"() {
     "use strict";
@@ -3808,10 +4452,26 @@ var init_init = __esm({
     init_gitignore();
     init_fs_ops();
     init_relay_client();
+    init_artifacts();
     init_cleanup();
+    init_ide_archive();
     init_workspace();
+    init_scan();
+    SERVER_MANAGED_DIRS = [
+      ".claude/skills",
+      ".claude/commands",
+      ".claude/hooks",
+      ".claude/agents",
+      ".cursor/rules",
+      ".cursor/commands"
+    ];
+    SERVER_MANAGED_FILES = [
+      ".claude/settings.json",
+      ".claude/CLAUDE.md",
+      "AGENTS.md"
+    ];
     execFileAsync = promisify(execFile);
-    init_default = defineCommand3({
+    init_default = defineCommand4({
       meta: {
         name: "init",
         description: "Initialize FlyDocs in this project (unified setup)"
@@ -3824,12 +4484,17 @@ var init_init = __esm({
         path: {
           type: "string",
           description: "Path to project directory"
+        },
+        scan: {
+          type: "boolean",
+          description: "Run AI scan after init to generate project context",
+          default: false
         }
       },
       async run({ args }) {
         const targetDir = args.path ?? process.cwd();
         console.log();
-        console.log(`  ${pc8.bold("FlyDocs Init")}`);
+        console.log(`  ${pc9.bold("FlyDocs Init")}`);
         console.log();
         if (await isParentDirectory(targetDir)) {
           await runMultiRepoInit(targetDir, args.key);
@@ -3876,7 +4541,7 @@ var init_init = __esm({
         actions.unshift("Stored credential globally (~/.flydocs/credentials)");
         const topology = serverResponse.config.topology;
         if (topology?.type === 4 && topology.label === "sibling-repos") {
-          const parentDir = join20(targetDir, "..");
+          const parentDir = join24(targetDir, "..");
           const existing = await readWorkspaceFile(parentDir);
           if (existing) {
             skipped.push(".flydocs-workspace.json (already exists)");
@@ -3900,6 +4565,402 @@ var init_init = __esm({
           serverResponse.warnings,
           !!serverResponse.context
         );
+        const shouldAutoScan = !args.scan && serverResponse.contextVersion === 0 && !serverResponse.context?.projectMd;
+        if (shouldAutoScan) {
+          const isAdmin = serverResponse.identity?.role === "admin";
+          if (isAdmin) {
+            console.log();
+            printInfo(
+              "No generated context found. AI scanning creates project.md and service.json."
+            );
+            const shouldScan = await confirm3({
+              message: "Run AI scan now?"
+            });
+            if (!isCancel4(shouldScan) && shouldScan) {
+              let repoName = null;
+              try {
+                const { stdout } = await execFileAsync(
+                  "git",
+                  ["-C", targetDir, "remote", "get-url", "origin"],
+                  { timeout: 5e3 }
+                );
+                const url = stdout.trim();
+                const match = url.match(/[/:]([\w.-]+\/[\w.-]+?)(?:\.git)?$/);
+                if (match) repoName = match[1];
+              } catch {
+              }
+              if (repoName) {
+                const { success, written } = await runScan(
+                  apiKey,
+                  workspaceId,
+                  targetDir,
+                  repoName,
+                  false
+                );
+                if (success) {
+                  for (const file of written) {
+                    printStatus(`Wrote ${file}`);
+                  }
+                }
+              } else {
+                printWarning(
+                  "Could not determine repo name from git remote. Run `flydocs scan --repo owner/name` manually."
+                );
+              }
+            }
+          } else {
+            console.log();
+            printInfo(
+              "No generated context yet. Ask a workspace admin to generate it from the portal, then run `flydocs sync`."
+            );
+          }
+        }
+        if (args.scan) {
+          const isAdmin = serverResponse.identity?.role === "admin";
+          if (!isAdmin) {
+            printWarning(
+              "Skipping scan: admin role required. Only workspace admins can trigger AI scans."
+            );
+          } else {
+            let repoName = null;
+            try {
+              const { stdout } = await execFileAsync(
+                "git",
+                ["-C", targetDir, "remote", "get-url", "origin"],
+                { timeout: 5e3 }
+              );
+              const url = stdout.trim();
+              const match = url.match(/[/:]([\w.-]+\/[\w.-]+?)(?:\.git)?$/);
+              if (match) repoName = match[1];
+            } catch {
+            }
+            if (!repoName) {
+              printWarning(
+                "Skipping scan: could not determine repo name from git remote."
+              );
+            } else {
+              console.log();
+              printInfo(`Running AI scan for ${pc9.bold(repoName)}...`);
+              const { success, written } = await runScan(
+                apiKey,
+                workspaceId,
+                targetDir,
+                repoName,
+                false
+                // not a forced regeneration on init
+              );
+              if (success) {
+                for (const file of written) {
+                  printStatus(`Wrote ${file}`);
+                }
+              }
+            }
+          }
+        }
+      }
+    });
+  }
+});
+
+// src/lib/skill-conflicts.ts
+import { join as join25 } from "path";
+import { readdir as readdir7, rm as rm6, cp as cp2, mkdir as mkdir13 } from "fs/promises";
+import { select as select3, isCancel as isCancel5 } from "@clack/prompts";
+async function resolveSkillConflicts(targetDir, keptPaths = []) {
+  const result = {
+    newKeptPaths: [],
+    archived: 0,
+    deleted: 0
+  };
+  const skillsDir = join25(targetDir, ".claude", "skills");
+  if (!await pathExists(skillsDir)) return result;
+  const entries = await readdir7(skillsDir, { withFileTypes: true });
+  for (const entry of entries) {
+    if (!entry.isDirectory()) continue;
+    if (entry.name.startsWith(CORE_SKILL_PREFIX2)) continue;
+    const relPath = `.claude/skills/${entry.name}`;
+    if (keptPaths.includes(relPath) || keptPaths.includes(relPath + "/")) {
+      continue;
+    }
+    await promptConflict(targetDir, skillsDir, entry.name, relPath, result);
+  }
+  if (result.archived > 0 || result.deleted > 0 || result.newKeptPaths.length > 0) {
+    const parts = [];
+    if (result.archived > 0) parts.push(`${result.archived} archived`);
+    if (result.deleted > 0) parts.push(`${result.deleted} deleted`);
+    if (result.newKeptPaths.length > 0)
+      parts.push(`${result.newKeptPaths.length} kept`);
+    printInfo(`Non-core skills: ${parts.join(", ")}`);
+  }
+  return result;
+}
+async function promptConflict(targetDir, skillsDir, name, relPath, result) {
+  const choice = await select3({
+    message: `Found non-managed skill: ${name}. What should we do?`,
+    options: [
+      {
+        value: "keep",
+        label: "Keep \u2014 leave in place, don't ask again"
+      },
+      {
+        value: "archive",
+        label: "Archive \u2014 move to flydocs/knowledge/archived/skills/"
+      },
+      {
+        value: "delete",
+        label: "Delete \u2014 remove permanently"
+      }
+    ]
+  });
+  if (isCancel5(choice)) {
+    result.newKeptPaths.push(relPath);
+    return;
+  }
+  const fullPath = join25(skillsDir, name);
+  switch (choice) {
+    case "keep":
+      result.newKeptPaths.push(relPath);
+      printInfo(`Keeping ${name} (won't ask again)`);
+      break;
+    case "archive": {
+      const archiveDir = join25(
+        targetDir,
+        "flydocs",
+        "knowledge",
+        "archived",
+        "skills"
+      );
+      await mkdir13(archiveDir, { recursive: true });
+      const archiveDest = join25(archiveDir, name);
+      if (await pathExists(archiveDest)) {
+        await rm6(archiveDest, { recursive: true, force: true });
+      }
+      await cp2(fullPath, archiveDest, { recursive: true });
+      await rm6(fullPath, { recursive: true, force: true });
+      result.archived++;
+      printStatus(`Archived ${name} \u2192 flydocs/knowledge/archived/skills/`);
+      break;
+    }
+    case "delete":
+      await rm6(fullPath, { recursive: true, force: true });
+      result.deleted++;
+      printStatus(`Deleted ${name}`);
+      break;
+  }
+}
+var CORE_SKILL_PREFIX2;
+var init_skill_conflicts = __esm({
+  "src/lib/skill-conflicts.ts"() {
+    "use strict";
+    init_fs_ops();
+    init_ui();
+    CORE_SKILL_PREFIX2 = "flydocs-";
+  }
+});
+
+// src/commands/sync.ts
+var sync_exports = {};
+__export(sync_exports, {
+  default: () => sync_default,
+  runSync: () => runSync
+});
+import { defineCommand as defineCommand5 } from "citty";
+import pc10 from "picocolors";
+import { join as join26, resolve as resolve4 } from "path";
+import { mkdir as mkdir14, writeFile as writeFile17 } from "fs/promises";
+async function runSync(targetDir) {
+  const changes = [];
+  printInfo("Syncing with server...");
+  const resolved = await resolveApiKey(void 0, targetDir);
+  if (!resolved) {
+    printError("No API key found. Run `flydocs auth` or `flydocs init` first.");
+    process.exit(1);
+  }
+  const apiKey = resolved.key;
+  const cred = await readGlobalCredential();
+  const workspaceId = cred?.workspaceId;
+  if (!workspaceId) {
+    printError(
+      "No workspace ID found. Run `flydocs init` to set up your workspace."
+    );
+    process.exit(1);
+  }
+  let currentTemplateVersion = 0;
+  let currentArtifactVersion = 0;
+  let localOverrides;
+  try {
+    const currentConfig = await readAnyConfig(targetDir);
+    if (isConfigV2(currentConfig)) {
+      currentTemplateVersion = currentConfig.configVersion ?? 0;
+      currentArtifactVersion = currentConfig.artifactVersion ?? 0;
+      localOverrides = currentConfig.artifactOverrides;
+    }
+  } catch {
+  }
+  let serverResponse;
+  try {
+    serverResponse = await fetchConfigV2(apiKey, { workspaceId });
+  } catch (err) {
+    if (err instanceof RelayError) {
+      printWarning(`Server unavailable (${err.status}), using cached config.`);
+    } else {
+      printWarning("Server unreachable, using cached config.");
+    }
+    console.log(`  ${pc10.dim("Config may be stale. Retry when connected.")}`);
+    return changes;
+  }
+  if (!serverResponse.valid) {
+    printWarning("Server returned invalid config. Keeping current config.");
+    return changes;
+  }
+  await mkdir14(join26(targetDir, ".flydocs"), { recursive: true });
+  const serverConfig = serverResponse.config;
+  if (localOverrides) {
+    serverConfig.artifactOverrides = localOverrides;
+  }
+  const configWithHash = applyConfigHash(serverConfig);
+  await writeConfig(targetDir, configWithHash);
+  changes.push("Updated .flydocs/config.json");
+  const serverTemplateVersion = serverResponse.templates.version;
+  if (serverTemplateVersion > currentTemplateVersion) {
+    try {
+      const templatesResponse = await fetchTemplates(
+        apiKey,
+        currentTemplateVersion,
+        workspaceId
+      );
+      if (templatesResponse.templates.length > 0) {
+        const templatesDir = join26(
+          targetDir,
+          ".claude",
+          "skills",
+          "flydocs-workflow",
+          "templates"
+        );
+        await mkdir14(templatesDir, { recursive: true });
+        for (const template of templatesResponse.templates) {
+          const filename = `${template.type}.md`;
+          const subdir = template.category === "issue" ? "issues" : template.category === "pr" ? "pr" : template.category === "comment" ? "." : ".";
+          const templateDir = join26(templatesDir, subdir);
+          await mkdir14(templateDir, { recursive: true });
+          await writeFile17(
+            join26(templateDir, filename),
+            template.content,
+            "utf-8"
+          );
+        }
+        changes.push(
+          `Updated ${templatesResponse.templates.length} templates (v${currentTemplateVersion} \u2192 v${serverTemplateVersion})`
+        );
+      }
+    } catch (err) {
+      if (err instanceof RelayError) {
+        printWarning("Could not fetch templates. Will retry on next sync.");
+      } else {
+        printWarning("Template sync failed. Will retry on next sync.");
+      }
+    }
+  }
+  const serverArtifactVersion = serverResponse.artifactVersion ?? 0;
+  const skipPaths = localOverrides?.skipPaths ?? [];
+  if (serverArtifactVersion > currentArtifactVersion) {
+    const artifactWriteRoot = await resolveArtifactWriteRoot(
+      targetDir,
+      serverResponse.config
+    );
+    const { changes: artifactChanges } = await syncAllArtifacts(
+      artifactWriteRoot,
+      apiKey,
+      workspaceId,
+      currentArtifactVersion,
+      skipPaths
+    );
+    changes.push(...artifactChanges);
+    if (artifactWriteRoot !== targetDir) {
+      changes.push(`Artifacts written to workspace root`);
+    }
+    const keptPaths = localOverrides?.keptPaths ?? [];
+    const conflicts = await resolveSkillConflicts(artifactWriteRoot, keptPaths);
+    if (conflicts.newKeptPaths.length > 0) {
+      try {
+        const updatedConfig = await readAnyConfig(targetDir);
+        if (isConfigV2(updatedConfig)) {
+          const existingKept = updatedConfig.artifactOverrides?.keptPaths ?? [];
+          const mergedKept = [
+            .../* @__PURE__ */ new Set([...existingKept, ...conflicts.newKeptPaths])
+          ];
+          updatedConfig.artifactOverrides = {
+            ...updatedConfig.artifactOverrides,
+            skipPaths: updatedConfig.artifactOverrides?.skipPaths ?? [],
+            keptPaths: mergedKept
+          };
+          const hashed = applyConfigHash(updatedConfig);
+          await writeConfig(targetDir, hashed);
+          changes.push(
+            `Persisted ${conflicts.newKeptPaths.length} kept path(s) to config`
+          );
+        }
+      } catch {
+      }
+    }
+    if (conflicts.archived > 0) {
+      changes.push(`Archived ${conflicts.archived} non-core skill(s)`);
+    }
+    if (conflicts.deleted > 0) {
+      changes.push(`Deleted ${conflicts.deleted} non-core skill(s)`);
+    }
+  }
+  await migrateGitignore(targetDir);
+  return changes;
+}
+async function resolveArtifactWriteRoot(targetDir, config) {
+  const topology = config.topology;
+  if (topology && topology.type === 4 && topology.label === "sibling-repos") {
+    const parentDir = join26(targetDir, "..");
+    const workspaceFile = await readWorkspaceFile(parentDir);
+    if (workspaceFile) {
+      return resolve4(parentDir);
+    }
+  }
+  return targetDir;
+}
+var sync_default;
+var init_sync = __esm({
+  "src/commands/sync.ts"() {
+    "use strict";
+    init_ui();
+    init_global_config();
+    init_config();
+    init_config_integrity();
+    init_types();
+    init_gitignore();
+    init_artifacts();
+    init_workspace();
+    init_relay_client();
+    init_skill_conflicts();
+    sync_default = defineCommand5({
+      meta: {
+        name: "sync",
+        description: "Pull latest config and templates from server"
+      },
+      args: {
+        path: {
+          type: "string",
+          description: "Path to project directory"
+        }
+      },
+      async run({ args }) {
+        const targetDir = args.path ?? process.cwd();
+        console.log();
+        const changes = await runSync(targetDir);
+        if (changes.length === 0) {
+          printStatus("Already up to date.");
+        } else {
+          for (const change of changes) {
+            printStatus(change);
+          }
+        }
+        console.log();
       }
     });
   }
@@ -3910,11 +4971,11 @@ var update_exports = {};
 __export(update_exports, {
   default: () => update_default
 });
-import { defineCommand as defineCommand4 } from "citty";
-import { resolve as resolve4, join as join21 } from "path";
-import { mkdir as mkdir10, cp as cp2, readFile as readFile15, readdir as readdir5, rm as rm5 } from "fs/promises";
-import { select as select3, text as text3, confirm as confirm4, isCancel as isCancel5, cancel as cancel4 } from "@clack/prompts";
-import pc9 from "picocolors";
+import { defineCommand as defineCommand6 } from "citty";
+import { resolve as resolve5, join as join27 } from "path";
+import { mkdir as mkdir15, cp as cp3, readFile as readFile16, readdir as readdir8, rm as rm7 } from "fs/promises";
+import { select as select4, text as text3, confirm as confirm4, isCancel as isCancel6, cancel as cancel4 } from "@clack/prompts";
+import pc11 from "picocolors";
 var update_default;
 var init_update = __esm({
   "src/commands/update.ts"() {
@@ -3933,7 +4994,11 @@ var init_update = __esm({
     init_update_check();
     init_telemetry();
     init_integrity();
-    update_default = defineCommand4({
+    init_config();
+    init_types();
+    init_managed_paths();
+    init_sync();
+    update_default = defineCommand6({
       meta: {
         name: "update",
         description: "Update an existing FlyDocs installation"
@@ -3978,11 +5043,11 @@ var init_update = __esm({
         await capture("update_started", { template_version: version });
         let targetDir;
         if (args.path) {
-          targetDir = resolve4(args.path.replace(/^~/, process.env.HOME ?? "~"));
+          targetDir = resolve5(args.path.replace(/^~/, process.env.HOME ?? "~"));
         } else if (args.here) {
           targetDir = process.cwd();
         } else {
-          const choice = await select3({
+          const choice = await select4({
             message: "Which project would you like to update?",
             options: [
               {
@@ -3995,7 +5060,7 @@ var init_update = __esm({
               }
             ]
           });
-          if (isCancel5(choice)) {
+          if (isCancel6(choice)) {
             cancel4("Update cancelled.");
             process.exit(0);
           }
@@ -4005,11 +5070,11 @@ var init_update = __esm({
             const enteredPath = await text3({
               message: "Enter project path:"
             });
-            if (isCancel5(enteredPath)) {
+            if (isCancel6(enteredPath)) {
               cancel4("Update cancelled.");
               process.exit(0);
             }
-            targetDir = resolve4(
+            targetDir = resolve5(
               enteredPath.replace(/^~/, process.env.HOME ?? "~")
             );
           }
@@ -4018,11 +5083,11 @@ var init_update = __esm({
           printError(`Directory does not exist: ${targetDir}`);
           process.exit(1);
         }
-        targetDir = resolve4(targetDir);
+        targetDir = resolve5(targetDir);
         process.chdir(targetDir);
-        const hasVersion = await pathExists(join21(targetDir, ".flydocs", "version"));
+        const hasVersion = await pathExists(join27(targetDir, ".flydocs", "version"));
         const hasConfig = await pathExists(
-          join21(targetDir, ".flydocs", "config.json")
+          join27(targetDir, ".flydocs", "config.json")
         );
         if (!hasVersion && !hasConfig) {
           printError(`Not a FlyDocs project: ${targetDir}`);
@@ -4033,8 +5098,8 @@ var init_update = __esm({
         console.log();
         let currentVersion = "0.1.0";
         if (hasVersion) {
-          const vContent = await readFile15(
-            join21(targetDir, ".flydocs", "version"),
+          const vContent = await readFile16(
+            join27(targetDir, ".flydocs", "version"),
             "utf-8"
           );
           currentVersion = vContent.trim();
@@ -4056,7 +5121,7 @@ var init_update = __esm({
           const shouldContinue = await confirm4({
             message: "Continue anyway?"
           });
-          if (isCancel5(shouldContinue) || !shouldContinue) {
+          if (isCancel6(shouldContinue) || !shouldContinue) {
             process.exit(0);
           }
         }
@@ -4068,35 +5133,65 @@ var init_update = __esm({
         });
         console.log(`Updating: v${currentVersion} \u2192 v${version}`);
         console.log();
-        const changelogPath = join21(templateDir, "CHANGELOG.md");
+        const changelogPath = join27(templateDir, "CHANGELOG.md");
         const whatsNew = await getWhatsNew(changelogPath, currentVersion, version);
         if (whatsNew.length > 0) {
-          console.log(pc9.cyan("What's new:"));
+          console.log(pc11.cyan("What's new:"));
           console.log();
           for (const entry of whatsNew) {
             console.log(`  ${entry}`);
           }
           console.log();
         }
+        if (hasConfig) {
+          try {
+            const existingConfig = await readAnyConfig(targetDir);
+            if (isConfigV2(existingConfig)) {
+              printInfo(
+                "Cloud project detected \u2014 running sync flow (wipe-and-replace)"
+              );
+              console.log();
+              const syncChanges = await runSync(targetDir);
+              if (syncChanges.length > 0) {
+                for (const change of syncChanges) {
+                  printStatus(change);
+                }
+              }
+              console.log();
+              console.log(
+                `  ${pc11.dim("Tip: use")} ${pc11.cyan("flydocs sync")} ${pc11.dim("for file-only refresh (no CLI update).")}`
+              );
+              await capture("update_completed", {
+                current_version: currentVersion,
+                version,
+                tier: "cloud",
+                mode: "sync-delegate"
+              });
+              await flush();
+              return;
+            }
+          } catch {
+          }
+        }
         const now = /* @__PURE__ */ new Date();
         const ts = `${now.getFullYear()}${String(now.getMonth() + 1).padStart(2, "0")}${String(now.getDate()).padStart(2, "0")}-${String(now.getHours()).padStart(2, "0")}${String(now.getMinutes()).padStart(2, "0")}${String(now.getSeconds()).padStart(2, "0")}`;
-        const backupDir = join21(targetDir, ".flydocs", `backup-${ts}`);
-        await mkdir10(backupDir, { recursive: true });
+        const backupDir = join27(targetDir, ".flydocs", `backup-${ts}`);
+        await mkdir15(backupDir, { recursive: true });
         if (hasConfig) {
-          await cp2(
-            join21(targetDir, ".flydocs", "config.json"),
-            join21(backupDir, "config.json")
+          await cp3(
+            join27(targetDir, ".flydocs", "config.json"),
+            join27(backupDir, "config.json")
           );
           printStatus(`Config backed up to .flydocs/backup-${ts}/`);
         }
         try {
-          const flydocsDir = join21(targetDir, ".flydocs");
-          const entries = await readdir5(flydocsDir);
+          const flydocsDir = join27(targetDir, ".flydocs");
+          const entries = await readdir8(flydocsDir);
           const backups = entries.filter((e) => e.startsWith("backup-")).sort();
           if (backups.length > 3) {
             const toRemove = backups.slice(0, backups.length - 3);
             for (const old of toRemove) {
-              await rm5(join21(flydocsDir, old), { recursive: true, force: true });
+              await rm7(join27(flydocsDir, old), { recursive: true, force: true });
             }
           }
         } catch {
@@ -4133,19 +5228,21 @@ var init_update = __esm({
           effectiveTier = preserved.tier;
         }
         await ensureDirectories(targetDir, effectiveTier);
+        console.log("Wiping server-managed paths...");
+        await wipeManagedPaths(targetDir);
         console.log("Replacing framework directories...");
         await replaceDirectory(
-          join21(templateDir, ".flydocs", "templates"),
-          join21(targetDir, ".flydocs", "templates")
+          join27(templateDir, ".flydocs", "templates"),
+          join27(targetDir, ".flydocs", "templates")
         );
         printStatus(".flydocs/templates");
         await replaceDirectory(
-          join21(templateDir, ".claude", "hooks"),
-          join21(targetDir, ".claude", "hooks")
+          join27(templateDir, ".claude", "hooks"),
+          join27(targetDir, ".claude", "hooks")
         );
         printStatus(".claude/hooks");
         const hasExistingAgents = await pathExists(
-          join21(targetDir, ".claude", "agents")
+          join27(targetDir, ".claude", "agents")
         );
         let installAgents;
         if (args.yes) {
@@ -4154,7 +5251,7 @@ var init_update = __esm({
           installAgents = true;
         } else {
           console.log();
-          console.log(`  ${pc9.bold(pc9.yellow("Sub-Agents (Recommended)"))}`);
+          console.log(`  ${pc11.bold(pc11.yellow("Sub-Agents (Recommended)"))}`);
           console.log();
           console.log(
             "  Sub-agents are specialized roles (PM, implementation, review,"
@@ -4170,27 +5267,27 @@ var init_update = __esm({
             message: "Install sub-agents?",
             initialValue: true
           });
-          if (isCancel5(agentConfirm)) {
+          if (isCancel6(agentConfirm)) {
             installAgents = false;
           } else {
             installAgents = agentConfirm;
           }
         }
         if (installAgents) {
-          const claudeAgentsSrc = join21(templateDir, ".claude", "agents");
+          const claudeAgentsSrc = join27(templateDir, ".claude", "agents");
           if (await pathExists(claudeAgentsSrc)) {
-            await mkdir10(join21(targetDir, ".claude", "agents"), { recursive: true });
+            await mkdir15(join27(targetDir, ".claude", "agents"), { recursive: true });
             await copyDirectoryContents(
               claudeAgentsSrc,
-              join21(targetDir, ".claude", "agents")
+              join27(targetDir, ".claude", "agents")
             );
           }
-          const cursorAgentsSrc = join21(templateDir, ".cursor", "agents");
+          const cursorAgentsSrc = join27(templateDir, ".cursor", "agents");
           if (await pathExists(cursorAgentsSrc)) {
-            await mkdir10(join21(targetDir, ".cursor", "agents"), { recursive: true });
+            await mkdir15(join27(targetDir, ".cursor", "agents"), { recursive: true });
             await copyDirectoryContents(
               cursorAgentsSrc,
-              join21(targetDir, ".cursor", "agents")
+              join27(targetDir, ".cursor", "agents")
             );
           }
           printStatus(
@@ -4204,58 +5301,58 @@ var init_update = __esm({
         console.log();
         console.log("Replacing framework files...");
         await copyFile(
-          join21(templateDir, ".claude", "CLAUDE.md"),
-          join21(targetDir, ".claude", "CLAUDE.md")
+          join27(templateDir, ".claude", "CLAUDE.md"),
+          join27(targetDir, ".claude", "CLAUDE.md")
         );
         await copyFile(
-          join21(templateDir, ".claude", "settings.json"),
-          join21(targetDir, ".claude", "settings.json")
+          join27(templateDir, ".claude", "settings.json"),
+          join27(targetDir, ".claude", "settings.json")
         );
         printStatus(".claude/CLAUDE.md, settings.json");
         await copyDirectoryContents(
-          join21(templateDir, ".claude", "commands"),
-          join21(targetDir, ".claude", "commands")
+          join27(templateDir, ".claude", "commands"),
+          join27(targetDir, ".claude", "commands")
         );
         await copyDirectoryContents(
-          join21(templateDir, ".claude", "commands"),
-          join21(targetDir, ".cursor", "commands")
+          join27(templateDir, ".claude", "commands"),
+          join27(targetDir, ".cursor", "commands")
         );
         printStatus(".claude/commands, .cursor/commands");
-        const skillsReadmeSrc = join21(templateDir, ".claude", "skills", "README.md");
+        const skillsReadmeSrc = join27(templateDir, ".claude", "skills", "README.md");
         if (await pathExists(skillsReadmeSrc)) {
           await copyFile(
             skillsReadmeSrc,
-            join21(targetDir, ".claude", "skills", "README.md")
+            join27(targetDir, ".claude", "skills", "README.md")
           );
         }
         printStatus(".claude/skills/README.md");
         await copyFile(
-          join21(templateDir, ".cursor", "hooks.json"),
-          join21(targetDir, ".cursor", "hooks.json")
+          join27(templateDir, ".cursor", "hooks.json"),
+          join27(targetDir, ".cursor", "hooks.json")
         );
         printStatus(".cursor/hooks.json");
         await copyFile(
-          join21(templateDir, "AGENTS.md"),
-          join21(targetDir, "AGENTS.md")
+          join27(templateDir, "AGENTS.md"),
+          join27(targetDir, "AGENTS.md")
         );
         printStatus("AGENTS.md");
-        const envExampleSrc = join21(templateDir, ".env.example");
+        const envExampleSrc = join27(templateDir, ".env.example");
         if (await pathExists(envExampleSrc)) {
-          await copyFile(envExampleSrc, join21(targetDir, ".env.example"));
+          await copyFile(envExampleSrc, join27(targetDir, ".env.example"));
           printStatus(".env.example");
         }
-        const knowledgeTemplatesDir = join21(
+        const knowledgeTemplatesDir = join27(
           targetDir,
           "flydocs",
           "knowledge",
           "templates"
         );
         if (!await pathExists(knowledgeTemplatesDir)) {
-          await mkdir10(knowledgeTemplatesDir, { recursive: true });
+          await mkdir15(knowledgeTemplatesDir, { recursive: true });
         }
         for (const tmpl of ["decision.md", "feature.md", "note.md"]) {
-          const src = join21(templateDir, "flydocs", "knowledge", "templates", tmpl);
-          const dest = join21(knowledgeTemplatesDir, tmpl);
+          const src = join27(templateDir, "flydocs", "knowledge", "templates", tmpl);
+          const dest = join27(knowledgeTemplatesDir, tmpl);
           if (await pathExists(src) && !await pathExists(dest)) {
             await copyFile(src, dest);
           }
@@ -4282,18 +5379,18 @@ var init_update = __esm({
           printWarning("Config merge failed \u2014 config.json preserved as-is");
         }
         await copyFile(
-          join21(templateDir, ".flydocs", "version"),
-          join21(targetDir, ".flydocs", "version")
+          join27(templateDir, ".flydocs", "version"),
+          join27(targetDir, ".flydocs", "version")
         );
         printStatus(`.flydocs/version \u2192 ${version}`);
-        const clSrc = join21(templateDir, "CHANGELOG.md");
+        const clSrc = join27(templateDir, "CHANGELOG.md");
         if (await pathExists(clSrc)) {
-          await copyFile(clSrc, join21(targetDir, ".flydocs", "CHANGELOG.md"));
+          await copyFile(clSrc, join27(targetDir, ".flydocs", "CHANGELOG.md"));
           printStatus(".flydocs/CHANGELOG.md");
         }
-        const mfSrc = join21(templateDir, "manifest.json");
+        const mfSrc = join27(templateDir, "manifest.json");
         if (await pathExists(mfSrc)) {
-          await copyFile(mfSrc, join21(targetDir, ".flydocs", "manifest.json"));
+          await copyFile(mfSrc, join27(targetDir, ".flydocs", "manifest.json"));
           printStatus(".flydocs/manifest.json");
         }
         await generateIntegrity(targetDir, version);
@@ -4355,22 +5452,22 @@ var uninstall_exports = {};
 __export(uninstall_exports, {
   default: () => uninstall_default
 });
-import { defineCommand as defineCommand5 } from "citty";
-import { resolve as resolve5, join as join22 } from "path";
-import { readdir as readdir6, rm as rm6, rename as rename2 } from "fs/promises";
-import { confirm as confirm5, select as select4, isCancel as isCancel6, cancel as cancel5 } from "@clack/prompts";
-import pc10 from "picocolors";
+import { defineCommand as defineCommand7 } from "citty";
+import { resolve as resolve6, join as join28 } from "path";
+import { readdir as readdir9, rm as rm8, rename as rename2 } from "fs/promises";
+import { confirm as confirm5, select as select5, isCancel as isCancel7, cancel as cancel5 } from "@clack/prompts";
+import pc12 from "picocolors";
 async function removeOwnedSkills(targetDir) {
-  const skillsDir = join22(targetDir, ".claude", "skills");
+  const skillsDir = join28(targetDir, ".claude", "skills");
   const removed = [];
   if (!await pathExists(skillsDir)) {
     return removed;
   }
   try {
-    const entries = await readdir6(skillsDir);
+    const entries = await readdir9(skillsDir);
     for (const entry of entries) {
       if (entry.startsWith(OWNED_SKILL_PREFIX)) {
-        await rm6(join22(skillsDir, entry), { recursive: true, force: true });
+        await rm8(join28(skillsDir, entry), { recursive: true, force: true });
         removed.push(`.claude/skills/${entry}`);
       }
     }
@@ -4379,16 +5476,16 @@ async function removeOwnedSkills(targetDir) {
   return removed;
 }
 async function removeOwnedCursorRules(targetDir) {
-  const rulesDir = join22(targetDir, ".cursor", "rules");
+  const rulesDir = join28(targetDir, ".cursor", "rules");
   const removed = [];
   if (!await pathExists(rulesDir)) {
     return removed;
   }
   try {
-    const entries = await readdir6(rulesDir);
+    const entries = await readdir9(rulesDir);
     for (const entry of entries) {
       if (entry.startsWith(OWNED_RULE_PREFIX) && entry.endsWith(".mdc")) {
-        await rm6(join22(rulesDir, entry), { force: true });
+        await rm8(join28(rulesDir, entry), { force: true });
         removed.push(`.cursor/rules/${entry}`);
       }
     }
@@ -4398,7 +5495,7 @@ async function removeOwnedCursorRules(targetDir) {
 }
 async function isEmptyDir(dirPath) {
   try {
-    const entries = await readdir6(dirPath);
+    const entries = await readdir9(dirPath);
     return entries.length === 0;
   } catch {
     return false;
@@ -4407,9 +5504,9 @@ async function isEmptyDir(dirPath) {
 async function cleanupEmptyParents(targetDir, dirs) {
   const cleaned = [];
   for (const dir of dirs) {
-    const fullPath = join22(targetDir, dir);
+    const fullPath = join28(targetDir, dir);
     if (await pathExists(fullPath) && await isEmptyDir(fullPath)) {
-      await rm6(fullPath, { recursive: true, force: true });
+      await rm8(fullPath, { recursive: true, force: true });
       cleaned.push(dir);
     }
   }
@@ -4439,7 +5536,7 @@ var init_uninstall = __esm({
     ];
     OWNED_SKILL_PREFIX = "flydocs-";
     OWNED_RULE_PREFIX = "flydocs-";
-    uninstall_default = defineCommand5({
+    uninstall_default = defineCommand7({
       meta: {
         name: "uninstall",
         description: "Remove FlyDocs from a project directory"
@@ -4475,7 +5572,7 @@ var init_uninstall = __esm({
         printBanner(CLI_VERSION);
         let targetDir;
         if (args.path) {
-          targetDir = resolve5(args.path.replace(/^~/, process.env.HOME ?? "~"));
+          targetDir = resolve6(args.path.replace(/^~/, process.env.HOME ?? "~"));
         } else if (args.here) {
           targetDir = process.cwd();
         } else {
@@ -4485,9 +5582,9 @@ var init_uninstall = __esm({
           printError(`Directory does not exist: ${targetDir}`);
           process.exit(1);
         }
-        targetDir = resolve5(targetDir);
-        const hasFlydocs = await pathExists(join22(targetDir, ".flydocs"));
-        const hasAgentsMd = await pathExists(join22(targetDir, "AGENTS.md"));
+        targetDir = resolve6(targetDir);
+        const hasFlydocs = await pathExists(join28(targetDir, ".flydocs"));
+        const hasAgentsMd = await pathExists(join28(targetDir, "AGENTS.md"));
         if (!hasFlydocs && !hasAgentsMd) {
           printError(`Not a FlyDocs project: ${targetDir}`);
           printInfo("No .flydocs/ directory or AGENTS.md found.");
@@ -4499,12 +5596,12 @@ var init_uninstall = __esm({
         const removeAll = forceAll || args.all;
         const skipPrompts = forceAll || args.yes;
         let contentAction = "preserve";
-        const hasUserContent = await pathExists(join22(targetDir, "flydocs"));
+        const hasUserContent = await pathExists(join28(targetDir, "flydocs"));
         if (hasUserContent) {
           if (removeAll) {
             contentAction = "remove";
           } else if (!skipPrompts) {
-            const choice = await select4({
+            const choice = await select5({
               message: "What should happen to your flydocs/ content (project docs, knowledge base)?",
               options: [
                 {
@@ -4524,7 +5621,7 @@ var init_uninstall = __esm({
                 }
               ]
             });
-            if (isCancel6(choice)) {
+            if (isCancel7(choice)) {
               cancel5("Uninstall cancelled.");
               process.exit(0);
             }
@@ -4533,39 +5630,39 @@ var init_uninstall = __esm({
         }
         if (!skipPrompts) {
           console.log();
-          console.log(pc10.bold("The following will be removed:"));
+          console.log(pc12.bold("The following will be removed:"));
           console.log();
           console.log("  Framework files:");
           for (const [path] of ALWAYS_REMOVED) {
-            console.log(`    ${pc10.dim(path)}`);
+            console.log(`    ${pc12.dim(path)}`);
           }
-          console.log(`    ${pc10.dim(".claude/skills/flydocs-*")}`);
-          console.log(`    ${pc10.dim(".cursor/rules/flydocs-*.mdc")}`);
+          console.log(`    ${pc12.dim(".claude/skills/flydocs-*")}`);
+          console.log(`    ${pc12.dim(".cursor/rules/flydocs-*.mdc")}`);
           if (hasUserContent) {
             if (contentAction === "archive") {
               console.log();
               console.log(
-                `  User content: ${pc10.yellow("flydocs/ -> flydocs-archive/")}`
+                `  User content: ${pc12.yellow("flydocs/ -> flydocs-archive/")}`
               );
             } else if (contentAction === "remove") {
               console.log();
-              console.log(`  User content: ${pc10.red("flydocs/ (deleted)")}`);
+              console.log(`  User content: ${pc12.red("flydocs/ (deleted)")}`);
             } else {
               console.log();
-              console.log(`  User content: ${pc10.green("flydocs/ (preserved)")}`);
+              console.log(`  User content: ${pc12.green("flydocs/ (preserved)")}`);
             }
           }
           console.log();
-          console.log(pc10.bold("Preserved:"));
+          console.log(pc12.bold("Preserved:"));
           console.log(
-            `    ${pc10.dim(".claude/skills/ (non-flydocs community skills)")}`
+            `    ${pc12.dim(".claude/skills/ (non-flydocs community skills)")}`
           );
-          console.log(`    ${pc10.dim(".env, .env.local")}`);
+          console.log(`    ${pc12.dim(".env, .env.local")}`);
           console.log();
           const shouldContinue = await confirm5({
             message: "Proceed with uninstall?"
           });
-          if (isCancel6(shouldContinue) || !shouldContinue) {
+          if (isCancel7(shouldContinue) || !shouldContinue) {
             cancel5("Uninstall cancelled.");
             process.exit(0);
           }
@@ -4582,16 +5679,16 @@ var init_uninstall = __esm({
         const removedRules = await removeOwnedCursorRules(targetDir);
         result.removed.push(...removedRules);
         for (const [relativePath, type] of ALWAYS_REMOVED) {
-          const fullPath = join22(targetDir, relativePath);
+          const fullPath = join28(targetDir, relativePath);
           if (!await pathExists(fullPath)) {
             result.skipped.push(relativePath);
             continue;
           }
           try {
             if (type === "dir") {
-              await rm6(fullPath, { recursive: true, force: true });
+              await rm8(fullPath, { recursive: true, force: true });
             } else {
-              await rm6(fullPath, { force: true });
+              await rm8(fullPath, { force: true });
             }
             result.removed.push(relativePath);
           } catch {
@@ -4600,16 +5697,16 @@ var init_uninstall = __esm({
           }
         }
         if (hasUserContent) {
-          const flydocsPath = join22(targetDir, "flydocs");
+          const flydocsPath = join28(targetDir, "flydocs");
           if (contentAction === "archive") {
-            const archivePath = join22(targetDir, "flydocs-archive");
+            const archivePath = join28(targetDir, "flydocs-archive");
             if (await pathExists(archivePath)) {
-              await rm6(archivePath, { recursive: true, force: true });
+              await rm8(archivePath, { recursive: true, force: true });
             }
             await rename2(flydocsPath, archivePath);
             result.archived.push("flydocs/ -> flydocs-archive/");
           } else if (contentAction === "remove") {
-            await rm6(flydocsPath, { recursive: true, force: true });
+            await rm8(flydocsPath, { recursive: true, force: true });
             result.removed.push("flydocs/");
           }
         }
@@ -4628,17 +5725,17 @@ var init_uninstall = __esm({
           result.restored = originals.map((f) => f.relativePath);
         }
         console.log();
-        console.log(pc10.bold("Uninstall Summary"));
+        console.log(pc12.bold("Uninstall Summary"));
         console.log();
         if (result.removed.length > 0) {
-          console.log(`  ${pc10.green("Removed")} (${result.removed.length}):`);
+          console.log(`  ${pc12.green("Removed")} (${result.removed.length}):`);
           for (const item of result.removed) {
             printStatus(item);
           }
         }
         if (result.archived.length > 0) {
           console.log();
-          console.log(`  ${pc10.yellow("Archived")} (${result.archived.length}):`);
+          console.log(`  ${pc12.yellow("Archived")} (${result.archived.length}):`);
           for (const item of result.archived) {
             printInfo(item);
           }
@@ -4646,7 +5743,7 @@ var init_uninstall = __esm({
         if (result.restored.length > 0) {
           console.log();
           console.log(
-            `  ${pc10.green("Restored")} (${result.restored.length} pre-FlyDocs original(s)):`
+            `  ${pc12.green("Restored")} (${result.restored.length} pre-FlyDocs original(s)):`
           );
           for (const item of result.restored) {
             printInfo(item);
@@ -4655,16 +5752,16 @@ var init_uninstall = __esm({
         if (result.skipped.length > 0) {
           console.log();
           console.log(
-            `  ${pc10.dim("Skipped")} (${result.skipped.length} \u2014 not found):`
+            `  ${pc12.dim("Skipped")} (${result.skipped.length} \u2014 not found):`
           );
           for (const item of result.skipped) {
-            console.log(`  ${pc10.dim(item)}`);
+            console.log(`  ${pc12.dim(item)}`);
           }
         }
         console.log();
         printStatus("FlyDocs has been removed from this project.");
         console.log();
-        printInfo(`To reinstall: ${pc10.cyan("npx @flydocs/cli install --here")}`);
+        printInfo(`To reinstall: ${pc12.cyan("npx @flydocs/cli install --here")}`);
         console.log();
       }
     });
@@ -4676,28 +5773,28 @@ var setup_exports = {};
 __export(setup_exports, {
   default: () => setup_default
 });
-import { defineCommand as defineCommand6 } from "citty";
-import pc11 from "picocolors";
+import { defineCommand as defineCommand8 } from "citty";
+import pc13 from "picocolors";
 var setup_default;
 var init_setup = __esm({
   "src/commands/setup.ts"() {
     "use strict";
-    setup_default = defineCommand6({
+    setup_default = defineCommand8({
       meta: {
         name: "setup",
         description: "Configure FlyDocs settings for this project"
       },
       run() {
         console.log();
-        console.log(`  ${pc11.bold("FlyDocs Setup")}`);
+        console.log(`  ${pc13.bold("FlyDocs Setup")}`);
         console.log();
         console.log(`  Setup runs inside your IDE as an interactive AI command.`);
         console.log();
         console.log(
-          `  ${pc11.cyan("Claude Code:")}  Type ${pc11.bold("/flydocs-setup")} in chat`
+          `  ${pc13.cyan("Claude Code:")}  Type ${pc13.bold("/flydocs-setup")} in chat`
         );
         console.log(
-          `  ${pc11.cyan("Cursor:")}      Type ${pc11.bold("/flydocs-setup")} in chat`
+          `  ${pc13.cyan("Cursor:")}      Type ${pc13.bold("/flydocs-setup")} in chat`
         );
         console.log();
         console.log(`  This configures your project context, detects your stack,`);
@@ -4713,14 +5810,14 @@ var skills_exports = {};
 __export(skills_exports, {
   default: () => skills_default
 });
-import { defineCommand as defineCommand7 } from "citty";
-import pc12 from "picocolors";
+import { defineCommand as defineCommand9 } from "citty";
+import pc14 from "picocolors";
 var list, search, add, remove, skills_default;
 var init_skills2 = __esm({
   "src/commands/skills.ts"() {
     "use strict";
     init_skill_manager();
-    list = defineCommand7({
+    list = defineCommand9({
       meta: {
         name: "list",
         description: "List installed skills"
@@ -4736,26 +5833,26 @@ var init_skills2 = __esm({
         console.log(`${total} skill(s) installed:`);
         if (result.platform.length > 0) {
           console.log();
-          console.log(pc12.bold("Platform"));
+          console.log(pc14.bold("Platform"));
           for (const skill of result.platform) {
             console.log(
-              `  ${skill.name} ${pc12.dim(`(${skill.triggers} triggers)`)}`
+              `  ${skill.name} ${pc14.dim(`(${skill.triggers} triggers)`)}`
             );
           }
         }
         if (result.community.length > 0) {
           console.log();
-          console.log(pc12.bold("Community"));
+          console.log(pc14.bold("Community"));
           for (const skill of result.community) {
             console.log(
-              `  ${skill.name} ${pc12.dim(`(${skill.triggers} triggers)`)}`
+              `  ${skill.name} ${pc14.dim(`(${skill.triggers} triggers)`)}`
             );
           }
         }
         console.log();
       }
     });
-    search = defineCommand7({
+    search = defineCommand9({
       meta: {
         name: "search",
         description: "Search community skills"
@@ -4771,24 +5868,24 @@ var init_skills2 = __esm({
         const results = await searchCatalog(args.keyword);
         if (results.length === 0) {
           console.log(`No skills found for "${args.keyword}".`);
-          console.log(`  Browse the catalog at: ${pc12.cyan("https://skills.sh/")}`);
+          console.log(`  Browse the catalog at: ${pc14.cyan("https://skills.sh/")}`);
           return;
         }
         console.log();
         console.log(`${results.length} skill(s) matching "${args.keyword}":`);
         console.log();
         for (const skill of results) {
-          console.log(`  ${pc12.bold(skill.name)}`);
+          console.log(`  ${pc14.bold(skill.name)}`);
           console.log(`  ${skill.description}`);
-          console.log(`  ${pc12.dim(skill.repo)}`);
+          console.log(`  ${pc14.dim(skill.repo)}`);
           if (skill.tags.length > 0) {
-            console.log(`  ${pc12.dim(skill.tags.join(", "))}`);
+            console.log(`  ${pc14.dim(skill.tags.join(", "))}`);
           }
           console.log();
         }
       }
     });
-    add = defineCommand7({
+    add = defineCommand9({
       meta: {
         name: "add",
         description: "Install a community skill"
@@ -4804,7 +5901,7 @@ var init_skills2 = __esm({
         await addSkill(process.cwd(), args.source);
       }
     });
-    remove = defineCommand7({
+    remove = defineCommand9({
       meta: {
         name: "remove",
         description: "Remove an installed community skill"
@@ -4820,7 +5917,7 @@ var init_skills2 = __esm({
         await removeSkill(process.cwd(), args.name);
       }
     });
-    skills_default = defineCommand7({
+    skills_default = defineCommand9({
       meta: {
         name: "skills",
         description: "Manage FlyDocs skills (list, search, add, remove)"
@@ -4840,10 +5937,10 @@ var connect_exports = {};
 __export(connect_exports, {
   default: () => connect_default
 });
-import { defineCommand as defineCommand8 } from "citty";
-import { text as text4, confirm as confirm6, isCancel as isCancel7, cancel as cancel6 } from "@clack/prompts";
-import pc13 from "picocolors";
-import { join as join23 } from "path";
+import { defineCommand as defineCommand10 } from "citty";
+import { text as text4, confirm as confirm6, isCancel as isCancel8, cancel as cancel6 } from "@clack/prompts";
+import pc15 from "picocolors";
+import { join as join29 } from "path";
 var connect_default;
 var init_connect = __esm({
   "src/commands/connect.ts"() {
@@ -4853,7 +5950,7 @@ var init_connect = __esm({
     init_template();
     init_ui();
     init_api_key();
-    connect_default = defineCommand8({
+    connect_default = defineCommand10({
       meta: {
         name: "connect",
         description: "Connect FlyDocs to a cloud provider"
@@ -4878,11 +5975,11 @@ var init_connect = __esm({
       },
       async run({ args }) {
         const targetDir = args.path ?? process.cwd();
-        const configPath = join23(targetDir, ".flydocs", "config.json");
+        const configPath = join29(targetDir, ".flydocs", "config.json");
         if (!await pathExists(configPath)) {
           printError("Not a FlyDocs project (.flydocs/config.json not found).");
           console.log(
-            `  Run ${pc13.cyan("flydocs")} first to install FlyDocs in this project.`
+            `  Run ${pc15.cyan("flydocs")} first to install FlyDocs in this project.`
           );
           process.exit(1);
         }
@@ -4893,16 +5990,16 @@ var init_connect = __esm({
           const reconnect = await confirm6({
             message: "Want to update your API key?"
           });
-          if (isCancel7(reconnect) || !reconnect) {
+          if (isCancel8(reconnect) || !reconnect) {
             console.log(`  No changes made.`);
             return;
           }
         }
         console.log();
-        console.log(`  ${pc13.bold("Connect to FlyDocs Cloud")}`);
+        console.log(`  ${pc15.bold("Connect to FlyDocs Cloud")}`);
         console.log();
         console.log(
-          `  ${pc13.dim("Get your API key (fdk_...) from your FlyDocs dashboard")}`
+          `  ${pc15.dim("Get your API key (fdk_...) from your FlyDocs dashboard")}`
         );
         console.log();
         let apiKey = args.key ?? "";
@@ -4918,7 +6015,7 @@ var init_connect = __esm({
               return void 0;
             }
           });
-          if (isCancel7(keyInput)) {
+          if (isCancel8(keyInput)) {
             cancel6("Connection cancelled.");
             process.exit(0);
           }
@@ -4940,7 +6037,7 @@ var init_connect = __esm({
               console.log(`  Check your key and try again.`);
               process.exit(1);
             }
-            printStatus(`Connected to ${pc13.bold(result.org)}`);
+            printStatus(`Connected to ${pc15.bold(result.org)}`);
           } catch {
             printError(
               "Could not reach relay API. Check your network and try again."
@@ -4948,7 +6045,7 @@ var init_connect = __esm({
             process.exit(1);
           }
           const envFile = await storeEnvKey(targetDir, "FLYDOCS_API_KEY", apiKey);
-          printStatus(`API key stored in ${pc13.dim(envFile)}`);
+          printStatus(`API key stored in ${pc15.dim(envFile)}`);
         } else {
           try {
             const result = await validateLinearKey(apiKey);
@@ -4958,7 +6055,7 @@ var init_connect = __esm({
               process.exit(1);
             }
             printStatus(
-              `Authenticated as ${pc13.bold(result.name)} (${result.email})`
+              `Authenticated as ${pc15.bold(result.name)} (${result.email})`
             );
           } catch {
             printError("Invalid API key or network error.");
@@ -4966,7 +6063,7 @@ var init_connect = __esm({
             process.exit(1);
           }
           const envFile = await storeEnvKey(targetDir, "LINEAR_API_KEY", apiKey);
-          printStatus(`API key stored in ${pc13.dim(envFile)}`);
+          printStatus(`API key stored in ${pc15.dim(envFile)}`);
         }
         const wasLocal = config.tier === "local";
         config.tier = "cloud";
@@ -4982,14 +6079,14 @@ var init_connect = __esm({
         }
         console.log();
         console.log(
-          `  ${pc13.bold("Connected!")} Your project is now on the cloud tier.`
+          `  ${pc15.bold("Connected!")} Your project is now on the cloud tier.`
         );
         console.log();
         console.log(`  Next steps:`);
         console.log(
-          `    1. Run ${pc13.cyan("/flydocs-setup")} in your IDE to configure your project`
+          `    1. Run ${pc15.cyan("/flydocs-setup")} in your IDE to configure your project`
         );
-        console.log(`    2. Run ${pc13.cyan("/start-session")} to begin working`);
+        console.log(`    2. Run ${pc15.cyan("/start-session")} to begin working`);
         console.log();
       }
     });
@@ -5001,9 +6098,9 @@ var auth_exports = {};
 __export(auth_exports, {
   default: () => auth_default
 });
-import { defineCommand as defineCommand9 } from "citty";
-import { text as text5, confirm as confirm7, isCancel as isCancel8, cancel as cancel7 } from "@clack/prompts";
-import pc14 from "picocolors";
+import { defineCommand as defineCommand11 } from "citty";
+import { text as text5, confirm as confirm7, isCancel as isCancel9, cancel as cancel7 } from "@clack/prompts";
+import pc16 from "picocolors";
 var auth_default;
 var init_auth = __esm({
   "src/commands/auth.ts"() {
@@ -5011,7 +6108,7 @@ var init_auth = __esm({
     init_ui();
     init_api_key();
     init_global_config();
-    auth_default = defineCommand9({
+    auth_default = defineCommand11({
       meta: {
         name: "auth",
         description: "Store API key globally (~/.flydocs/credentials)"
@@ -5025,25 +6122,25 @@ var init_auth = __esm({
       },
       async run({ args }) {
         console.log();
-        console.log(`  ${pc14.bold("FlyDocs Authentication")}`);
+        console.log(`  ${pc16.bold("FlyDocs Authentication")}`);
         console.log();
         let apiKey = args.key ?? "";
         const existing = await readGlobalCredential();
         if (existing?.apiKey && !apiKey) {
           printInfo(
-            `Existing key found: ${pc14.dim(existing.apiKey.slice(0, 8) + "...")}`
+            `Existing key found: ${pc16.dim(existing.apiKey.slice(0, 8) + "...")}`
           );
           const replace = await confirm7({
             message: "Replace with a new key?"
           });
-          if (isCancel8(replace) || !replace) {
+          if (isCancel9(replace) || !replace) {
             console.log(`  No changes made.`);
             return;
           }
         }
         if (!apiKey) {
           console.log(
-            `  ${pc14.dim("Get your API key (fdk_...) from your FlyDocs dashboard")}`
+            `  ${pc16.dim("Get your API key (fdk_...) from your FlyDocs dashboard")}`
           );
           console.log();
           const keyInput = await text5({
@@ -5057,7 +6154,7 @@ var init_auth = __esm({
               return void 0;
             }
           });
-          if (isCancel8(keyInput)) {
+          if (isCancel9(keyInput)) {
             cancel7("Authentication cancelled.");
             process.exit(0);
           }
@@ -5079,7 +6176,7 @@ var init_auth = __esm({
             printError("Invalid API key. Check your key and try again.");
             process.exit(1);
           }
-          printStatus(`Authenticated with ${pc14.bold(result.org)}`);
+          printStatus(`Authenticated with ${pc16.bold(result.org)}`);
         } catch {
           printError(
             "Could not reach FlyDocs API. Check your network and try again."
@@ -5094,10 +6191,10 @@ var init_auth = __esm({
           createdAt: (/* @__PURE__ */ new Date()).toISOString(),
           lastValidated: (/* @__PURE__ */ new Date()).toISOString()
         });
-        printStatus(`Key stored at ${pc14.dim(credentialsPath())}`);
+        printStatus(`Key stored at ${pc16.dim(credentialsPath())}`);
         await checkCredentialPermissions();
         console.log();
-        console.log(`  ${pc14.bold("Authenticated!")} Key stored globally.`);
+        console.log(`  ${pc16.bold("Authenticated!")} Key stored globally.`);
         console.log(`  All FlyDocs projects on this machine will use this key.`);
         console.log();
       }
@@ -5105,155 +6202,20 @@ var init_auth = __esm({
   }
 });
 
-// src/commands/sync.ts
-var sync_exports = {};
-__export(sync_exports, {
-  default: () => sync_default
-});
-import { defineCommand as defineCommand10 } from "citty";
-import pc15 from "picocolors";
-import { join as join24 } from "path";
-import { mkdir as mkdir11, writeFile as writeFile14 } from "fs/promises";
-var sync_default;
-var init_sync = __esm({
-  "src/commands/sync.ts"() {
-    "use strict";
-    init_ui();
-    init_global_config();
-    init_config();
-    init_config_integrity();
-    init_fs_ops();
-    init_types();
-    init_relay_client();
-    sync_default = defineCommand10({
-      meta: {
-        name: "sync",
-        description: "Pull latest config and templates from server"
-      },
-      args: {
-        path: {
-          type: "string",
-          description: "Path to project directory"
-        }
-      },
-      async run({ args }) {
-        const targetDir = args.path ?? process.cwd();
-        const changes = [];
-        console.log();
-        printInfo("Syncing with server...");
-        const resolved = await resolveApiKey(void 0, targetDir);
-        if (!resolved) {
-          printError(
-            "No API key found. Run `flydocs auth` or `flydocs init` first."
-          );
-          process.exit(1);
-        }
-        const apiKey = resolved.key;
-        const cred = await readGlobalCredential();
-        const workspaceId = cred?.workspaceId;
-        if (!workspaceId) {
-          printError(
-            "No workspace ID found. Run `flydocs init` to set up your workspace."
-          );
-          process.exit(1);
-        }
-        let currentTemplateVersion = 0;
-        try {
-          const currentConfig = await readAnyConfig(targetDir);
-          if (isConfigV2(currentConfig)) {
-            currentTemplateVersion = currentConfig.configVersion ?? 0;
-          }
-        } catch {
-        }
-        let serverResponse;
-        try {
-          serverResponse = await fetchConfigV2(apiKey, { workspaceId });
-        } catch (err) {
-          if (err instanceof RelayError) {
-            printWarning(
-              `Server unavailable (${err.status}), using cached config.`
-            );
-          } else {
-            printWarning("Server unreachable, using cached config.");
-          }
-          console.log(`  ${pc15.dim("Config may be stale. Retry when connected.")}`);
-          return;
-        }
-        if (!serverResponse.valid) {
-          printWarning("Server returned invalid config. Keeping current config.");
-          return;
-        }
-        await mkdir11(join24(targetDir, ".flydocs"), { recursive: true });
-        const configWithHash = applyConfigHash(serverResponse.config);
-        await writeConfig(targetDir, configWithHash);
-        changes.push("Updated .flydocs/config.json");
-        const serverTemplateVersion = serverResponse.templates.version;
-        if (serverTemplateVersion > currentTemplateVersion) {
-          try {
-            const templatesResponse = await fetchTemplates(
-              apiKey,
-              currentTemplateVersion,
-              workspaceId
-            );
-            if (templatesResponse.templates.length > 0) {
-              const templatesDir = join24(
-                targetDir,
-                ".claude",
-                "skills",
-                "flydocs-workflow",
-                "templates"
-              );
-              await mkdir11(templatesDir, { recursive: true });
-              for (const template of templatesResponse.templates) {
-                const filename = `${template.type}.md`;
-                const subdir = template.category === "issue" ? "issues" : template.category === "pr" ? "pr" : template.category === "comment" ? "." : ".";
-                const templateDir = join24(templatesDir, subdir);
-                await mkdir11(templateDir, { recursive: true });
-                await writeFile14(
-                  join24(templateDir, filename),
-                  template.content,
-                  "utf-8"
-                );
-              }
-              changes.push(
-                `Updated ${templatesResponse.templates.length} templates (v${currentTemplateVersion} \u2192 v${serverTemplateVersion})`
-              );
-            }
-          } catch (err) {
-            if (err instanceof RelayError) {
-              printWarning("Could not fetch templates. Will retry on next sync.");
-            } else {
-              printWarning("Template sync failed. Will retry on next sync.");
-            }
-          }
-        }
-        if (changes.length === 0) {
-          printStatus("Already up to date.");
-        } else {
-          for (const change of changes) {
-            printStatus(change);
-          }
-        }
-        console.log();
-      }
-    });
-  }
-});
-
 // src/commands/upgrade.ts
 var upgrade_exports = {};
 __export(upgrade_exports, {
   default: () => upgrade_default
 });
-import { defineCommand as defineCommand11 } from "citty";
-import pc16 from "picocolors";
+import { defineCommand as defineCommand12 } from "citty";
+import pc17 from "picocolors";
 var upgrade_default;
 var init_upgrade = __esm({
   "src/commands/upgrade.ts"() {
     "use strict";
     init_config();
     init_fs_ops();
-    upgrade_default = defineCommand11({
+    upgrade_default = defineCommand12({
       meta: {
         name: "upgrade",
         description: "Learn about FlyDocs Cloud tier and upgrade from local"
@@ -5282,34 +6244,34 @@ var init_upgrade = __esm({
         console.log();
         if (currentTier === "cloud") {
           console.log(
-            `  ${pc16.green("\u2713")} You're already on the ${pc16.bold("cloud")} tier.`
+            `  ${pc17.green("\u2713")} You're already on the ${pc17.bold("cloud")} tier.`
           );
           console.log();
           console.log(`  Your issues sync with your provider via the relay API.`);
           console.log(
-            `  Run ${pc16.cyan("flydocs connect")} to update your connection settings.`
+            `  Run ${pc17.cyan("flydocs connect")} to update your connection settings.`
           );
           console.log();
           return;
         }
-        console.log(`  ${pc16.bold("FlyDocs Cloud Tier")}`);
+        console.log(`  ${pc17.bold("FlyDocs Cloud Tier")}`);
         console.log();
-        console.log(`  You're currently on the ${pc16.yellow("local")} tier.`);
+        console.log(`  You're currently on the ${pc17.yellow("local")} tier.`);
         console.log(`  Upgrade to cloud for:`);
         console.log();
-        console.log(`    ${pc16.cyan("\u2192")} Issue sync with Linear, Jira, and more`);
-        console.log(`    ${pc16.cyan("\u2192")} Project milestones and cycle management`);
-        console.log(`    ${pc16.cyan("\u2192")} Team assignment and priority tracking`);
-        console.log(`    ${pc16.cyan("\u2192")} Project health updates and dashboards`);
-        console.log(`    ${pc16.cyan("\u2192")} Cross-project issue linking`);
+        console.log(`    ${pc17.cyan("\u2192")} Issue sync with Linear, Jira, and more`);
+        console.log(`    ${pc17.cyan("\u2192")} Project milestones and cycle management`);
+        console.log(`    ${pc17.cyan("\u2192")} Team assignment and priority tracking`);
+        console.log(`    ${pc17.cyan("\u2192")} Project health updates and dashboards`);
+        console.log(`    ${pc17.cyan("\u2192")} Cross-project issue linking`);
         console.log();
-        console.log(`  ${pc16.bold("How to upgrade:")}`);
+        console.log(`  ${pc17.bold("How to upgrade:")}`);
         console.log();
-        console.log(`    Option 1: Run ${pc16.cyan("/flydocs-upgrade")} in your IDE`);
+        console.log(`    Option 1: Run ${pc17.cyan("/flydocs-upgrade")} in your IDE`);
         console.log(`              Guided migration with issue transfer`);
         console.log();
         console.log(
-          `    Option 2: Run ${pc16.cyan("flydocs connect")} from terminal`
+          `    Option 2: Run ${pc17.cyan("flydocs connect")} from terminal`
         );
         console.log(`              Quick tier swap (no issue migration)`);
         console.log();
@@ -5323,23 +6285,23 @@ var self_update_exports = {};
 __export(self_update_exports, {
   default: () => self_update_default
 });
-import { defineCommand as defineCommand12 } from "citty";
+import { defineCommand as defineCommand13 } from "citty";
 import { execSync } from "child_process";
-import pc17 from "picocolors";
+import pc18 from "picocolors";
 var self_update_default;
 var init_self_update = __esm({
   "src/commands/self-update.ts"() {
     "use strict";
     init_constants();
     init_ui();
-    self_update_default = defineCommand12({
+    self_update_default = defineCommand13({
       meta: {
         name: "self-update",
         description: "Update FlyDocs CLI to the latest version"
       },
       async run() {
         console.log();
-        console.log(`  Updating ${pc17.cyan(PACKAGE_NAME)}...`);
+        console.log(`  Updating ${pc18.cyan(PACKAGE_NAME)}...`);
         console.log();
         try {
           execSync(`npm install -g ${PACKAGE_NAME}@beta`, {
@@ -5364,15 +6326,15 @@ var telemetry_exports = {};
 __export(telemetry_exports, {
   default: () => telemetry_default
 });
-import { defineCommand as defineCommand13 } from "citty";
-import pc18 from "picocolors";
+import { defineCommand as defineCommand14 } from "citty";
+import pc19 from "picocolors";
 var enable, disable, status, telemetry_default;
 var init_telemetry2 = __esm({
   "src/commands/telemetry.ts"() {
     "use strict";
     init_telemetry();
     init_ui();
-    enable = defineCommand13({
+    enable = defineCommand14({
       meta: {
         name: "enable",
         description: "Enable anonymous usage analytics"
@@ -5387,7 +6349,7 @@ var init_telemetry2 = __esm({
         }
       }
     });
-    disable = defineCommand13({
+    disable = defineCommand14({
       meta: {
         name: "disable",
         description: "Disable anonymous usage analytics"
@@ -5405,7 +6367,7 @@ var init_telemetry2 = __esm({
         }
       }
     });
-    status = defineCommand13({
+    status = defineCommand14({
       meta: {
         name: "status",
         description: "Show current telemetry status"
@@ -5413,37 +6375,37 @@ var init_telemetry2 = __esm({
       async run() {
         const info = await getStatus();
         console.log();
-        console.log(pc18.bold("Telemetry Status"));
+        console.log(pc19.bold("Telemetry Status"));
         console.log();
         const effectivelyEnabled = info.enabled && !info.envOverride;
         console.log(
-          `  Enabled:        ${effectivelyEnabled ? pc18.green("yes") : pc18.yellow("no")}`
+          `  Enabled:        ${effectivelyEnabled ? pc19.green("yes") : pc19.yellow("no")}`
         );
         if (info.envOverride) {
           console.log(
-            `  Env override:   ${pc18.yellow("FLYDOCS_TELEMETRY=0 (disabled via env)")}`
+            `  Env override:   ${pc19.yellow("FLYDOCS_TELEMETRY=0 (disabled via env)")}`
           );
         }
         if (info.anonymousId) {
-          console.log(`  Anonymous ID:   ${pc18.dim(info.anonymousId)}`);
+          console.log(`  Anonymous ID:   ${pc19.dim(info.anonymousId)}`);
         } else {
           console.log(
-            `  Anonymous ID:   ${pc18.dim("(not yet created \u2014 generated on first run)")}`
+            `  Anonymous ID:   ${pc19.dim("(not yet created \u2014 generated on first run)")}`
           );
         }
         console.log();
         console.log(
-          pc18.dim(
+          pc19.dim(
             "  FlyDocs collects anonymous usage analytics to improve the CLI."
           )
         );
         console.log(
-          pc18.dim("  No personal data, file contents, or code is ever collected.")
+          pc19.dim("  No personal data, file contents, or code is ever collected.")
         );
         console.log();
       }
     });
-    telemetry_default = defineCommand13({
+    telemetry_default = defineCommand14({
       meta: {
         name: "telemetry",
         description: "Manage anonymous usage analytics (enable, disable, status)"
@@ -5459,7 +6421,7 @@ var init_telemetry2 = __esm({
 
 // src/cli.ts
 init_constants();
-import { defineCommand as defineCommand14, runMain } from "citty";
+import { defineCommand as defineCommand15, runMain } from "citty";
 var SUB_COMMANDS = /* @__PURE__ */ new Set([
   "install",
   "init",
@@ -5470,6 +6432,7 @@ var SUB_COMMANDS = /* @__PURE__ */ new Set([
   "connect",
   "auth",
   "sync",
+  "scan",
   "cleanup",
   "upgrade",
   "self-update",
@@ -5483,7 +6446,7 @@ var firstPositional = userArgs.find((a) => !a.startsWith("-"));
 if (!hasMetaFlag && (!firstPositional || !SUB_COMMANDS.has(firstPositional))) {
   process.argv.splice(2, 0, "install");
 }
-var main = defineCommand14({
+var main = defineCommand15({
   meta: {
     name: CLI_NAME,
     version: CLI_VERSION,
@@ -5499,6 +6462,7 @@ var main = defineCommand14({
     connect: () => Promise.resolve().then(() => (init_connect(), connect_exports)).then((m) => m.default),
     auth: () => Promise.resolve().then(() => (init_auth(), auth_exports)).then((m) => m.default),
     sync: () => Promise.resolve().then(() => (init_sync(), sync_exports)).then((m) => m.default),
+    scan: () => Promise.resolve().then(() => (init_scan(), scan_exports)).then((m) => m.default),
     cleanup: () => Promise.resolve().then(() => (init_cleanup(), cleanup_exports)).then((m) => m.default),
     upgrade: () => Promise.resolve().then(() => (init_upgrade(), upgrade_exports)).then((m) => m.default),
     "self-update": () => Promise.resolve().then(() => (init_self_update(), self_update_exports)).then((m) => m.default),