@flydocs/cli 0.6.0-alpha.32 → 0.6.0-alpha.34

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.32";
+    CLI_VERSION = "0.6.0-alpha.34";
     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: mkdir15 } = await import("fs/promises");
+  const { mkdir: mkdir16 } = await import("fs/promises");
   const rulesDir = join4(targetDir, ".cursor", "rules");
-  await mkdir15(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 });
     }
   }
 }
@@ -1328,6 +1328,11 @@ async function scanDeprecated(targetDir) {
       found.push(item);
     }
   }
+  for (const file of DEPRECATED_CONTEXT_FILES) {
+    if (await pathExists(join10(targetDir, file))) {
+      found.push(file);
+    }
+  }
   for (const skill of DEPRECATED_SKILLS) {
     const p = join10(targetDir, ".claude", "skills", skill);
     if (await pathExists(p)) {
@@ -1436,7 +1441,7 @@ async function promptCleanup(targetDir, paths) {
     printStatus(`Deleted: ${p}`);
   }
 }
-var DEPRECATED_DIRS, DEPRECATED_FILES, DEPRECATED_SKILLS, DEPRECATED_RULES_DIR, DEPRECATED_FLYDOCS_DIRS, DEPRECATED_HOOKS, DEPRECATED_CURSOR_RULES, DEPRECATED_CURSOR_RULE_DIRS, DEPRECATED_COMMANDS;
+var DEPRECATED_DIRS, DEPRECATED_FILES, DEPRECATED_CONTEXT_FILES, DEPRECATED_SKILLS, DEPRECATED_RULES_DIR, DEPRECATED_FLYDOCS_DIRS, DEPRECATED_HOOKS, DEPRECATED_CURSOR_RULES, DEPRECATED_CURSOR_RULE_DIRS, DEPRECATED_COMMANDS;
 var init_deprecated = __esm({
   "src/lib/deprecated.ts"() {
     "use strict";
@@ -1444,6 +1449,11 @@ var init_deprecated = __esm({
     init_ui();
     DEPRECATED_DIRS = [".docflow", "docflow"];
     DEPRECATED_FILES = ["AGENTS.md.bak", ".cursor/mcp.json"];
+    DEPRECATED_CONTEXT_FILES = [
+      "flydocs/context/overview.md",
+      "flydocs/context/stack.md",
+      "flydocs/context/standards.md"
+    ];
     DEPRECATED_SKILLS = [
       "linear-workflow",
       "session-workflow",
@@ -3027,11 +3037,11 @@ async function fetchTemplates(apiKey, sinceVersion, workspaceId) {
   }
   return await response.json();
 }
-async function fetchArtifacts(apiKey, sinceVersion) {
+async function fetchArtifacts(apiKey, sinceVersion, workspaceId) {
   const baseUrl = resolveRelayUrl();
   const response = await fetch(`${baseUrl}/artifacts?since=${sinceVersion}`, {
     method: "GET",
-    headers: headers(apiKey),
+    headers: headers(apiKey, workspaceId),
     signal: AbortSignal.timeout(3e4)
   });
   if (!response.ok) {
@@ -3044,23 +3054,6 @@ async function fetchArtifacts(apiKey, sinceVersion) {
   }
   return await response.json();
 }
-async function fetchAgentConfigs(apiKey, workspaceId) {
-  const baseUrl = resolveRelayUrl();
-  const response = await fetch(`${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 = {
@@ -3102,78 +3095,156 @@ 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 join18, dirname as dirname3 } from "path";
-async function syncArtifacts(targetDir, apiKey, workspaceId, currentVersion) {
-  const response = await fetchArtifacts(apiKey, currentVersion);
+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, workspaceId);
   if (response.artifacts.length === 0) {
-    return { written: 0, version: currentVersion };
+    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})`
   );
-  return { written, version: response.version };
-}
-async function syncAgentConfigs(targetDir, apiKey, workspaceId) {
-  const response = await fetchAgentConfigs(apiKey, workspaceId);
-  let written = 0;
-  for (const file of response.files) {
-    const filePath = join18(targetDir, file.path);
-    await mkdir9(dirname3(filePath), { recursive: true });
-    await writeFile11(filePath, file.content, "utf-8");
-    written++;
+  if (skipped > 0) {
+    printInfo(`Skipped ${skipped} artifact(s) via artifactOverrides.skipPaths`);
   }
-  if (written > 0) {
-    printStatus(`Wrote ${written} agent config(s) (CLAUDE.md, AGENTS.md)`);
-  }
-  return written;
+  return { written, skipped, version: response.version };
 }
 async function writeArtifact(targetDir, artifact) {
-  const filePath = join18(targetDir, artifact.path);
+  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) {
+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
+      currentArtifactVersion,
+      skipPaths
     );
     if (result.written > 0) {
       changes.push(`Synced ${result.written} artifact(s)`);
       artifactVersion = result.version;
     }
-  } catch (err) {
-    if (err instanceof RelayError) {
-      printWarning(
-        `Could not fetch artifacts (${err.status}). Will retry on next sync.`
+    if (result.skipped > 0) {
+      changes.push(
+        `Skipped ${result.skipped} artifact(s) (skipPaths override)`
       );
-    } else {
-      printWarning("Artifact sync failed. Will retry on next sync.");
-    }
-  }
-  try {
-    const configCount = await syncAgentConfigs(targetDir, apiKey, workspaceId);
-    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.`
+        `Could not fetch artifacts (${err.status}). Will retry on next sync.`
       );
     } else {
-      printWarning("Agent config sync failed. Will retry on next sync.");
+      printWarning("Artifact sync failed. Will retry on next sync.");
     }
   }
   return { artifactVersion, changes };
@@ -3183,6 +3254,7 @@ var init_artifacts = __esm({
     "use strict";
     init_ui();
     init_relay_client();
+    init_managed_paths();
   }
 });
 
@@ -3195,11 +3267,11 @@ __export(cleanup_exports, {
 });
 import { defineCommand as defineCommand2 } from "citty";
 import pc7 from "picocolors";
-import { join as join19 } from "path";
-import { readFile as readFile13, writeFile as writeFile12, 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 = join19(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)",
@@ -3207,7 +3279,7 @@ async function scanArtifacts(targetDir) {
       type: "file"
     });
   }
-  const validationCachePath = join19(
+  const validationCachePath = join20(
     targetDir,
     ".flydocs",
     "validation-cache.json"
@@ -3221,7 +3293,7 @@ async function scanArtifacts(targetDir) {
   }
   const hasGlobalCreds = await pathExists(credentialsPath());
   for (const envFile of [".env", ".env.local"]) {
-    const envPath = join19(targetDir, envFile);
+    const envPath = join20(targetDir, envFile);
     if (!await pathExists(envPath)) continue;
     const content = await readFile13(envPath, "utf-8");
     const lines = content.split("\n");
@@ -3246,7 +3318,7 @@ async function scanArtifacts(targetDir) {
   try {
     const config = await readAnyConfig(targetDir);
     const rawContent = await readFile13(
-      join19(targetDir, ".flydocs", "config.json"),
+      join20(targetDir, ".flydocs", "config.json"),
       "utf-8"
     );
     const raw = JSON.parse(rawContent);
@@ -3255,7 +3327,7 @@ async function scanArtifacts(targetDir) {
       if (field in raw) {
         actions.push({
           description: `Remove ghost field "${field}" from config.json`,
-          path: join19(targetDir, ".flydocs", "config.json"),
+          path: join20(targetDir, ".flydocs", "config.json"),
           type: "field"
         });
       }
@@ -3274,7 +3346,7 @@ async function scanArtifacts(targetDir) {
         if (field in raw) {
           actions.push({
             description: `Remove v1 field "${field}" from config.json (server-owned in v2)`,
-            path: join19(targetDir, ".flydocs", "config.json"),
+            path: join20(targetDir, ".flydocs", "config.json"),
             type: "field"
           });
         }
@@ -3289,7 +3361,7 @@ 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) {
@@ -3307,13 +3379,13 @@ 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 writeFile12(envPath, filtered.join("\n"), "utf-8");
     }
   }
   if (fieldRemovals.length > 0) {
-    const configPath = join19(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) {
@@ -3360,7 +3432,7 @@ var init_cleanup = __esm({
         console.log(`  ${pc7.bold("FlyDocs Cleanup")}`);
         console.log();
         const hasConfig = await pathExists(
-          join19(targetDir, ".flydocs", "config.json")
+          join20(targetDir, ".flydocs", "config.json")
         );
         if (!hasConfig) {
           printError("No .flydocs/config.json found. Run flydocs init first.");
@@ -3404,16 +3476,16 @@ var init_cleanup = __esm({
 });
 
 // src/lib/ide-archive.ts
-import { readFile as readFile14, writeFile as writeFile13, mkdir as mkdir10, readdir as readdir4 } from "fs/promises";
-import { join as join20, basename } from "path";
+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 = join20(targetDir, cfg.source);
+    const absSource = join21(targetDir, cfg.source);
     if (!await pathExists(absSource)) continue;
     const content = await readFile14(absSource, "utf-8");
-    const absDest = join20(targetDir, cfg.archive);
-    await mkdir10(join20(absDest, ".."), { recursive: true });
+    const absDest = join21(targetDir, cfg.archive);
+    await mkdir10(join21(absDest, ".."), { recursive: true });
     await writeFile13(absDest, content, "utf-8");
     archived.push({
       sourcePath: cfg.source,
@@ -3422,17 +3494,17 @@ async function archiveIdeConfigs(targetDir) {
     });
     printStatus(`Archived ${cfg.source}`);
   }
-  const cursorRulesDir = join20(targetDir, ".cursor", "rules");
+  const cursorRulesDir = join21(targetDir, ".cursor", "rules");
   if (await pathExists(cursorRulesDir)) {
     let entries;
     try {
-      entries = await readdir4(cursorRulesDir);
+      entries = await readdir5(cursorRulesDir);
     } catch {
       entries = [];
     }
     const mdFiles = entries.filter((f) => f.endsWith(".md"));
     if (mdFiles.length > 0) {
-      const archiveSubdir = join20(
+      const archiveSubdir = join21(
         targetDir,
         "flydocs",
         "knowledge",
@@ -3441,10 +3513,10 @@ async function archiveIdeConfigs(targetDir) {
       );
       await mkdir10(archiveSubdir, { recursive: true });
       for (const file of mdFiles) {
-        const absSource = join20(cursorRulesDir, file);
+        const absSource = join21(cursorRulesDir, file);
         const content = await readFile14(absSource, "utf-8");
         const archivePath = `flydocs/knowledge/archived/cursor-rules/${basename(file)}`;
-        const absDest = join20(targetDir, archivePath);
+        const absDest = join21(targetDir, archivePath);
         await writeFile13(absDest, content, "utf-8");
         archived.push({
           sourcePath: `.cursor/rules/${file}`,
@@ -3477,10 +3549,10 @@ var init_ide_archive = __esm({
 });
 
 // src/lib/workspace.ts
-import { readFile as readFile15, writeFile as writeFile14, readdir as readdir5, stat as stat2 } from "fs/promises";
-import { join as join21, dirname as dirname4, 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 = join21(dir, WORKSPACE_FILENAME);
+  const filePath = join22(dir, WORKSPACE_FILENAME);
   if (!await pathExists(filePath)) return null;
   const content = await readFile15(filePath, "utf-8");
   const parsed = JSON.parse(content);
@@ -3488,21 +3560,21 @@ async function readWorkspaceFile(dir) {
   return parsed;
 }
 async function writeWorkspaceFile(dir, workspace) {
-  const filePath = join21(dir, WORKSPACE_FILENAME);
+  const filePath = join22(dir, WORKSPACE_FILENAME);
   const content = JSON.stringify(workspace, null, 2) + "\n";
   await writeFile14(filePath, content, "utf-8");
 }
 async function detectSiblingRepos(parentDir) {
   const repos = {};
-  const entries = await readdir5(parentDir);
+  const entries = await readdir6(parentDir);
   for (const entry of entries) {
     if (entry.startsWith(".")) continue;
-    const entryPath = join21(parentDir, entry);
+    const entryPath = join22(parentDir, entry);
     const entryStat = await stat2(entryPath).catch(() => null);
     if (!entryStat?.isDirectory()) continue;
-    const hasGit = await pathExists(join21(entryPath, ".git"));
+    const hasGit = await pathExists(join22(entryPath, ".git"));
     const hasFlydocs = await pathExists(
-      join21(entryPath, ".flydocs", "config.json")
+      join22(entryPath, ".flydocs", "config.json")
     );
     if (hasGit || hasFlydocs) {
       repos[entry] = { path: `./${entry}` };
@@ -3517,7 +3589,7 @@ async function readSiblingDescriptors(workspaceDir, repos) {
   const descriptors = [];
   for (const [name, entry] of Object.entries(repos)) {
     const repoDir = resolve3(workspaceDir, entry.path);
-    const serviceJsonPath = join21(repoDir, "flydocs", "context", "service.json");
+    const serviceJsonPath = join22(repoDir, "flydocs", "context", "service.json");
     if (!await pathExists(serviceJsonPath)) continue;
     try {
       const content = await readFile15(serviceJsonPath, "utf-8");
@@ -3632,7 +3704,7 @@ __export(scan_exports, {
 import { defineCommand as defineCommand3 } from "citty";
 import { spinner } from "@clack/prompts";
 import pc8 from "picocolors";
-import { join as join22 } from "path";
+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;
@@ -3661,15 +3733,15 @@ async function resolveRepoName(targetDir, repoArg) {
 }
 async function writeScanResults(targetDir, response) {
   const written = [];
-  const contextDir = join22(targetDir, "flydocs", "context");
+  const contextDir = join23(targetDir, "flydocs", "context");
   await mkdir11(contextDir, { recursive: true });
   if (response.projectMd) {
-    const projectMdPath = join22(contextDir, "project.md");
+    const projectMdPath = join23(contextDir, "project.md");
     await writeFile15(projectMdPath, response.projectMd, "utf-8");
     written.push("flydocs/context/project.md");
   }
   if (response.serviceJson) {
-    const serviceJsonPath = join22(contextDir, "service.json");
+    const serviceJsonPath = join23(contextDir, "service.json");
     await writeFile15(
       serviceJsonPath,
       JSON.stringify(response.serviceJson, null, 2) + "\n",
@@ -3825,7 +3897,7 @@ __export(init_exports, {
 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 join23 } from "path";
+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";
@@ -3906,7 +3978,7 @@ async function resolveAndValidateKey(keyArg, targetDir) {
 }
 async function pullServerConfig(apiKey, targetDir, workspaceId, forceIncludeContext = false) {
   printInfo("Pulling config from server...");
-  const isFirstInit = forceIncludeContext || !await pathExists(join23(targetDir, ".flydocs", "config.json"));
+  const isFirstInit = forceIncludeContext || !await pathExists(join24(targetDir, ".flydocs", "config.json"));
   try {
     const response = await fetchConfigV2(apiKey, {
       includeContext: isFirstInit,
@@ -3935,7 +4007,7 @@ async function initSingleRepo(targetDir, apiKey, serverResponse, options = {}) {
   const actions = [];
   const skipped = [];
   const { childRepoMode = false } = options;
-  await mkdir12(join23(targetDir, ".flydocs"), { recursive: true });
+  await mkdir12(join24(targetDir, ".flydocs"), { recursive: true });
   const configWithHash = applyConfigHash(serverResponse.config);
   await writeConfig(targetDir, configWithHash);
   actions.push("Wrote .flydocs/config.json (from server)");
@@ -3948,16 +4020,16 @@ async function initSingleRepo(targetDir, apiKey, serverResponse, options = {}) {
     actions.push("Wrote ~/.flydocs/me.json");
   }
   if (serverResponse.context) {
-    const contextDir = join23(targetDir, "flydocs", "context");
+    const contextDir = join24(targetDir, "flydocs", "context");
     await mkdir12(contextDir, { recursive: true });
-    const projectMdPath = join23(contextDir, "project.md");
+    const projectMdPath = join24(contextDir, "project.md");
     if (!await pathExists(projectMdPath)) {
       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 = join23(contextDir, "service.json");
+    const serviceJsonPath = join24(contextDir, "service.json");
     if (serverResponse.context.serviceJson && !await pathExists(serviceJsonPath)) {
       await writeFile16(
         serviceJsonPath,
@@ -4004,26 +4076,26 @@ async function initSingleRepo(targetDir, apiKey, serverResponse, options = {}) {
   };
 }
 async function cleanServerManagedFiles(targetDir) {
-  const { rm: rm7 } = await import("fs/promises");
+  const { rm: rm9 } = await import("fs/promises");
   let cleaned = 0;
   for (const dir of SERVER_MANAGED_DIRS) {
-    const fullPath = join23(targetDir, dir);
+    const fullPath = join24(targetDir, dir);
     if (await pathExists(fullPath)) {
-      await rm7(fullPath, { recursive: true, force: true });
+      await rm9(fullPath, { recursive: true, force: true });
       cleaned++;
     }
   }
   for (const file of SERVER_MANAGED_FILES) {
-    const fullPath = join23(targetDir, file);
+    const fullPath = join24(targetDir, file);
     if (await pathExists(fullPath)) {
-      await rm7(fullPath, { force: true });
+      await rm9(fullPath, { force: true });
       cleaned++;
     }
   }
   return cleaned;
 }
 async function checkGitFreshness(repoDir) {
-  const hasGit = await pathExists(join23(repoDir, ".git"));
+  const hasGit = await pathExists(join24(repoDir, ".git"));
   if (!hasGit) return;
   try {
     await execFileAsync("git", ["-C", repoDir, "fetch", "--quiet"], {
@@ -4052,7 +4124,7 @@ async function checkGitFreshness(repoDir) {
   }
 }
 async function isEmptyOrNonRepo(dir) {
-  const hasGit = await pathExists(join23(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;
@@ -4122,9 +4194,9 @@ 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 = join23(targetDir, shortName);
+      const cloneDir = join24(targetDir, shortName);
       console.log();
-      if (await pathExists(join23(cloneDir, ".git"))) {
+      if (await pathExists(join24(cloneDir, ".git"))) {
         printInfo(`${pc9.bold(shortName)} already cloned, initializing...`);
         await checkGitFreshness(cloneDir);
       } else {
@@ -4167,8 +4239,8 @@ async function runCloneAndInit(targetDir, keyArg, repos, apiKey, workspaceId) {
       );
       await writeWorkspaceFile(targetDir, workspaceFile);
       allActions.push(`.flydocs-workspace.json (${repos.length} repos)`);
-      const contextDir = join23(targetDir, "flydocs", "context");
-      const workspaceMdPath = join23(contextDir, "workspace.md");
+      const contextDir = join24(targetDir, "flydocs", "context");
+      const workspaceMdPath = join24(contextDir, "workspace.md");
       if (!await pathExists(workspaceMdPath)) {
         await mkdir12(contextDir, { recursive: true });
         const content = firstResponse.context?.workspaceMd ?? await generateWorkspaceMd(targetDir, workspaceFile);
@@ -4187,7 +4259,7 @@ async function runCloneAndInit(targetDir, keyArg, repos, apiKey, workspaceId) {
   }
 }
 async function isParentDirectory(dir) {
-  const hasGit = await pathExists(join23(dir, ".git"));
+  const hasGit = await pathExists(join24(dir, ".git"));
   if (hasGit) return false;
   const repos = await detectSiblingRepos(dir);
   return Object.keys(repos).length >= 2;
@@ -4207,7 +4279,7 @@ async function runMultiRepoInit(parentDir, keyArg) {
     cancel3("Init cancelled.");
     process.exit(0);
   }
-  const firstRepoDir = join23(parentDir, repoNames[0]);
+  const firstRepoDir = join24(parentDir, repoNames[0]);
   const { apiKey, workspaceId } = await resolveAndValidateKey(
     keyArg,
     firstRepoDir
@@ -4240,7 +4312,7 @@ async function runMultiRepoInit(parentDir, keyArg) {
   await ensureGitignore(parentDir);
   allActions.push("Updated workspace root .gitignore");
   for (const repoName of repoNames) {
-    const repoDir = join23(parentDir, repoName);
+    const repoDir = join24(parentDir, repoName);
     console.log();
     printInfo(`Initializing ${pc9.bold(repoName)}...`);
     await checkGitFreshness(repoDir);
@@ -4272,8 +4344,8 @@ async function runMultiRepoInit(parentDir, keyArg) {
       await writeWorkspaceFile(parentDir, workspaceFile);
       allActions.push(`.flydocs-workspace.json (${repoNames.length} repos)`);
     }
-    const contextDir = join23(parentDir, "flydocs", "context");
-    const workspaceMdPath = join23(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 {
@@ -4426,7 +4498,7 @@ 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 = join23(targetDir, "..");
+          const parentDir = join24(targetDir, "..");
           const existing = await readWorkspaceFile(parentDir);
           if (existing) {
             skipped.push(".flydocs-workspace.json (already exists)");
@@ -4547,16 +4619,320 @@ var init_init = __esm({
   }
 });
 
+// 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();
+      }
+    });
+  }
+});
+
 // src/commands/update.ts
 var update_exports = {};
 __export(update_exports, {
   default: () => update_default
 });
-import { defineCommand as defineCommand5 } from "citty";
-import { resolve as resolve4, join as join24 } from "path";
-import { mkdir as mkdir13, cp as cp2, readFile as readFile16, readdir as readdir6, 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 pc10 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"() {
@@ -4575,7 +4951,11 @@ var init_update = __esm({
     init_update_check();
     init_telemetry();
     init_integrity();
-    update_default = defineCommand5({
+    init_config();
+    init_types();
+    init_managed_paths();
+    init_sync();
+    update_default = defineCommand6({
       meta: {
         name: "update",
         description: "Update an existing FlyDocs installation"
@@ -4620,11 +5000,11 @@ 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: [
               {
@@ -4637,7 +5017,7 @@ var init_update = __esm({
               }
             ]
           });
-          if (isCancel5(choice)) {
+          if (isCancel6(choice)) {
             cancel4("Update cancelled.");
             process.exit(0);
           }
@@ -4647,11 +5027,11 @@ 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 ?? "~")
             );
           }
@@ -4660,11 +5040,11 @@ 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(join24(targetDir, ".flydocs", "version"));
+        const hasVersion = await pathExists(join27(targetDir, ".flydocs", "version"));
         const hasConfig = await pathExists(
-          join24(targetDir, ".flydocs", "config.json")
+          join27(targetDir, ".flydocs", "config.json")
         );
         if (!hasVersion && !hasConfig) {
           printError(`Not a FlyDocs project: ${targetDir}`);
@@ -4676,7 +5056,7 @@ var init_update = __esm({
         let currentVersion = "0.1.0";
         if (hasVersion) {
           const vContent = await readFile16(
-            join24(targetDir, ".flydocs", "version"),
+            join27(targetDir, ".flydocs", "version"),
             "utf-8"
           );
           currentVersion = vContent.trim();
@@ -4698,7 +5078,7 @@ var init_update = __esm({
           const shouldContinue = await confirm4({
             message: "Continue anyway?"
           });
-          if (isCancel5(shouldContinue) || !shouldContinue) {
+          if (isCancel6(shouldContinue) || !shouldContinue) {
             process.exit(0);
           }
         }
@@ -4710,35 +5090,65 @@ var init_update = __esm({
         });
         console.log(`Updating: v${currentVersion} \u2192 v${version}`);
         console.log();
-        const changelogPath = join24(templateDir, "CHANGELOG.md");
+        const changelogPath = join27(templateDir, "CHANGELOG.md");
         const whatsNew = await getWhatsNew(changelogPath, currentVersion, version);
         if (whatsNew.length > 0) {
-          console.log(pc10.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")}${String(now.getSeconds()).padStart(2, "0")}`;
-        const backupDir = join24(targetDir, ".flydocs", `backup-${ts}`);
-        await mkdir13(backupDir, { recursive: true });
+        const backupDir = join27(targetDir, ".flydocs", `backup-${ts}`);
+        await mkdir15(backupDir, { recursive: true });
         if (hasConfig) {
-          await cp2(
-            join24(targetDir, ".flydocs", "config.json"),
-            join24(backupDir, "config.json")
+          await cp3(
+            join27(targetDir, ".flydocs", "config.json"),
+            join27(backupDir, "config.json")
           );
           printStatus(`Config backed up to .flydocs/backup-${ts}/`);
         }
         try {
-          const flydocsDir = join24(targetDir, ".flydocs");
-          const entries = await readdir6(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(join24(flydocsDir, old), { recursive: true, force: true });
+              await rm7(join27(flydocsDir, old), { recursive: true, force: true });
             }
           }
         } catch {
@@ -4775,19 +5185,21 @@ 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(
-          join24(templateDir, ".flydocs", "templates"),
-          join24(targetDir, ".flydocs", "templates")
+          join27(templateDir, ".flydocs", "templates"),
+          join27(targetDir, ".flydocs", "templates")
         );
         printStatus(".flydocs/templates");
         await replaceDirectory(
-          join24(templateDir, ".claude", "hooks"),
-          join24(targetDir, ".claude", "hooks")
+          join27(templateDir, ".claude", "hooks"),
+          join27(targetDir, ".claude", "hooks")
         );
         printStatus(".claude/hooks");
         const hasExistingAgents = await pathExists(
-          join24(targetDir, ".claude", "agents")
+          join27(targetDir, ".claude", "agents")
         );
         let installAgents;
         if (args.yes) {
@@ -4796,7 +5208,7 @@ var init_update = __esm({
           installAgents = true;
         } else {
           console.log();
-          console.log(`  ${pc10.bold(pc10.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,"
@@ -4812,27 +5224,27 @@ 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 = join24(templateDir, ".claude", "agents");
+          const claudeAgentsSrc = join27(templateDir, ".claude", "agents");
           if (await pathExists(claudeAgentsSrc)) {
-            await mkdir13(join24(targetDir, ".claude", "agents"), { recursive: true });
+            await mkdir15(join27(targetDir, ".claude", "agents"), { recursive: true });
             await copyDirectoryContents(
               claudeAgentsSrc,
-              join24(targetDir, ".claude", "agents")
+              join27(targetDir, ".claude", "agents")
             );
           }
-          const cursorAgentsSrc = join24(templateDir, ".cursor", "agents");
+          const cursorAgentsSrc = join27(templateDir, ".cursor", "agents");
           if (await pathExists(cursorAgentsSrc)) {
-            await mkdir13(join24(targetDir, ".cursor", "agents"), { recursive: true });
+            await mkdir15(join27(targetDir, ".cursor", "agents"), { recursive: true });
             await copyDirectoryContents(
               cursorAgentsSrc,
-              join24(targetDir, ".cursor", "agents")
+              join27(targetDir, ".cursor", "agents")
             );
           }
           printStatus(
@@ -4846,58 +5258,58 @@ var init_update = __esm({
         console.log();
         console.log("Replacing framework files...");
         await copyFile(
-          join24(templateDir, ".claude", "CLAUDE.md"),
-          join24(targetDir, ".claude", "CLAUDE.md")
+          join27(templateDir, ".claude", "CLAUDE.md"),
+          join27(targetDir, ".claude", "CLAUDE.md")
         );
         await copyFile(
-          join24(templateDir, ".claude", "settings.json"),
-          join24(targetDir, ".claude", "settings.json")
+          join27(templateDir, ".claude", "settings.json"),
+          join27(targetDir, ".claude", "settings.json")
         );
         printStatus(".claude/CLAUDE.md, settings.json");
         await copyDirectoryContents(
-          join24(templateDir, ".claude", "commands"),
-          join24(targetDir, ".claude", "commands")
+          join27(templateDir, ".claude", "commands"),
+          join27(targetDir, ".claude", "commands")
         );
         await copyDirectoryContents(
-          join24(templateDir, ".claude", "commands"),
-          join24(targetDir, ".cursor", "commands")
+          join27(templateDir, ".claude", "commands"),
+          join27(targetDir, ".cursor", "commands")
         );
         printStatus(".claude/commands, .cursor/commands");
-        const skillsReadmeSrc = join24(templateDir, ".claude", "skills", "README.md");
+        const skillsReadmeSrc = join27(templateDir, ".claude", "skills", "README.md");
         if (await pathExists(skillsReadmeSrc)) {
           await copyFile(
             skillsReadmeSrc,
-            join24(targetDir, ".claude", "skills", "README.md")
+            join27(targetDir, ".claude", "skills", "README.md")
           );
         }
         printStatus(".claude/skills/README.md");
         await copyFile(
-          join24(templateDir, ".cursor", "hooks.json"),
-          join24(targetDir, ".cursor", "hooks.json")
+          join27(templateDir, ".cursor", "hooks.json"),
+          join27(targetDir, ".cursor", "hooks.json")
         );
         printStatus(".cursor/hooks.json");
         await copyFile(
-          join24(templateDir, "AGENTS.md"),
-          join24(targetDir, "AGENTS.md")
+          join27(templateDir, "AGENTS.md"),
+          join27(targetDir, "AGENTS.md")
         );
         printStatus("AGENTS.md");
-        const envExampleSrc = join24(templateDir, ".env.example");
+        const envExampleSrc = join27(templateDir, ".env.example");
         if (await pathExists(envExampleSrc)) {
-          await copyFile(envExampleSrc, join24(targetDir, ".env.example"));
+          await copyFile(envExampleSrc, join27(targetDir, ".env.example"));
           printStatus(".env.example");
         }
-        const knowledgeTemplatesDir = join24(
+        const knowledgeTemplatesDir = join27(
           targetDir,
           "flydocs",
           "knowledge",
           "templates"
         );
         if (!await pathExists(knowledgeTemplatesDir)) {
-          await mkdir13(knowledgeTemplatesDir, { recursive: true });
+          await mkdir15(knowledgeTemplatesDir, { recursive: true });
         }
         for (const tmpl of ["decision.md", "feature.md", "note.md"]) {
-          const src = join24(templateDir, "flydocs", "knowledge", "templates", tmpl);
-          const dest = join24(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);
           }
@@ -4924,18 +5336,18 @@ var init_update = __esm({
           printWarning("Config merge failed \u2014 config.json preserved as-is");
         }
         await copyFile(
-          join24(templateDir, ".flydocs", "version"),
-          join24(targetDir, ".flydocs", "version")
+          join27(templateDir, ".flydocs", "version"),
+          join27(targetDir, ".flydocs", "version")
         );
         printStatus(`.flydocs/version \u2192 ${version}`);
-        const clSrc = join24(templateDir, "CHANGELOG.md");
+        const clSrc = join27(templateDir, "CHANGELOG.md");
         if (await pathExists(clSrc)) {
-          await copyFile(clSrc, join24(targetDir, ".flydocs", "CHANGELOG.md"));
+          await copyFile(clSrc, join27(targetDir, ".flydocs", "CHANGELOG.md"));
           printStatus(".flydocs/CHANGELOG.md");
         }
-        const mfSrc = join24(templateDir, "manifest.json");
+        const mfSrc = join27(templateDir, "manifest.json");
         if (await pathExists(mfSrc)) {
-          await copyFile(mfSrc, join24(targetDir, ".flydocs", "manifest.json"));
+          await copyFile(mfSrc, join27(targetDir, ".flydocs", "manifest.json"));
           printStatus(".flydocs/manifest.json");
         }
         await generateIntegrity(targetDir, version);
@@ -4997,22 +5409,22 @@ var uninstall_exports = {};
 __export(uninstall_exports, {
   default: () => uninstall_default
 });
-import { defineCommand as defineCommand6 } from "citty";
-import { resolve as resolve5, join as join25 } from "path";
-import { readdir as readdir7, 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 pc11 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 = join25(targetDir, ".claude", "skills");
+  const skillsDir = join28(targetDir, ".claude", "skills");
   const removed = [];
   if (!await pathExists(skillsDir)) {
     return removed;
   }
   try {
-    const entries = await readdir7(skillsDir);
+    const entries = await readdir9(skillsDir);
     for (const entry of entries) {
       if (entry.startsWith(OWNED_SKILL_PREFIX)) {
-        await rm6(join25(skillsDir, entry), { recursive: true, force: true });
+        await rm8(join28(skillsDir, entry), { recursive: true, force: true });
         removed.push(`.claude/skills/${entry}`);
       }
     }
@@ -5021,16 +5433,16 @@ async function removeOwnedSkills(targetDir) {
   return removed;
 }
 async function removeOwnedCursorRules(targetDir) {
-  const rulesDir = join25(targetDir, ".cursor", "rules");
+  const rulesDir = join28(targetDir, ".cursor", "rules");
   const removed = [];
   if (!await pathExists(rulesDir)) {
     return removed;
   }
   try {
-    const entries = await readdir7(rulesDir);
+    const entries = await readdir9(rulesDir);
     for (const entry of entries) {
       if (entry.startsWith(OWNED_RULE_PREFIX) && entry.endsWith(".mdc")) {
-        await rm6(join25(rulesDir, entry), { force: true });
+        await rm8(join28(rulesDir, entry), { force: true });
         removed.push(`.cursor/rules/${entry}`);
       }
     }
@@ -5040,7 +5452,7 @@ async function removeOwnedCursorRules(targetDir) {
 }
 async function isEmptyDir(dirPath) {
   try {
-    const entries = await readdir7(dirPath);
+    const entries = await readdir9(dirPath);
     return entries.length === 0;
   } catch {
     return false;
@@ -5049,9 +5461,9 @@ async function isEmptyDir(dirPath) {
 async function cleanupEmptyParents(targetDir, dirs) {
   const cleaned = [];
   for (const dir of dirs) {
-    const fullPath = join25(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);
     }
   }
@@ -5081,7 +5493,7 @@ var init_uninstall = __esm({
     ];
     OWNED_SKILL_PREFIX = "flydocs-";
     OWNED_RULE_PREFIX = "flydocs-";
-    uninstall_default = defineCommand6({
+    uninstall_default = defineCommand7({
       meta: {
         name: "uninstall",
         description: "Remove FlyDocs from a project directory"
@@ -5117,7 +5529,7 @@ 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 {
@@ -5127,9 +5539,9 @@ var init_uninstall = __esm({
           printError(`Directory does not exist: ${targetDir}`);
           process.exit(1);
         }
-        targetDir = resolve5(targetDir);
-        const hasFlydocs = await pathExists(join25(targetDir, ".flydocs"));
-        const hasAgentsMd = await pathExists(join25(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.");
@@ -5141,12 +5553,12 @@ var init_uninstall = __esm({
         const removeAll = forceAll || args.all;
         const skipPrompts = forceAll || args.yes;
         let contentAction = "preserve";
-        const hasUserContent = await pathExists(join25(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: [
                 {
@@ -5166,7 +5578,7 @@ var init_uninstall = __esm({
                 }
               ]
             });
-            if (isCancel6(choice)) {
+            if (isCancel7(choice)) {
               cancel5("Uninstall cancelled.");
               process.exit(0);
             }
@@ -5175,39 +5587,39 @@ var init_uninstall = __esm({
         }
         if (!skipPrompts) {
           console.log();
-          console.log(pc11.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(`    ${pc11.dim(path)}`);
+            console.log(`    ${pc12.dim(path)}`);
           }
-          console.log(`    ${pc11.dim(".claude/skills/flydocs-*")}`);
-          console.log(`    ${pc11.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: ${pc11.yellow("flydocs/ -> flydocs-archive/")}`
+                `  User content: ${pc12.yellow("flydocs/ -> flydocs-archive/")}`
               );
             } else if (contentAction === "remove") {
               console.log();
-              console.log(`  User content: ${pc11.red("flydocs/ (deleted)")}`);
+              console.log(`  User content: ${pc12.red("flydocs/ (deleted)")}`);
             } else {
               console.log();
-              console.log(`  User content: ${pc11.green("flydocs/ (preserved)")}`);
+              console.log(`  User content: ${pc12.green("flydocs/ (preserved)")}`);
             }
           }
           console.log();
-          console.log(pc11.bold("Preserved:"));
+          console.log(pc12.bold("Preserved:"));
           console.log(
-            `    ${pc11.dim(".claude/skills/ (non-flydocs community skills)")}`
+            `    ${pc12.dim(".claude/skills/ (non-flydocs community skills)")}`
           );
-          console.log(`    ${pc11.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);
           }
@@ -5224,16 +5636,16 @@ var init_uninstall = __esm({
         const removedRules = await removeOwnedCursorRules(targetDir);
         result.removed.push(...removedRules);
         for (const [relativePath, type] of ALWAYS_REMOVED) {
-          const fullPath = join25(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 {
@@ -5242,16 +5654,16 @@ var init_uninstall = __esm({
           }
         }
         if (hasUserContent) {
-          const flydocsPath = join25(targetDir, "flydocs");
+          const flydocsPath = join28(targetDir, "flydocs");
           if (contentAction === "archive") {
-            const archivePath = join25(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/");
           }
         }
@@ -5270,17 +5682,17 @@ var init_uninstall = __esm({
           result.restored = originals.map((f) => f.relativePath);
         }
         console.log();
-        console.log(pc11.bold("Uninstall Summary"));
+        console.log(pc12.bold("Uninstall Summary"));
         console.log();
         if (result.removed.length > 0) {
-          console.log(`  ${pc11.green("Removed")} (${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(`  ${pc11.yellow("Archived")} (${result.archived.length}):`);
+          console.log(`  ${pc12.yellow("Archived")} (${result.archived.length}):`);
           for (const item of result.archived) {
             printInfo(item);
           }
@@ -5288,7 +5700,7 @@ var init_uninstall = __esm({
         if (result.restored.length > 0) {
           console.log();
           console.log(
-            `  ${pc11.green("Restored")} (${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);
@@ -5297,16 +5709,16 @@ var init_uninstall = __esm({
         if (result.skipped.length > 0) {
           console.log();
           console.log(
-            `  ${pc11.dim("Skipped")} (${result.skipped.length} \u2014 not found):`
+            `  ${pc12.dim("Skipped")} (${result.skipped.length} \u2014 not found):`
           );
           for (const item of result.skipped) {
-            console.log(`  ${pc11.dim(item)}`);
+            console.log(`  ${pc12.dim(item)}`);
           }
         }
         console.log();
         printStatus("FlyDocs has been removed from this project.");
         console.log();
-        printInfo(`To reinstall: ${pc11.cyan("npx @flydocs/cli install --here")}`);
+        printInfo(`To reinstall: ${pc12.cyan("npx @flydocs/cli install --here")}`);
         console.log();
       }
     });
@@ -5318,28 +5730,28 @@ var setup_exports = {};
 __export(setup_exports, {
   default: () => setup_default
 });
-import { defineCommand as defineCommand7 } from "citty";
-import pc12 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 = defineCommand7({
+    setup_default = defineCommand8({
       meta: {
         name: "setup",
         description: "Configure FlyDocs settings for this project"
       },
       run() {
         console.log();
-        console.log(`  ${pc12.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(
-          `  ${pc12.cyan("Claude Code:")}  Type ${pc12.bold("/flydocs-setup")} in chat`
+          `  ${pc13.cyan("Claude Code:")}  Type ${pc13.bold("/flydocs-setup")} in chat`
         );
         console.log(
-          `  ${pc12.cyan("Cursor:")}      Type ${pc12.bold("/flydocs-setup")} in chat`
+          `  ${pc13.cyan("Cursor:")}      Type ${pc13.bold("/flydocs-setup")} in chat`
         );
         console.log();
         console.log(`  This configures your project context, detects your stack,`);
@@ -5355,14 +5767,14 @@ var skills_exports = {};
 __export(skills_exports, {
   default: () => skills_default
 });
-import { defineCommand as defineCommand8 } from "citty";
-import pc13 from "picocolors";
+import { defineCommand as defineCommand9 } from "citty";
+import pc14 from "picocolors";
 var list, search, add, remove, skills_default;
 var init_skills2 = __esm({
   "src/commands/skills.ts"() {
     "use strict";
     init_skill_manager();
-    list = defineCommand8({
+    list = defineCommand9({
       meta: {
         name: "list",
         description: "List installed skills"
@@ -5378,26 +5790,26 @@ var init_skills2 = __esm({
         console.log(`${total} skill(s) installed:`);
         if (result.platform.length > 0) {
           console.log();
-          console.log(pc13.bold("Platform"));
+          console.log(pc14.bold("Platform"));
           for (const skill of result.platform) {
             console.log(
-              `  ${skill.name} ${pc13.dim(`(${skill.triggers} triggers)`)}`
+              `  ${skill.name} ${pc14.dim(`(${skill.triggers} triggers)`)}`
             );
           }
         }
         if (result.community.length > 0) {
           console.log();
-          console.log(pc13.bold("Community"));
+          console.log(pc14.bold("Community"));
           for (const skill of result.community) {
             console.log(
-              `  ${skill.name} ${pc13.dim(`(${skill.triggers} triggers)`)}`
+              `  ${skill.name} ${pc14.dim(`(${skill.triggers} triggers)`)}`
             );
           }
         }
         console.log();
       }
     });
-    search = defineCommand8({
+    search = defineCommand9({
       meta: {
         name: "search",
         description: "Search community skills"
@@ -5413,24 +5825,24 @@ 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: ${pc13.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(`  ${pc13.bold(skill.name)}`);
+          console.log(`  ${pc14.bold(skill.name)}`);
           console.log(`  ${skill.description}`);
-          console.log(`  ${pc13.dim(skill.repo)}`);
+          console.log(`  ${pc14.dim(skill.repo)}`);
           if (skill.tags.length > 0) {
-            console.log(`  ${pc13.dim(skill.tags.join(", "))}`);
+            console.log(`  ${pc14.dim(skill.tags.join(", "))}`);
           }
           console.log();
         }
       }
     });
-    add = defineCommand8({
+    add = defineCommand9({
       meta: {
         name: "add",
         description: "Install a community skill"
@@ -5446,7 +5858,7 @@ var init_skills2 = __esm({
         await addSkill(process.cwd(), args.source);
       }
     });
-    remove = defineCommand8({
+    remove = defineCommand9({
       meta: {
         name: "remove",
         description: "Remove an installed community skill"
@@ -5462,7 +5874,7 @@ var init_skills2 = __esm({
         await removeSkill(process.cwd(), args.name);
       }
     });
-    skills_default = defineCommand8({
+    skills_default = defineCommand9({
       meta: {
         name: "skills",
         description: "Manage FlyDocs skills (list, search, add, remove)"
@@ -5482,10 +5894,10 @@ var connect_exports = {};
 __export(connect_exports, {
   default: () => connect_default
 });
-import { defineCommand as defineCommand9 } from "citty";
-import { text as text4, confirm as confirm6, isCancel as isCancel7, cancel as cancel6 } from "@clack/prompts";
-import pc14 from "picocolors";
-import { join as join26 } 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"() {
@@ -5495,7 +5907,7 @@ var init_connect = __esm({
     init_template();
     init_ui();
     init_api_key();
-    connect_default = defineCommand9({
+    connect_default = defineCommand10({
       meta: {
         name: "connect",
         description: "Connect FlyDocs to a cloud provider"
@@ -5520,11 +5932,11 @@ var init_connect = __esm({
       },
       async run({ args }) {
         const targetDir = args.path ?? process.cwd();
-        const configPath = join26(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 ${pc14.cyan("flydocs")} first to install FlyDocs in this project.`
+            `  Run ${pc15.cyan("flydocs")} first to install FlyDocs in this project.`
           );
           process.exit(1);
         }
@@ -5535,16 +5947,16 @@ 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(`  ${pc14.bold("Connect to FlyDocs Cloud")}`);
+        console.log(`  ${pc15.bold("Connect to FlyDocs Cloud")}`);
         console.log();
         console.log(
-          `  ${pc14.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 ?? "";
@@ -5560,7 +5972,7 @@ var init_connect = __esm({
               return void 0;
             }
           });
-          if (isCancel7(keyInput)) {
+          if (isCancel8(keyInput)) {
             cancel6("Connection cancelled.");
             process.exit(0);
           }
@@ -5582,7 +5994,7 @@ var init_connect = __esm({
               console.log(`  Check your key and try again.`);
               process.exit(1);
             }
-            printStatus(`Connected to ${pc14.bold(result.org)}`);
+            printStatus(`Connected to ${pc15.bold(result.org)}`);
           } catch {
             printError(
               "Could not reach relay API. Check your network and try again."
@@ -5590,7 +6002,7 @@ var init_connect = __esm({
             process.exit(1);
           }
           const envFile = await storeEnvKey(targetDir, "FLYDOCS_API_KEY", apiKey);
-          printStatus(`API key stored in ${pc14.dim(envFile)}`);
+          printStatus(`API key stored in ${pc15.dim(envFile)}`);
         } else {
           try {
             const result = await validateLinearKey(apiKey);
@@ -5600,7 +6012,7 @@ var init_connect = __esm({
               process.exit(1);
             }
             printStatus(
-              `Authenticated as ${pc14.bold(result.name)} (${result.email})`
+              `Authenticated as ${pc15.bold(result.name)} (${result.email})`
             );
           } catch {
             printError("Invalid API key or network error.");
@@ -5608,7 +6020,7 @@ var init_connect = __esm({
             process.exit(1);
           }
           const envFile = await storeEnvKey(targetDir, "LINEAR_API_KEY", apiKey);
-          printStatus(`API key stored in ${pc14.dim(envFile)}`);
+          printStatus(`API key stored in ${pc15.dim(envFile)}`);
         }
         const wasLocal = config.tier === "local";
         config.tier = "cloud";
@@ -5624,14 +6036,14 @@ var init_connect = __esm({
         }
         console.log();
         console.log(
-          `  ${pc14.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 ${pc14.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 ${pc14.cyan("/start-session")} to begin working`);
+        console.log(`    2. Run ${pc15.cyan("/start-session")} to begin working`);
         console.log();
       }
     });
@@ -5643,9 +6055,9 @@ var auth_exports = {};
 __export(auth_exports, {
   default: () => auth_default
 });
-import { defineCommand as defineCommand10 } from "citty";
-import { text as text5, confirm as confirm7, isCancel as isCancel8, cancel as cancel7 } from "@clack/prompts";
-import pc15 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"() {
@@ -5653,7 +6065,7 @@ var init_auth = __esm({
     init_ui();
     init_api_key();
     init_global_config();
-    auth_default = defineCommand10({
+    auth_default = defineCommand11({
       meta: {
         name: "auth",
         description: "Store API key globally (~/.flydocs/credentials)"
@@ -5667,25 +6079,25 @@ var init_auth = __esm({
       },
       async run({ args }) {
         console.log();
-        console.log(`  ${pc15.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: ${pc15.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(
-            `  ${pc15.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({
@@ -5699,7 +6111,7 @@ var init_auth = __esm({
               return void 0;
             }
           });
-          if (isCancel8(keyInput)) {
+          if (isCancel9(keyInput)) {
             cancel7("Authentication cancelled.");
             process.exit(0);
           }
@@ -5721,7 +6133,7 @@ var init_auth = __esm({
             printError("Invalid API key. Check your key and try again.");
             process.exit(1);
           }
-          printStatus(`Authenticated with ${pc15.bold(result.org)}`);
+          printStatus(`Authenticated with ${pc16.bold(result.org)}`);
         } catch {
           printError(
             "Could not reach FlyDocs API. Check your network and try again."
@@ -5736,10 +6148,10 @@ var init_auth = __esm({
           createdAt: (/* @__PURE__ */ new Date()).toISOString(),
           lastValidated: (/* @__PURE__ */ new Date()).toISOString()
         });
-        printStatus(`Key stored at ${pc15.dim(credentialsPath())}`);
+        printStatus(`Key stored at ${pc16.dim(credentialsPath())}`);
         await checkCredentialPermissions();
         console.log();
-        console.log(`  ${pc15.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();
       }
@@ -5747,175 +6159,6 @@ var init_auth = __esm({
   }
 });
 
-// src/commands/sync.ts
-var sync_exports = {};
-__export(sync_exports, {
-  default: () => sync_default
-});
-import { defineCommand as defineCommand11 } from "citty";
-import pc16 from "picocolors";
-import { join as join27, resolve as resolve6 } from "path";
-import { mkdir as mkdir14, writeFile as writeFile17 } from "fs/promises";
-async function resolveArtifactWriteRoot(targetDir, config) {
-  const topology = config.topology;
-  if (topology && topology.type === 4 && topology.label === "sibling-repos") {
-    const parentDir = join27(targetDir, "..");
-    const workspaceFile = await readWorkspaceFile(parentDir);
-    if (workspaceFile) {
-      return resolve6(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_fs_ops();
-    init_types();
-    init_gitignore();
-    init_artifacts();
-    init_workspace();
-    init_relay_client();
-    sync_default = defineCommand11({
-      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;
-        let currentArtifactVersion = 0;
-        try {
-          const currentConfig = await readAnyConfig(targetDir);
-          if (isConfigV2(currentConfig)) {
-            currentTemplateVersion = currentConfig.configVersion ?? 0;
-            currentArtifactVersion = currentConfig.artifactVersion ?? 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(`  ${pc16.dim("Config may be stale. Retry when connected.")}`);
-          return;
-        }
-        if (!serverResponse.valid) {
-          printWarning("Server returned invalid config. Keeping current config.");
-          return;
-        }
-        await mkdir14(join27(targetDir, ".flydocs"), { recursive: true });
-        const configWithHash = applyConfigHash(serverResponse.config);
-        await writeConfig(targetDir, configWithHash);
-        changes.push("Updated .flydocs/config.json");
-        const serverTemplateVersion = serverResponse.templates.version;
-        if (serverTemplateVersion > currentTemplateVersion) {
-          try {
-            const templatesResponse = await fetchTemplates(
-              apiKey,
-              currentTemplateVersion,
-              workspaceId
-            );
-            if (templatesResponse.templates.length > 0) {
-              const templatesDir = join27(
-                targetDir,
-                ".claude",
-                "skills",
-                "flydocs-workflow",
-                "templates"
-              );
-              await mkdir14(templatesDir, { recursive: true });
-              for (const template of templatesResponse.templates) {
-                const filename = `${template.type}.md`;
-                const subdir = template.category === "issue" ? "issues" : template.category === "pr" ? "pr" : template.category === "comment" ? "." : ".";
-                const templateDir = join27(templatesDir, subdir);
-                await mkdir14(templateDir, { recursive: true });
-                await writeFile17(
-                  join27(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;
-        if (serverArtifactVersion > currentArtifactVersion) {
-          const artifactWriteRoot = await resolveArtifactWriteRoot(
-            targetDir,
-            serverResponse.config
-          );
-          const { changes: artifactChanges } = await syncAllArtifacts(
-            artifactWriteRoot,
-            apiKey,
-            workspaceId,
-            currentArtifactVersion
-          );
-          changes.push(...artifactChanges);
-          if (artifactWriteRoot !== targetDir) {
-            changes.push(`Artifacts written to workspace root`);
-          }
-        }
-        await migrateGitignore(targetDir);
-        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, {