@flydocs/cli 0.6.0-alpha.23 → 0.6.0-alpha.26

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.23";
+    CLI_VERSION = "0.6.0-alpha.26";
     CLI_NAME = "flydocs";
     PACKAGE_NAME = "@flydocs/cli";
     POSTHOG_API_KEY = "phc_v1MSJTQDFkMS90CBh3mxIz3v8bYCCnKU6v1ir6bz0Xn";
@@ -136,8 +136,8 @@ var init_template = __esm({
 
 // src/lib/ui.ts
 import pc2 from "picocolors";
-function shadow(text4) {
-  return `\x1B[38;2;55;45;70m${text4}\x1B[0m`;
+function shadow(text6) {
+  return `\x1B[38;2;55;45;70m${text6}\x1B[0m`;
 }
 function renderBannerBlock() {
   const height = BANNER_ROWS.length;
@@ -268,12 +268,70 @@ var init_ui = __esm({
   }
 });
 
+// src/lib/types.ts
+function isConfigV2(config) {
+  return config.configFormat === 2;
+}
+var init_types = __esm({
+  "src/lib/types.ts"() {
+    "use strict";
+  }
+});
+
+// src/lib/config-integrity.ts
+import { createHash } from "crypto";
+function computeConfigHash(config) {
+  const { configHash: _, ...rest } = config;
+  const serialized = JSON.stringify(rest, Object.keys(rest).sort());
+  return `sha256:${createHash("sha256").update(serialized, "utf-8").digest("hex")}`;
+}
+function validateConfigIntegrity(config) {
+  if (!config.configHash) return false;
+  const computed = computeConfigHash(config);
+  return computed === config.configHash;
+}
+function checkConfigIntegrity(config) {
+  if (!config.configHash) {
+    return true;
+  }
+  const valid = validateConfigIntegrity(config);
+  if (!valid) {
+    printWarning(
+      "Config modified locally \u2014 will restore from server on next sync."
+    );
+  }
+  return valid;
+}
+function applyConfigHash(config) {
+  const hash = computeConfigHash(config);
+  return { ...config, configHash: hash };
+}
+var init_config_integrity = __esm({
+  "src/lib/config-integrity.ts"() {
+    "use strict";
+    init_ui();
+  }
+});
+
 // src/lib/config.ts
 import { readFile as readFile2, writeFile } from "fs/promises";
 import { join as join3 } from "path";
-async function readConfig(dir) {
+async function readAnyConfig(dir) {
   const content = await readFile2(join3(dir, ".flydocs", "config.json"), "utf-8");
-  return JSON.parse(content);
+  const config = JSON.parse(content);
+  if (isConfigV2(config)) {
+    checkConfigIntegrity(config);
+  }
+  return config;
+}
+async function readConfig(dir) {
+  const config = await readAnyConfig(dir);
+  if (isConfigV2(config)) {
+    throw new Error(
+      "This command requires v1 config format. Run `flydocs sync` to use v2 commands."
+    );
+  }
+  return config;
 }
 async function writeConfig(dir, config) {
   const content = JSON.stringify(config, null, 2) + "\n";
@@ -343,6 +401,8 @@ async function mergeConfig(templateDir, version, tierFlag, preserved) {
 var init_config = __esm({
   "src/lib/config.ts"() {
     "use strict";
+    init_types();
+    init_config_integrity();
   }
 });
 
@@ -363,7 +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: rm6 } = await import("fs/promises");
+  const { rm: rm7 } = await import("fs/promises");
   await replaceDirectory(
     join4(templateSkillsDir, OWNED_SKILL),
     join4(skillsDir, OWNED_SKILL)
@@ -371,7 +431,7 @@ async function replaceOwnedSkills(templateDir, targetDir, _tier) {
   for (const legacy of LEGACY_SKILLS) {
     const legacyPath = join4(skillsDir, legacy);
     if (await pathExists(legacyPath)) {
-      await rm6(legacyPath, { recursive: true, force: true });
+      await rm7(legacyPath, { recursive: true, force: true });
     }
   }
   const readmeSrc = join4(templateSkillsDir, "README.md");
@@ -380,9 +440,9 @@ async function replaceOwnedSkills(templateDir, targetDir, _tier) {
   }
 }
 async function copyCursorRules(targetDir) {
-  const { mkdir: mkdir9 } = await import("fs/promises");
+  const { mkdir: mkdir12 } = await import("fs/promises");
   const rulesDir = join4(targetDir, ".cursor", "rules");
-  await mkdir9(rulesDir, { recursive: true });
+  await mkdir12(rulesDir, { recursive: true });
   const workflowRule = join4(
     targetDir,
     ".claude",
@@ -393,11 +453,11 @@ async function copyCursorRules(targetDir) {
   if (await pathExists(workflowRule)) {
     await copyFile(workflowRule, join4(rulesDir, "flydocs-workflow.mdc"));
   }
-  const { rm: rm6 } = await import("fs/promises");
+  const { rm: rm7 } = await import("fs/promises");
   for (const legacy of ["flydocs-mechanism.mdc", "flydocs-context7.mdc"]) {
     const legacyRule = join4(rulesDir, legacy);
     if (await pathExists(legacyRule)) {
-      await rm6(legacyRule, { force: true });
+      await rm7(legacyRule, { force: true });
     }
   }
 }
@@ -715,8 +775,8 @@ function flushFrontmatterValue(mode, lines) {
       return lines.join("\n").trim();
   }
 }
-function parseFrontmatter(text4) {
-  const match = text4.match(/^---\s*\n([\s\S]*?)\n---/);
+function parseFrontmatter(text6) {
+  const match = text6.match(/^---\s*\n([\s\S]*?)\n---/);
   if (!match) return null;
   const block = match[1];
   const result = {};
@@ -1481,7 +1541,7 @@ async function ensurePlatformIgnores(targetDir) {
     if (!await pathExists(filePath)) continue;
     const content = await readFile6(filePath, "utf-8");
     if (content.includes("# FlyDocs")) continue;
-    const section = "\n# FlyDocs \u2014 exclude from builds and deploys\n" + FLYDOCS_DEPLOY_EXCLUSIONS.join("\n") + "\n";
+    const section = "\n# FlyDocs \u2014 managed by flydocs-cli, do not edit this section\n" + FLYDOCS_DEPLOY_EXCLUSIONS.join("\n") + "\n";
     await appendFile(filePath, section, "utf-8");
     printStatus(`Added FlyDocs exclusions to ${filename}`);
   }
@@ -1496,14 +1556,19 @@ var init_gitignore = __esm({
       ".gcloudignore",
       ".dockerignore",
       ".vercelignore",
-      ".npmignore"
+      ".npmignore",
+      ".cfignore",
+      ".ebignore",
+      ".funcignore"
     ];
     FLYDOCS_DEPLOY_EXCLUSIONS = [
       ".flydocs/",
       ".claude/",
       ".cursor/",
       "flydocs/",
-      "AGENTS.md"
+      ".flydocs-workspace.json",
+      "AGENTS.md",
+      ".cursorrules"
     ];
     FLYDOCS_GITIGNORE_ENTRIES = [
       ".env",
@@ -2759,16 +2824,630 @@ var init_install = __esm({
   }
 });
 
+// src/lib/global-config.ts
+import { readFile as readFile12, writeFile as writeFile10, mkdir as mkdir8, stat, chmod } from "fs/promises";
+import { join as join17 } from "path";
+import { homedir as homedir3 } from "os";
+function globalDir() {
+  return join17(homedir3(), ".flydocs");
+}
+function credentialsPath() {
+  return join17(globalDir(), "credentials");
+}
+function globalMePath() {
+  return join17(globalDir(), "me.json");
+}
+async function ensureGlobalDir() {
+  const dir = globalDir();
+  if (!await pathExists(dir)) {
+    await mkdir8(dir, { recursive: true, mode: 448 });
+  }
+  return dir;
+}
+async function readGlobalCredential() {
+  const path = credentialsPath();
+  if (!await pathExists(path)) return null;
+  try {
+    const content = await readFile12(path, "utf-8");
+    return JSON.parse(content);
+  } catch {
+    return null;
+  }
+}
+async function writeGlobalCredential(credential) {
+  await ensureGlobalDir();
+  const path = credentialsPath();
+  await writeFile10(path, JSON.stringify(credential, null, 2) + "\n", {
+    encoding: "utf-8",
+    mode: 384
+  });
+  await chmod(path, 384);
+}
+async function checkCredentialPermissions() {
+  const path = credentialsPath();
+  if (!await pathExists(path)) return;
+  try {
+    const stats = await stat(path);
+    const mode = stats.mode & 511;
+    if (mode !== 384) {
+      printWarning(
+        `Credential file permissions are too open (${mode.toString(8)}). Expected 0600. Run: chmod 600 ${path}`
+      );
+    }
+  } catch {
+  }
+}
+async function writeGlobalIdentity(identity) {
+  await ensureGlobalDir();
+  const path = globalMePath();
+  await writeFile10(path, JSON.stringify(identity, null, 2) + "\n", "utf-8");
+}
+async function resolveApiKey(explicitKey, projectDir) {
+  if (explicitKey) {
+    return { key: explicitKey, source: "--key flag" };
+  }
+  const envKey = process.env.FLYDOCS_API_KEY;
+  if (envKey) {
+    return { key: envKey, source: "FLYDOCS_API_KEY env var" };
+  }
+  const globalCred = await readGlobalCredential();
+  if (globalCred?.apiKey) {
+    return { key: globalCred.apiKey, source: "~/.flydocs/credentials" };
+  }
+  if (projectDir) {
+    const envLocalKey = await readEnvKey(projectDir, "FLYDOCS_API_KEY");
+    if (envLocalKey) {
+      return { key: envLocalKey, source: ".env.local (legacy)" };
+    }
+  }
+  return null;
+}
+async function readEnvKey(dir, varName) {
+  for (const filename of [".env.local", ".env"]) {
+    const filePath = join17(dir, filename);
+    if (!await pathExists(filePath)) continue;
+    try {
+      const content = await readFile12(filePath, "utf-8");
+      const match = content.match(new RegExp(`^${varName}=(.+)$`, "m"));
+      if (match) return match[1].trim();
+    } catch {
+      continue;
+    }
+  }
+  return null;
+}
+var init_global_config = __esm({
+  "src/lib/global-config.ts"() {
+    "use strict";
+    init_fs_ops();
+    init_ui();
+  }
+});
+
+// src/lib/relay-client.ts
+function resolveRelayUrl() {
+  return process.env.FLYDOCS_RELAY_URL?.replace(/\/$/, "") ?? DEFAULT_RELAY_URL;
+}
+function headers(apiKey) {
+  return {
+    Authorization: `Bearer ${apiKey}`,
+    "Content-Type": "application/json",
+    Accept: "application/json"
+  };
+}
+async function fetchConfigV2(apiKey, options = {}) {
+  const baseUrl = resolveRelayUrl();
+  const params = new URLSearchParams({ format: "2" });
+  if (options.includeContext) params.set("includeContext", "true");
+  const response = await fetch(`${baseUrl}/config/generate?${params}`, {
+    method: "GET",
+    headers: headers(apiKey),
+    signal: AbortSignal.timeout(3e4)
+  });
+  if (!response.ok) {
+    const body = await response.text().catch(() => "");
+    throw new RelayError(
+      `config/generate failed (${response.status})`,
+      response.status,
+      body
+    );
+  }
+  return await response.json();
+}
+async function fetchTemplates(apiKey, sinceVersion) {
+  const baseUrl = resolveRelayUrl();
+  const response = await fetch(`${baseUrl}/templates?since=${sinceVersion}`, {
+    method: "GET",
+    headers: headers(apiKey),
+    signal: AbortSignal.timeout(15e3)
+  });
+  if (!response.ok) {
+    const body = await response.text().catch(() => "");
+    throw new RelayError(
+      `templates fetch failed (${response.status})`,
+      response.status,
+      body
+    );
+  }
+  return await response.json();
+}
+var DEFAULT_RELAY_URL, RelayError;
+var init_relay_client = __esm({
+  "src/lib/relay-client.ts"() {
+    "use strict";
+    DEFAULT_RELAY_URL = "https://app.flydocs.ai/api/relay";
+    RelayError = class extends Error {
+      constructor(message, status2, body) {
+        super(message);
+        this.status = status2;
+        this.body = body;
+        this.name = "RelayError";
+      }
+    };
+  }
+});
+
+// src/lib/workspace.ts
+import { readFile as readFile13, writeFile as writeFile11, readdir as readdir4, stat as stat2 } from "fs/promises";
+import { join as join18, dirname as dirname3, relative, resolve as resolve3 } from "path";
+async function readWorkspaceFile(dir) {
+  const filePath = join18(dir, WORKSPACE_FILENAME);
+  if (!await pathExists(filePath)) return null;
+  const content = await readFile13(filePath, "utf-8");
+  const parsed = JSON.parse(content);
+  validateWorkspaceFile(parsed);
+  return parsed;
+}
+async function writeWorkspaceFile(dir, workspace) {
+  const filePath = join18(dir, WORKSPACE_FILENAME);
+  const content = JSON.stringify(workspace, null, 2) + "\n";
+  await writeFile11(filePath, content, "utf-8");
+}
+async function detectSiblingRepos(parentDir) {
+  const repos = {};
+  const entries = await readdir4(parentDir);
+  for (const entry of entries) {
+    if (entry.startsWith(".")) continue;
+    const entryPath = join18(parentDir, entry);
+    const entryStat = await stat2(entryPath).catch(() => null);
+    if (!entryStat?.isDirectory()) continue;
+    const hasGit = await pathExists(join18(entryPath, ".git"));
+    const hasFlydocs = await pathExists(
+      join18(entryPath, ".flydocs", "config.json")
+    );
+    if (hasGit || hasFlydocs) {
+      repos[entry] = { path: `./${entry}` };
+    }
+  }
+  return repos;
+}
+function buildWorkspaceFile(workspaceId, repos) {
+  return { workspaceId, repos };
+}
+async function readSiblingDescriptors(workspaceDir, repos) {
+  const descriptors = [];
+  for (const [name, entry] of Object.entries(repos)) {
+    const repoDir = resolve3(workspaceDir, entry.path);
+    const serviceJsonPath = join18(repoDir, "flydocs", "context", "service.json");
+    if (!await pathExists(serviceJsonPath)) continue;
+    try {
+      const content = await readFile13(serviceJsonPath, "utf-8");
+      const descriptor = JSON.parse(content);
+      descriptors.push({ name, path: entry.path, descriptor });
+    } catch {
+    }
+  }
+  return descriptors;
+}
+async function generateWorkspaceMd(workspaceDir, workspace, productName) {
+  const descriptors = await readSiblingDescriptors(
+    workspaceDir,
+    workspace.repos
+  );
+  const repoCount = Object.keys(workspace.repos).length;
+  const lines = [];
+  const title = productName ?? "Workspace";
+  lines.push(`# Product: ${title}`);
+  lines.push("");
+  lines.push("## Overview");
+  lines.push("");
+  if (descriptors.length > 0) {
+    const purposes = descriptors.map((d) => d.descriptor.purpose).filter(Boolean);
+    if (purposes.length > 0) {
+      lines.push(purposes.join(". ") + ".");
+    } else {
+      lines.push(`Multi-repo workspace with ${repoCount} repositories.`);
+    }
+  } else {
+    lines.push(`Multi-repo workspace with ${repoCount} repositories.`);
+  }
+  lines.push("");
+  lines.push("## Architecture");
+  lines.push("");
+  lines.push(`${repoCount}-repo sibling topology.`);
+  lines.push("");
+  lines.push("## Repos");
+  lines.push("");
+  for (const [name, entry] of Object.entries(workspace.repos)) {
+    const desc = descriptors.find((d) => d.name === name);
+    const purpose = desc?.descriptor.purpose ?? "";
+    const stack = desc?.descriptor.stack?.join(", ") ?? "";
+    const detail = [purpose, stack].filter(Boolean).join(". ");
+    const projectMdLink = `${entry.path}/flydocs/context/project.md`;
+    lines.push(
+      `- **${name}** \u2014 ${detail || "No description"}. [Details](${projectMdLink})`
+    );
+  }
+  lines.push("");
+  const edges = [];
+  for (const desc of descriptors) {
+    for (const dep of desc.descriptor.dependencies ?? []) {
+      const target = dep.service;
+      const iface = dep.interface;
+      edges.push(`- ${desc.name} \u2192 ${target} (${iface})`);
+    }
+  }
+  lines.push("## Cross-Repo Dependencies");
+  lines.push("");
+  if (edges.length > 0) {
+    lines.push(...edges);
+  } else {
+    lines.push("No cross-repo dependencies detected.");
+  }
+  lines.push("");
+  return lines.join("\n");
+}
+function validateWorkspaceFile(value) {
+  if (typeof value !== "object" || value === null) {
+    throw new Error("Invalid workspace file: expected an object");
+  }
+  const obj = value;
+  if (typeof obj.workspaceId !== "string" || obj.workspaceId.length === 0) {
+    throw new Error(
+      "Invalid workspace file: workspaceId must be a non-empty string"
+    );
+  }
+  if (typeof obj.repos !== "object" || obj.repos === null) {
+    throw new Error("Invalid workspace file: repos must be an object");
+  }
+  const repos = obj.repos;
+  for (const [name, entry] of Object.entries(repos)) {
+    if (typeof entry !== "object" || entry === null) {
+      throw new Error(
+        `Invalid workspace file: repos.${name} must be an object`
+      );
+    }
+    const repoEntry = entry;
+    if (typeof repoEntry.path !== "string" || repoEntry.path.length === 0) {
+      throw new Error(
+        `Invalid workspace file: repos.${name}.path must be a non-empty string`
+      );
+    }
+  }
+}
+var WORKSPACE_FILENAME;
+var init_workspace = __esm({
+  "src/lib/workspace.ts"() {
+    "use strict";
+    init_fs_ops();
+    WORKSPACE_FILENAME = ".flydocs-workspace.json";
+  }
+});
+
+// src/commands/init.ts
+var init_exports = {};
+__export(init_exports, {
+  default: () => init_default
+});
+import { defineCommand as defineCommand2 } from "citty";
+import { text as text2, confirm as confirm3, isCancel as isCancel4, cancel as cancel3 } from "@clack/prompts";
+import pc7 from "picocolors";
+import { join as join19 } from "path";
+import { mkdir as mkdir9, writeFile as writeFile12 } from "fs/promises";
+async function resolveAndValidateKey(keyArg, targetDir) {
+  let resolved = await resolveApiKey(keyArg, targetDir);
+  if (!resolved) {
+    console.log(
+      `  ${pc7.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 ${pc7.bold(result.org)}`);
+  } catch {
+    printError(
+      "Could not reach FlyDocs API. Check your network and try again."
+    );
+    console.log(
+      `  ${pc7.dim("flydocs init requires server access. For offline use, run flydocs install instead.")}`
+    );
+    process.exit(1);
+  }
+  await writeGlobalCredential({
+    apiKey,
+    createdAt: (/* @__PURE__ */ new Date()).toISOString(),
+    lastValidated: (/* @__PURE__ */ new Date()).toISOString()
+  });
+  await checkCredentialPermissions();
+  return apiKey;
+}
+async function pullServerConfig(apiKey, targetDir) {
+  printInfo("Pulling config from server...");
+  const isFirstInit = !await pathExists(
+    join19(targetDir, ".flydocs", "config.json")
+  );
+  try {
+    const response = await fetchConfigV2(apiKey, {
+      includeContext: isFirstInit
+    });
+    if (!response.valid) {
+      printError("Server returned invalid config. Contact support.");
+      process.exit(1);
+    }
+    return response;
+  } catch (err) {
+    if (err instanceof RelayError) {
+      printError(`Server error: ${err.message}`);
+      if (err.status === 401) {
+        console.log(
+          `  ${pc7.dim("Your API key may be revoked. Run flydocs auth with a new key.")}`
+        );
+      }
+    } else {
+      printError("Could not reach server. Check your network.");
+    }
+    process.exit(1);
+  }
+}
+async function initSingleRepo(targetDir, apiKey, serverResponse) {
+  const actions = [];
+  const skipped = [];
+  await mkdir9(join19(targetDir, ".flydocs"), { recursive: true });
+  const configWithHash = applyConfigHash(serverResponse.config);
+  await writeConfig(targetDir, configWithHash);
+  actions.push("Wrote .flydocs/config.json (from server)");
+  if (serverResponse.identity) {
+    await writeGlobalIdentity({
+      name: serverResponse.identity.name,
+      email: serverResponse.identity.email,
+      providerIdentities: serverResponse.identity.providerIdentities
+    });
+    actions.push("Wrote ~/.flydocs/me.json");
+  }
+  if (serverResponse.context) {
+    const contextDir = join19(targetDir, "flydocs", "context");
+    await mkdir9(contextDir, { recursive: true });
+    const projectMdPath = join19(contextDir, "project.md");
+    if (!await pathExists(projectMdPath)) {
+      await writeFile12(projectMdPath, serverResponse.context.projectMd, "utf-8");
+      actions.push("Wrote flydocs/context/project.md");
+    } else {
+      skipped.push("flydocs/context/project.md (already exists)");
+    }
+    const serviceJsonPath = join19(contextDir, "service.json");
+    if (serverResponse.context.serviceJson && !await pathExists(serviceJsonPath)) {
+      await writeFile12(
+        serviceJsonPath,
+        JSON.stringify(serverResponse.context.serviceJson, null, 2) + "\n",
+        "utf-8"
+      );
+      actions.push("Wrote flydocs/context/service.json");
+    } else if (await pathExists(serviceJsonPath)) {
+      skipped.push("flydocs/context/service.json (already exists)");
+    }
+  }
+  await ensureGitignore(targetDir);
+  await ensurePlatformIgnores(targetDir);
+  actions.push("Updated ignore files");
+  return { actions, skipped };
+}
+async function isParentDirectory(dir) {
+  const hasGit = await pathExists(join19(dir, ".git"));
+  if (hasGit) return false;
+  const repos = await detectSiblingRepos(dir);
+  return Object.keys(repos).length >= 2;
+}
+async function runMultiRepoInit(parentDir, keyArg) {
+  const repos = await detectSiblingRepos(parentDir);
+  const repoNames = Object.keys(repos).sort();
+  printInfo(`Detected ${repoNames.length} repos:`);
+  for (const name of repoNames) {
+    console.log(`    ${pc7.cyan(name)}`);
+  }
+  console.log();
+  const shouldContinue = await confirm3({
+    message: `Initialize all ${repoNames.length} repos?`
+  });
+  if (isCancel4(shouldContinue) || !shouldContinue) {
+    cancel3("Init cancelled.");
+    process.exit(0);
+  }
+  const firstRepoDir = join19(parentDir, repoNames[0]);
+  const apiKey = await resolveAndValidateKey(keyArg, firstRepoDir);
+  const allActions = [
+    "Stored credential globally (~/.flydocs/credentials)"
+  ];
+  const allSkipped = [];
+  let allWarnings = [];
+  let firstResponse;
+  for (const repoName of repoNames) {
+    const repoDir = join19(parentDir, repoName);
+    console.log();
+    printInfo(`Initializing ${pc7.bold(repoName)}...`);
+    const serverResponse = await pullServerConfig(apiKey, repoDir);
+    if (!firstResponse) firstResponse = serverResponse;
+    const { actions, skipped } = await initSingleRepo(
+      repoDir,
+      apiKey,
+      serverResponse
+    );
+    for (const action of actions) {
+      allActions.push(`[${repoName}] ${action}`);
+    }
+    for (const skip of skipped) {
+      allSkipped.push(`[${repoName}] ${skip}`);
+    }
+    allWarnings = [...allWarnings, ...serverResponse.warnings];
+    printStatus(`${repoName} initialized`);
+  }
+  if (firstResponse) {
+    const existing = await readWorkspaceFile(parentDir);
+    if (existing) {
+      allSkipped.push(".flydocs-workspace.json (already exists)");
+    } else {
+      const workspaceFile = buildWorkspaceFile(
+        firstResponse.workspaceId,
+        repos
+      );
+      await writeWorkspaceFile(parentDir, workspaceFile);
+      allActions.push(`.flydocs-workspace.json (${repoNames.length} repos)`);
+    }
+    const contextDir = join19(parentDir, "flydocs", "context");
+    const workspaceMdPath = join19(contextDir, "workspace.md");
+    if (await pathExists(workspaceMdPath)) {
+      allSkipped.push("flydocs/context/workspace.md (already exists)");
+    } else {
+      await mkdir9(contextDir, { recursive: true });
+      const workspaceJson = await readWorkspaceFile(parentDir) ?? buildWorkspaceFile(firstResponse.workspaceId, repos);
+      const content = firstResponse.context?.workspaceMd ?? await generateWorkspaceMd(parentDir, workspaceJson);
+      await writeFile12(workspaceMdPath, content, "utf-8");
+      const source = firstResponse.context?.workspaceMd ? "from server" : "generated locally";
+      allActions.push(`Wrote flydocs/context/workspace.md (${source})`);
+    }
+  }
+  console.log();
+  printInitReport(allActions, allSkipped, allWarnings);
+}
+function printInitReport(actions, skipped, warnings) {
+  console.log();
+  const lines = [];
+  for (const action of actions) {
+    lines.push(`${pc7.green("+")} ${action}`);
+  }
+  for (const skip of skipped) {
+    lines.push(`${pc7.dim("-")} ${skip}`);
+  }
+  if (warnings.length > 0) {
+    lines.push("");
+    for (const warning of warnings) {
+      lines.push(`${pc7.yellow("!")} ${warning}`);
+    }
+  }
+  printCompletionBox("FlyDocs Initialized", lines);
+  console.log();
+  console.log(`  Next steps:`);
+  console.log(
+    `    ${pc7.cyan("flydocs sync")}    \u2014 pull latest config and templates`
+  );
+  console.log(`    ${pc7.cyan("/start-session")} \u2014 begin working`);
+  console.log();
+}
+var init_default;
+var init_init = __esm({
+  "src/commands/init.ts"() {
+    "use strict";
+    init_ui();
+    init_api_key();
+    init_global_config();
+    init_config();
+    init_config_integrity();
+    init_gitignore();
+    init_fs_ops();
+    init_relay_client();
+    init_workspace();
+    init_default = defineCommand2({
+      meta: {
+        name: "init",
+        description: "Initialize FlyDocs in this project (unified setup)"
+      },
+      args: {
+        key: {
+          type: "string",
+          description: "FlyDocs API key (fdk_...)"
+        },
+        path: {
+          type: "string",
+          description: "Path to project directory"
+        }
+      },
+      async run({ args }) {
+        const targetDir = args.path ?? process.cwd();
+        console.log();
+        console.log(`  ${pc7.bold("FlyDocs Init")}`);
+        console.log();
+        if (await isParentDirectory(targetDir)) {
+          await runMultiRepoInit(targetDir, args.key);
+          return;
+        }
+        const apiKey = await resolveAndValidateKey(args.key, targetDir);
+        const serverResponse = await pullServerConfig(apiKey, targetDir);
+        const { actions, skipped } = await initSingleRepo(
+          targetDir,
+          apiKey,
+          serverResponse
+        );
+        actions.unshift("Stored credential globally (~/.flydocs/credentials)");
+        const topology = serverResponse.config.topology;
+        if (topology?.type === 4 && topology.label === "sibling-repos") {
+          const parentDir = join19(targetDir, "..");
+          const existing = await readWorkspaceFile(parentDir);
+          if (existing) {
+            skipped.push(".flydocs-workspace.json (already exists)");
+          } else {
+            const repos = await detectSiblingRepos(parentDir);
+            if (Object.keys(repos).length > 0) {
+              const workspaceFile = buildWorkspaceFile(
+                serverResponse.workspaceId,
+                repos
+              );
+              await writeWorkspaceFile(parentDir, workspaceFile);
+              actions.push(
+                `.flydocs-workspace.json (${Object.keys(repos).length} repos detected)`
+              );
+            }
+          }
+        }
+        printInitReport(actions, skipped, serverResponse.warnings);
+      }
+    });
+  }
+});
+
 // src/commands/update.ts
 var update_exports = {};
 __export(update_exports, {
   default: () => update_default
 });
-import { defineCommand as defineCommand2 } from "citty";
-import { resolve as resolve3, join as join17 } from "path";
-import { mkdir as mkdir8, cp as cp2, readFile as readFile12, readdir as readdir4, rm as rm4 } from "fs/promises";
-import { select as select2, text as text2, confirm as confirm3, isCancel as isCancel4, cancel as cancel3 } from "@clack/prompts";
-import pc7 from "picocolors";
+import { defineCommand as defineCommand3 } from "citty";
+import { resolve as resolve4, join as join20 } from "path";
+import { mkdir as mkdir10, cp as cp2, readFile as readFile14, readdir as readdir5, rm as rm4 } from "fs/promises";
+import { select as select2, text as text3, confirm as confirm4, isCancel as isCancel5, cancel as cancel4 } from "@clack/prompts";
+import pc8 from "picocolors";
 var update_default;
 var init_update = __esm({
   "src/commands/update.ts"() {
@@ -2787,7 +3466,7 @@ var init_update = __esm({
     init_update_check();
     init_telemetry();
     init_integrity();
-    update_default = defineCommand2({
+    update_default = defineCommand3({
       meta: {
         name: "update",
         description: "Update an existing FlyDocs installation"
@@ -2832,7 +3511,7 @@ var init_update = __esm({
         await capture("update_started", { template_version: version });
         let targetDir;
         if (args.path) {
-          targetDir = resolve3(args.path.replace(/^~/, process.env.HOME ?? "~"));
+          targetDir = resolve4(args.path.replace(/^~/, process.env.HOME ?? "~"));
         } else if (args.here) {
           targetDir = process.cwd();
         } else {
@@ -2849,21 +3528,21 @@ var init_update = __esm({
               }
             ]
           });
-          if (isCancel4(choice)) {
-            cancel3("Update cancelled.");
+          if (isCancel5(choice)) {
+            cancel4("Update cancelled.");
             process.exit(0);
           }
           if (choice === "cwd") {
             targetDir = process.cwd();
           } else {
-            const enteredPath = await text2({
+            const enteredPath = await text3({
               message: "Enter project path:"
             });
-            if (isCancel4(enteredPath)) {
-              cancel3("Update cancelled.");
+            if (isCancel5(enteredPath)) {
+              cancel4("Update cancelled.");
               process.exit(0);
             }
-            targetDir = resolve3(
+            targetDir = resolve4(
               enteredPath.replace(/^~/, process.env.HOME ?? "~")
             );
           }
@@ -2872,11 +3551,11 @@ var init_update = __esm({
           printError(`Directory does not exist: ${targetDir}`);
           process.exit(1);
         }
-        targetDir = resolve3(targetDir);
+        targetDir = resolve4(targetDir);
         process.chdir(targetDir);
-        const hasVersion = await pathExists(join17(targetDir, ".flydocs", "version"));
+        const hasVersion = await pathExists(join20(targetDir, ".flydocs", "version"));
         const hasConfig = await pathExists(
-          join17(targetDir, ".flydocs", "config.json")
+          join20(targetDir, ".flydocs", "config.json")
         );
         if (!hasVersion && !hasConfig) {
           printError(`Not a FlyDocs project: ${targetDir}`);
@@ -2887,8 +3566,8 @@ var init_update = __esm({
         console.log();
         let currentVersion = "0.1.0";
         if (hasVersion) {
-          const vContent = await readFile12(
-            join17(targetDir, ".flydocs", "version"),
+          const vContent = await readFile14(
+            join20(targetDir, ".flydocs", "version"),
             "utf-8"
           );
           currentVersion = vContent.trim();
@@ -2907,10 +3586,10 @@ var init_update = __esm({
           printWarning(
             `Project version (${currentVersion}) is newer than installer (${version})`
           );
-          const shouldContinue = await confirm3({
+          const shouldContinue = await confirm4({
             message: "Continue anyway?"
           });
-          if (isCancel4(shouldContinue) || !shouldContinue) {
+          if (isCancel5(shouldContinue) || !shouldContinue) {
             process.exit(0);
           }
         }
@@ -2922,10 +3601,10 @@ var init_update = __esm({
         });
         console.log(`Updating: v${currentVersion} \u2192 v${version}`);
         console.log();
-        const changelogPath = join17(templateDir, "CHANGELOG.md");
+        const changelogPath = join20(templateDir, "CHANGELOG.md");
         const whatsNew = await getWhatsNew(changelogPath, currentVersion, version);
         if (whatsNew.length > 0) {
-          console.log(pc7.cyan("What's new:"));
+          console.log(pc8.cyan("What's new:"));
           console.log();
           for (const entry of whatsNew) {
             console.log(`  ${entry}`);
@@ -2934,23 +3613,23 @@ var init_update = __esm({
         }
         const now = /* @__PURE__ */ new Date();
         const ts = `${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")}${String(now.getSeconds()).padStart(2, "0")}`;
-        const backupDir = join17(targetDir, ".flydocs", `backup-${ts}`);
-        await mkdir8(backupDir, { recursive: true });
+        const backupDir = join20(targetDir, ".flydocs", `backup-${ts}`);
+        await mkdir10(backupDir, { recursive: true });
         if (hasConfig) {
           await cp2(
-            join17(targetDir, ".flydocs", "config.json"),
-            join17(backupDir, "config.json")
+            join20(targetDir, ".flydocs", "config.json"),
+            join20(backupDir, "config.json")
           );
           printStatus(`Config backed up to .flydocs/backup-${ts}/`);
         }
         try {
-          const flydocsDir = join17(targetDir, ".flydocs");
-          const entries = await readdir4(flydocsDir);
+          const flydocsDir = join20(targetDir, ".flydocs");
+          const entries = await readdir5(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 rm4(join17(flydocsDir, old), { recursive: true, force: true });
+              await rm4(join20(flydocsDir, old), { recursive: true, force: true });
             }
           }
         } catch {
@@ -2989,17 +3668,17 @@ var init_update = __esm({
         await ensureDirectories(targetDir, effectiveTier);
         console.log("Replacing framework directories...");
         await replaceDirectory(
-          join17(templateDir, ".flydocs", "templates"),
-          join17(targetDir, ".flydocs", "templates")
+          join20(templateDir, ".flydocs", "templates"),
+          join20(targetDir, ".flydocs", "templates")
         );
         printStatus(".flydocs/templates");
         await replaceDirectory(
-          join17(templateDir, ".claude", "hooks"),
-          join17(targetDir, ".claude", "hooks")
+          join20(templateDir, ".claude", "hooks"),
+          join20(targetDir, ".claude", "hooks")
         );
         printStatus(".claude/hooks");
         const hasExistingAgents = await pathExists(
-          join17(targetDir, ".claude", "agents")
+          join20(targetDir, ".claude", "agents")
         );
         let installAgents;
         if (args.yes) {
@@ -3008,7 +3687,7 @@ var init_update = __esm({
           installAgents = true;
         } else {
           console.log();
-          console.log(`  ${pc7.bold(pc7.yellow("Sub-Agents (Recommended)"))}`);
+          console.log(`  ${pc8.bold(pc8.yellow("Sub-Agents (Recommended)"))}`);
           console.log();
           console.log(
             "  Sub-agents are specialized roles (PM, implementation, review,"
@@ -3020,31 +3699,31 @@ var init_update = __esm({
             "  structure work but are not required \u2014 everything works without them."
           );
           console.log();
-          const agentConfirm = await confirm3({
+          const agentConfirm = await confirm4({
             message: "Install sub-agents?",
             initialValue: true
           });
-          if (isCancel4(agentConfirm)) {
+          if (isCancel5(agentConfirm)) {
             installAgents = false;
           } else {
             installAgents = agentConfirm;
           }
         }
         if (installAgents) {
-          const claudeAgentsSrc = join17(templateDir, ".claude", "agents");
+          const claudeAgentsSrc = join20(templateDir, ".claude", "agents");
           if (await pathExists(claudeAgentsSrc)) {
-            await mkdir8(join17(targetDir, ".claude", "agents"), { recursive: true });
+            await mkdir10(join20(targetDir, ".claude", "agents"), { recursive: true });
             await copyDirectoryContents(
               claudeAgentsSrc,
-              join17(targetDir, ".claude", "agents")
+              join20(targetDir, ".claude", "agents")
             );
           }
-          const cursorAgentsSrc = join17(templateDir, ".cursor", "agents");
+          const cursorAgentsSrc = join20(templateDir, ".cursor", "agents");
           if (await pathExists(cursorAgentsSrc)) {
-            await mkdir8(join17(targetDir, ".cursor", "agents"), { recursive: true });
+            await mkdir10(join20(targetDir, ".cursor", "agents"), { recursive: true });
             await copyDirectoryContents(
               cursorAgentsSrc,
-              join17(targetDir, ".cursor", "agents")
+              join20(targetDir, ".cursor", "agents")
             );
           }
           printStatus(
@@ -3058,58 +3737,58 @@ var init_update = __esm({
         console.log();
         console.log("Replacing framework files...");
         await copyFile(
-          join17(templateDir, ".claude", "CLAUDE.md"),
-          join17(targetDir, ".claude", "CLAUDE.md")
+          join20(templateDir, ".claude", "CLAUDE.md"),
+          join20(targetDir, ".claude", "CLAUDE.md")
         );
         await copyFile(
-          join17(templateDir, ".claude", "settings.json"),
-          join17(targetDir, ".claude", "settings.json")
+          join20(templateDir, ".claude", "settings.json"),
+          join20(targetDir, ".claude", "settings.json")
         );
         printStatus(".claude/CLAUDE.md, settings.json");
         await copyDirectoryContents(
-          join17(templateDir, ".claude", "commands"),
-          join17(targetDir, ".claude", "commands")
+          join20(templateDir, ".claude", "commands"),
+          join20(targetDir, ".claude", "commands")
         );
         await copyDirectoryContents(
-          join17(templateDir, ".claude", "commands"),
-          join17(targetDir, ".cursor", "commands")
+          join20(templateDir, ".claude", "commands"),
+          join20(targetDir, ".cursor", "commands")
         );
         printStatus(".claude/commands, .cursor/commands");
-        const skillsReadmeSrc = join17(templateDir, ".claude", "skills", "README.md");
+        const skillsReadmeSrc = join20(templateDir, ".claude", "skills", "README.md");
         if (await pathExists(skillsReadmeSrc)) {
           await copyFile(
             skillsReadmeSrc,
-            join17(targetDir, ".claude", "skills", "README.md")
+            join20(targetDir, ".claude", "skills", "README.md")
           );
         }
         printStatus(".claude/skills/README.md");
         await copyFile(
-          join17(templateDir, ".cursor", "hooks.json"),
-          join17(targetDir, ".cursor", "hooks.json")
+          join20(templateDir, ".cursor", "hooks.json"),
+          join20(targetDir, ".cursor", "hooks.json")
         );
         printStatus(".cursor/hooks.json");
         await copyFile(
-          join17(templateDir, "AGENTS.md"),
-          join17(targetDir, "AGENTS.md")
+          join20(templateDir, "AGENTS.md"),
+          join20(targetDir, "AGENTS.md")
         );
         printStatus("AGENTS.md");
-        const envExampleSrc = join17(templateDir, ".env.example");
+        const envExampleSrc = join20(templateDir, ".env.example");
         if (await pathExists(envExampleSrc)) {
-          await copyFile(envExampleSrc, join17(targetDir, ".env.example"));
+          await copyFile(envExampleSrc, join20(targetDir, ".env.example"));
           printStatus(".env.example");
         }
-        const knowledgeTemplatesDir = join17(
+        const knowledgeTemplatesDir = join20(
           targetDir,
           "flydocs",
           "knowledge",
           "templates"
         );
         if (!await pathExists(knowledgeTemplatesDir)) {
-          await mkdir8(knowledgeTemplatesDir, { recursive: true });
+          await mkdir10(knowledgeTemplatesDir, { recursive: true });
         }
         for (const tmpl of ["decision.md", "feature.md", "note.md"]) {
-          const src = join17(templateDir, "flydocs", "knowledge", "templates", tmpl);
-          const dest = join17(knowledgeTemplatesDir, tmpl);
+          const src = join20(templateDir, "flydocs", "knowledge", "templates", tmpl);
+          const dest = join20(knowledgeTemplatesDir, tmpl);
           if (await pathExists(src) && !await pathExists(dest)) {
             await copyFile(src, dest);
           }
@@ -3136,18 +3815,18 @@ var init_update = __esm({
           printWarning("Config merge failed \u2014 config.json preserved as-is");
         }
         await copyFile(
-          join17(templateDir, ".flydocs", "version"),
-          join17(targetDir, ".flydocs", "version")
+          join20(templateDir, ".flydocs", "version"),
+          join20(targetDir, ".flydocs", "version")
         );
         printStatus(`.flydocs/version \u2192 ${version}`);
-        const clSrc = join17(templateDir, "CHANGELOG.md");
+        const clSrc = join20(templateDir, "CHANGELOG.md");
         if (await pathExists(clSrc)) {
-          await copyFile(clSrc, join17(targetDir, ".flydocs", "CHANGELOG.md"));
+          await copyFile(clSrc, join20(targetDir, ".flydocs", "CHANGELOG.md"));
           printStatus(".flydocs/CHANGELOG.md");
         }
-        const mfSrc = join17(templateDir, "manifest.json");
+        const mfSrc = join20(templateDir, "manifest.json");
         if (await pathExists(mfSrc)) {
-          await copyFile(mfSrc, join17(targetDir, ".flydocs", "manifest.json"));
+          await copyFile(mfSrc, join20(targetDir, ".flydocs", "manifest.json"));
           printStatus(".flydocs/manifest.json");
         }
         await generateIntegrity(targetDir, version);
@@ -3209,22 +3888,22 @@ var uninstall_exports = {};
 __export(uninstall_exports, {
   default: () => uninstall_default
 });
-import { defineCommand as defineCommand3 } from "citty";
-import { resolve as resolve4, join as join18 } from "path";
-import { readdir as readdir5, rm as rm5, rename as rename2 } from "fs/promises";
-import { confirm as confirm4, select as select3, isCancel as isCancel5, cancel as cancel4 } from "@clack/prompts";
-import pc8 from "picocolors";
+import { defineCommand as defineCommand4 } from "citty";
+import { resolve as resolve5, join as join21 } from "path";
+import { readdir as readdir6, rm as rm5, rename as rename2 } from "fs/promises";
+import { confirm as confirm5, select as select3, isCancel as isCancel6, cancel as cancel5 } from "@clack/prompts";
+import pc9 from "picocolors";
 async function removeOwnedSkills(targetDir) {
-  const skillsDir = join18(targetDir, ".claude", "skills");
+  const skillsDir = join21(targetDir, ".claude", "skills");
   const removed = [];
   if (!await pathExists(skillsDir)) {
     return removed;
   }
   try {
-    const entries = await readdir5(skillsDir);
+    const entries = await readdir6(skillsDir);
     for (const entry of entries) {
       if (entry.startsWith(OWNED_SKILL_PREFIX)) {
-        await rm5(join18(skillsDir, entry), { recursive: true, force: true });
+        await rm5(join21(skillsDir, entry), { recursive: true, force: true });
         removed.push(`.claude/skills/${entry}`);
       }
     }
@@ -3233,16 +3912,16 @@ async function removeOwnedSkills(targetDir) {
   return removed;
 }
 async function removeOwnedCursorRules(targetDir) {
-  const rulesDir = join18(targetDir, ".cursor", "rules");
+  const rulesDir = join21(targetDir, ".cursor", "rules");
   const removed = [];
   if (!await pathExists(rulesDir)) {
     return removed;
   }
   try {
-    const entries = await readdir5(rulesDir);
+    const entries = await readdir6(rulesDir);
     for (const entry of entries) {
       if (entry.startsWith(OWNED_RULE_PREFIX) && entry.endsWith(".mdc")) {
-        await rm5(join18(rulesDir, entry), { force: true });
+        await rm5(join21(rulesDir, entry), { force: true });
         removed.push(`.cursor/rules/${entry}`);
       }
     }
@@ -3252,7 +3931,7 @@ async function removeOwnedCursorRules(targetDir) {
 }
 async function isEmptyDir(dirPath) {
   try {
-    const entries = await readdir5(dirPath);
+    const entries = await readdir6(dirPath);
     return entries.length === 0;
   } catch {
     return false;
@@ -3261,7 +3940,7 @@ async function isEmptyDir(dirPath) {
 async function cleanupEmptyParents(targetDir, dirs) {
   const cleaned = [];
   for (const dir of dirs) {
-    const fullPath = join18(targetDir, dir);
+    const fullPath = join21(targetDir, dir);
     if (await pathExists(fullPath) && await isEmptyDir(fullPath)) {
       await rm5(fullPath, { recursive: true, force: true });
       cleaned.push(dir);
@@ -3293,7 +3972,7 @@ var init_uninstall = __esm({
     ];
     OWNED_SKILL_PREFIX = "flydocs-";
     OWNED_RULE_PREFIX = "flydocs-";
-    uninstall_default = defineCommand3({
+    uninstall_default = defineCommand4({
       meta: {
         name: "uninstall",
         description: "Remove FlyDocs from a project directory"
@@ -3329,7 +4008,7 @@ var init_uninstall = __esm({
         printBanner(CLI_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 {
@@ -3339,9 +4018,9 @@ var init_uninstall = __esm({
           printError(`Directory does not exist: ${targetDir}`);
           process.exit(1);
         }
-        targetDir = resolve4(targetDir);
-        const hasFlydocs = await pathExists(join18(targetDir, ".flydocs"));
-        const hasAgentsMd = await pathExists(join18(targetDir, "AGENTS.md"));
+        targetDir = resolve5(targetDir);
+        const hasFlydocs = await pathExists(join21(targetDir, ".flydocs"));
+        const hasAgentsMd = await pathExists(join21(targetDir, "AGENTS.md"));
         if (!hasFlydocs && !hasAgentsMd) {
           printError(`Not a FlyDocs project: ${targetDir}`);
           printInfo("No .flydocs/ directory or AGENTS.md found.");
@@ -3353,7 +4032,7 @@ var init_uninstall = __esm({
         const removeAll = forceAll || args.all;
         const skipPrompts = forceAll || args.yes;
         let contentAction = "preserve";
-        const hasUserContent = await pathExists(join18(targetDir, "flydocs"));
+        const hasUserContent = await pathExists(join21(targetDir, "flydocs"));
         if (hasUserContent) {
           if (removeAll) {
             contentAction = "remove";
@@ -3378,8 +4057,8 @@ var init_uninstall = __esm({
                 }
               ]
             });
-            if (isCancel5(choice)) {
-              cancel4("Uninstall cancelled.");
+            if (isCancel6(choice)) {
+              cancel5("Uninstall cancelled.");
               process.exit(0);
             }
             contentAction = choice;
@@ -3387,40 +4066,40 @@ var init_uninstall = __esm({
         }
         if (!skipPrompts) {
           console.log();
-          console.log(pc8.bold("The following will be removed:"));
+          console.log(pc9.bold("The following will be removed:"));
           console.log();
           console.log("  Framework files:");
           for (const [path] of ALWAYS_REMOVED) {
-            console.log(`    ${pc8.dim(path)}`);
+            console.log(`    ${pc9.dim(path)}`);
           }
-          console.log(`    ${pc8.dim(".claude/skills/flydocs-*")}`);
-          console.log(`    ${pc8.dim(".cursor/rules/flydocs-*.mdc")}`);
+          console.log(`    ${pc9.dim(".claude/skills/flydocs-*")}`);
+          console.log(`    ${pc9.dim(".cursor/rules/flydocs-*.mdc")}`);
           if (hasUserContent) {
             if (contentAction === "archive") {
               console.log();
               console.log(
-                `  User content: ${pc8.yellow("flydocs/ -> flydocs-archive/")}`
+                `  User content: ${pc9.yellow("flydocs/ -> flydocs-archive/")}`
               );
             } else if (contentAction === "remove") {
               console.log();
-              console.log(`  User content: ${pc8.red("flydocs/ (deleted)")}`);
+              console.log(`  User content: ${pc9.red("flydocs/ (deleted)")}`);
             } else {
               console.log();
-              console.log(`  User content: ${pc8.green("flydocs/ (preserved)")}`);
+              console.log(`  User content: ${pc9.green("flydocs/ (preserved)")}`);
             }
           }
           console.log();
-          console.log(pc8.bold("Preserved:"));
+          console.log(pc9.bold("Preserved:"));
           console.log(
-            `    ${pc8.dim(".claude/skills/ (non-flydocs community skills)")}`
+            `    ${pc9.dim(".claude/skills/ (non-flydocs community skills)")}`
           );
-          console.log(`    ${pc8.dim(".env, .env.local")}`);
+          console.log(`    ${pc9.dim(".env, .env.local")}`);
           console.log();
-          const shouldContinue = await confirm4({
+          const shouldContinue = await confirm5({
             message: "Proceed with uninstall?"
           });
-          if (isCancel5(shouldContinue) || !shouldContinue) {
-            cancel4("Uninstall cancelled.");
+          if (isCancel6(shouldContinue) || !shouldContinue) {
+            cancel5("Uninstall cancelled.");
             process.exit(0);
           }
         }
@@ -3436,7 +4115,7 @@ var init_uninstall = __esm({
         const removedRules = await removeOwnedCursorRules(targetDir);
         result.removed.push(...removedRules);
         for (const [relativePath, type] of ALWAYS_REMOVED) {
-          const fullPath = join18(targetDir, relativePath);
+          const fullPath = join21(targetDir, relativePath);
           if (!await pathExists(fullPath)) {
             result.skipped.push(relativePath);
             continue;
@@ -3454,9 +4133,9 @@ var init_uninstall = __esm({
           }
         }
         if (hasUserContent) {
-          const flydocsPath = join18(targetDir, "flydocs");
+          const flydocsPath = join21(targetDir, "flydocs");
           if (contentAction === "archive") {
-            const archivePath = join18(targetDir, "flydocs-archive");
+            const archivePath = join21(targetDir, "flydocs-archive");
             if (await pathExists(archivePath)) {
               await rm5(archivePath, { recursive: true, force: true });
             }
@@ -3482,17 +4161,17 @@ var init_uninstall = __esm({
           result.restored = originals.map((f) => f.relativePath);
         }
         console.log();
-        console.log(pc8.bold("Uninstall Summary"));
+        console.log(pc9.bold("Uninstall Summary"));
         console.log();
         if (result.removed.length > 0) {
-          console.log(`  ${pc8.green("Removed")} (${result.removed.length}):`);
+          console.log(`  ${pc9.green("Removed")} (${result.removed.length}):`);
           for (const item of result.removed) {
             printStatus(item);
           }
         }
         if (result.archived.length > 0) {
           console.log();
-          console.log(`  ${pc8.yellow("Archived")} (${result.archived.length}):`);
+          console.log(`  ${pc9.yellow("Archived")} (${result.archived.length}):`);
           for (const item of result.archived) {
             printInfo(item);
           }
@@ -3500,7 +4179,7 @@ var init_uninstall = __esm({
         if (result.restored.length > 0) {
           console.log();
           console.log(
-            `  ${pc8.green("Restored")} (${result.restored.length} pre-FlyDocs original(s)):`
+            `  ${pc9.green("Restored")} (${result.restored.length} pre-FlyDocs original(s)):`
           );
           for (const item of result.restored) {
             printInfo(item);
@@ -3509,16 +4188,16 @@ var init_uninstall = __esm({
         if (result.skipped.length > 0) {
           console.log();
           console.log(
-            `  ${pc8.dim("Skipped")} (${result.skipped.length} \u2014 not found):`
+            `  ${pc9.dim("Skipped")} (${result.skipped.length} \u2014 not found):`
           );
           for (const item of result.skipped) {
-            console.log(`  ${pc8.dim(item)}`);
+            console.log(`  ${pc9.dim(item)}`);
           }
         }
         console.log();
         printStatus("FlyDocs has been removed from this project.");
         console.log();
-        printInfo(`To reinstall: ${pc8.cyan("npx @flydocs/cli install --here")}`);
+        printInfo(`To reinstall: ${pc9.cyan("npx @flydocs/cli install --here")}`);
         console.log();
       }
     });
@@ -3530,28 +4209,28 @@ var setup_exports = {};
 __export(setup_exports, {
   default: () => setup_default
 });
-import { defineCommand as defineCommand4 } from "citty";
-import pc9 from "picocolors";
+import { defineCommand as defineCommand5 } from "citty";
+import pc10 from "picocolors";
 var setup_default;
 var init_setup = __esm({
   "src/commands/setup.ts"() {
     "use strict";
-    setup_default = defineCommand4({
+    setup_default = defineCommand5({
       meta: {
         name: "setup",
         description: "Configure FlyDocs settings for this project"
       },
       run() {
         console.log();
-        console.log(`  ${pc9.bold("FlyDocs Setup")}`);
+        console.log(`  ${pc10.bold("FlyDocs Setup")}`);
         console.log();
         console.log(`  Setup runs inside your IDE as an interactive AI command.`);
         console.log();
         console.log(
-          `  ${pc9.cyan("Claude Code:")}  Type ${pc9.bold("/flydocs-setup")} in chat`
+          `  ${pc10.cyan("Claude Code:")}  Type ${pc10.bold("/flydocs-setup")} in chat`
         );
         console.log(
-          `  ${pc9.cyan("Cursor:")}      Type ${pc9.bold("/flydocs-setup")} in chat`
+          `  ${pc10.cyan("Cursor:")}      Type ${pc10.bold("/flydocs-setup")} in chat`
         );
         console.log();
         console.log(`  This configures your project context, detects your stack,`);
@@ -3567,14 +4246,14 @@ var skills_exports = {};
 __export(skills_exports, {
   default: () => skills_default
 });
-import { defineCommand as defineCommand5 } from "citty";
-import pc10 from "picocolors";
+import { defineCommand as defineCommand6 } from "citty";
+import pc11 from "picocolors";
 var list, search, add, remove, skills_default;
 var init_skills2 = __esm({
   "src/commands/skills.ts"() {
     "use strict";
     init_skill_manager();
-    list = defineCommand5({
+    list = defineCommand6({
       meta: {
         name: "list",
         description: "List installed skills"
@@ -3590,26 +4269,26 @@ var init_skills2 = __esm({
         console.log(`${total} skill(s) installed:`);
         if (result.platform.length > 0) {
           console.log();
-          console.log(pc10.bold("Platform"));
+          console.log(pc11.bold("Platform"));
           for (const skill of result.platform) {
             console.log(
-              `  ${skill.name} ${pc10.dim(`(${skill.triggers} triggers)`)}`
+              `  ${skill.name} ${pc11.dim(`(${skill.triggers} triggers)`)}`
             );
           }
         }
         if (result.community.length > 0) {
           console.log();
-          console.log(pc10.bold("Community"));
+          console.log(pc11.bold("Community"));
           for (const skill of result.community) {
             console.log(
-              `  ${skill.name} ${pc10.dim(`(${skill.triggers} triggers)`)}`
+              `  ${skill.name} ${pc11.dim(`(${skill.triggers} triggers)`)}`
             );
           }
         }
         console.log();
       }
     });
-    search = defineCommand5({
+    search = defineCommand6({
       meta: {
         name: "search",
         description: "Search community skills"
@@ -3625,24 +4304,24 @@ 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: ${pc10.cyan("https://skills.sh/")}`);
+          console.log(`  Browse the catalog at: ${pc11.cyan("https://skills.sh/")}`);
           return;
         }
         console.log();
         console.log(`${results.length} skill(s) matching "${args.keyword}":`);
         console.log();
         for (const skill of results) {
-          console.log(`  ${pc10.bold(skill.name)}`);
+          console.log(`  ${pc11.bold(skill.name)}`);
           console.log(`  ${skill.description}`);
-          console.log(`  ${pc10.dim(skill.repo)}`);
+          console.log(`  ${pc11.dim(skill.repo)}`);
           if (skill.tags.length > 0) {
-            console.log(`  ${pc10.dim(skill.tags.join(", "))}`);
+            console.log(`  ${pc11.dim(skill.tags.join(", "))}`);
           }
           console.log();
         }
       }
     });
-    add = defineCommand5({
+    add = defineCommand6({
       meta: {
         name: "add",
         description: "Install a community skill"
@@ -3658,7 +4337,7 @@ var init_skills2 = __esm({
         await addSkill(process.cwd(), args.source);
       }
     });
-    remove = defineCommand5({
+    remove = defineCommand6({
       meta: {
         name: "remove",
         description: "Remove an installed community skill"
@@ -3674,7 +4353,7 @@ var init_skills2 = __esm({
         await removeSkill(process.cwd(), args.name);
       }
     });
-    skills_default = defineCommand5({
+    skills_default = defineCommand6({
       meta: {
         name: "skills",
         description: "Manage FlyDocs skills (list, search, add, remove)"
@@ -3694,10 +4373,10 @@ var connect_exports = {};
 __export(connect_exports, {
   default: () => connect_default
 });
-import { defineCommand as defineCommand6 } from "citty";
-import { text as text3, confirm as confirm5, isCancel as isCancel6, cancel as cancel5 } from "@clack/prompts";
-import pc11 from "picocolors";
-import { join as join19 } from "path";
+import { defineCommand as defineCommand7 } from "citty";
+import { text as text4, confirm as confirm6, isCancel as isCancel7, cancel as cancel6 } from "@clack/prompts";
+import pc12 from "picocolors";
+import { join as join22 } from "path";
 var connect_default;
 var init_connect = __esm({
   "src/commands/connect.ts"() {
@@ -3707,7 +4386,7 @@ var init_connect = __esm({
     init_template();
     init_ui();
     init_api_key();
-    connect_default = defineCommand6({
+    connect_default = defineCommand7({
       meta: {
         name: "connect",
         description: "Connect FlyDocs to a cloud provider"
@@ -3732,11 +4411,11 @@ var init_connect = __esm({
       },
       async run({ args }) {
         const targetDir = args.path ?? process.cwd();
-        const configPath = join19(targetDir, ".flydocs", "config.json");
+        const configPath = join22(targetDir, ".flydocs", "config.json");
         if (!await pathExists(configPath)) {
           printError("Not a FlyDocs project (.flydocs/config.json not found).");
           console.log(
-            `  Run ${pc11.cyan("flydocs")} first to install FlyDocs in this project.`
+            `  Run ${pc12.cyan("flydocs")} first to install FlyDocs in this project.`
           );
           process.exit(1);
         }
@@ -3744,24 +4423,24 @@ var init_connect = __esm({
         if (config.tier === "cloud") {
           printInfo("This project is already connected to the cloud tier.");
           console.log();
-          const reconnect = await confirm5({
+          const reconnect = await confirm6({
             message: "Want to update your API key?"
           });
-          if (isCancel6(reconnect) || !reconnect) {
+          if (isCancel7(reconnect) || !reconnect) {
             console.log(`  No changes made.`);
             return;
           }
         }
         console.log();
-        console.log(`  ${pc11.bold("Connect to FlyDocs Cloud")}`);
+        console.log(`  ${pc12.bold("Connect to FlyDocs Cloud")}`);
         console.log();
         console.log(
-          `  ${pc11.dim("Get your API key (fdk_...) from your FlyDocs dashboard")}`
+          `  ${pc12.dim("Get your API key (fdk_...) from your FlyDocs dashboard")}`
         );
         console.log();
         let apiKey = args.key ?? "";
         if (!apiKey) {
-          const keyInput = await text3({
+          const keyInput = await text4({
             message: "Enter your API key",
             placeholder: "fdk_...",
             validate(value) {
@@ -3772,8 +4451,8 @@ var init_connect = __esm({
               return void 0;
             }
           });
-          if (isCancel6(keyInput)) {
-            cancel5("Connection cancelled.");
+          if (isCancel7(keyInput)) {
+            cancel6("Connection cancelled.");
             process.exit(0);
           }
           apiKey = keyInput.trim();
@@ -3794,7 +4473,7 @@ var init_connect = __esm({
               console.log(`  Check your key and try again.`);
               process.exit(1);
             }
-            printStatus(`Connected to ${pc11.bold(result.org)}`);
+            printStatus(`Connected to ${pc12.bold(result.org)}`);
           } catch {
             printError(
               "Could not reach relay API. Check your network and try again."
@@ -3802,7 +4481,7 @@ var init_connect = __esm({
             process.exit(1);
           }
           const envFile = await storeEnvKey(targetDir, "FLYDOCS_API_KEY", apiKey);
-          printStatus(`API key stored in ${pc11.dim(envFile)}`);
+          printStatus(`API key stored in ${pc12.dim(envFile)}`);
         } else {
           try {
             const result = await validateLinearKey(apiKey);
@@ -3812,7 +4491,7 @@ var init_connect = __esm({
               process.exit(1);
             }
             printStatus(
-              `Authenticated as ${pc11.bold(result.name)} (${result.email})`
+              `Authenticated as ${pc12.bold(result.name)} (${result.email})`
             );
           } catch {
             printError("Invalid API key or network error.");
@@ -3820,7 +4499,7 @@ var init_connect = __esm({
             process.exit(1);
           }
           const envFile = await storeEnvKey(targetDir, "LINEAR_API_KEY", apiKey);
-          printStatus(`API key stored in ${pc11.dim(envFile)}`);
+          printStatus(`API key stored in ${pc12.dim(envFile)}`);
         }
         const wasLocal = config.tier === "local";
         config.tier = "cloud";
@@ -3836,14 +4515,464 @@ var init_connect = __esm({
         }
         console.log();
         console.log(
-          `  ${pc11.bold("Connected!")} Your project is now on the cloud tier.`
+          `  ${pc12.bold("Connected!")} Your project is now on the cloud tier.`
         );
         console.log();
         console.log(`  Next steps:`);
         console.log(
-          `    1. Run ${pc11.cyan("/flydocs-setup")} in your IDE to configure your project`
+          `    1. Run ${pc12.cyan("/flydocs-setup")} in your IDE to configure your project`
         );
-        console.log(`    2. Run ${pc11.cyan("/start-session")} to begin working`);
+        console.log(`    2. Run ${pc12.cyan("/start-session")} to begin working`);
+        console.log();
+      }
+    });
+  }
+});
+
+// src/commands/auth.ts
+var auth_exports = {};
+__export(auth_exports, {
+  default: () => auth_default
+});
+import { defineCommand as defineCommand8 } from "citty";
+import { text as text5, confirm as confirm7, isCancel as isCancel8, cancel as cancel7 } from "@clack/prompts";
+import pc13 from "picocolors";
+var auth_default;
+var init_auth = __esm({
+  "src/commands/auth.ts"() {
+    "use strict";
+    init_ui();
+    init_api_key();
+    init_global_config();
+    auth_default = defineCommand8({
+      meta: {
+        name: "auth",
+        description: "Store API key globally (~/.flydocs/credentials)"
+      },
+      args: {
+        key: {
+          type: "positional",
+          description: "FlyDocs API key (fdk_...)",
+          required: false
+        }
+      },
+      async run({ args }) {
+        console.log();
+        console.log(`  ${pc13.bold("FlyDocs Authentication")}`);
+        console.log();
+        let apiKey = args.key ?? "";
+        const existing = await readGlobalCredential();
+        if (existing?.apiKey && !apiKey) {
+          printInfo(
+            `Existing key found: ${pc13.dim(existing.apiKey.slice(0, 8) + "...")}`
+          );
+          const replace = await confirm7({
+            message: "Replace with a new key?"
+          });
+          if (isCancel8(replace) || !replace) {
+            console.log(`  No changes made.`);
+            return;
+          }
+        }
+        if (!apiKey) {
+          console.log(
+            `  ${pc13.dim("Get your API key (fdk_...) from your FlyDocs dashboard")}`
+          );
+          console.log();
+          const keyInput = await text5({
+            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 (isCancel8(keyInput)) {
+            cancel7("Authentication cancelled.");
+            process.exit(0);
+          }
+          apiKey = keyInput.trim();
+        }
+        if (detectKeyType(apiKey) !== "relay") {
+          printError("Invalid key format. Expected fdk_ prefix (FlyDocs API key).");
+          process.exit(1);
+        }
+        if (existing?.apiKey === apiKey) {
+          printInfo("This key is already stored.");
+          await checkCredentialPermissions();
+          return;
+        }
+        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 ${pc13.bold(result.org)}`);
+        } catch {
+          printError(
+            "Could not reach FlyDocs API. Check your network and try again."
+          );
+          process.exit(1);
+        }
+        if (existing?.apiKey && existing.apiKey !== apiKey) {
+          printWarning("Replacing existing key.");
+        }
+        await writeGlobalCredential({
+          apiKey,
+          createdAt: (/* @__PURE__ */ new Date()).toISOString(),
+          lastValidated: (/* @__PURE__ */ new Date()).toISOString()
+        });
+        printStatus(`Key stored at ${pc13.dim(credentialsPath())}`);
+        await checkCredentialPermissions();
+        console.log();
+        console.log(`  ${pc13.bold("Authenticated!")} Key stored globally.`);
+        console.log(`  All FlyDocs projects on this machine will use this key.`);
+        console.log();
+      }
+    });
+  }
+});
+
+// src/commands/sync.ts
+var sync_exports = {};
+__export(sync_exports, {
+  default: () => sync_default
+});
+import { defineCommand as defineCommand9 } from "citty";
+import pc14 from "picocolors";
+import { join as join23 } from "path";
+import { mkdir as mkdir11, writeFile as writeFile13 } 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 = defineCommand9({
+      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;
+        let currentTemplateVersion = 0;
+        try {
+          const currentConfig = await readAnyConfig(targetDir);
+          if (isConfigV2(currentConfig)) {
+            currentTemplateVersion = currentConfig.configVersion ?? 0;
+          }
+        } catch {
+        }
+        let serverResponse;
+        try {
+          serverResponse = await fetchConfigV2(apiKey);
+        } catch (err) {
+          if (err instanceof RelayError) {
+            printWarning(
+              `Server unavailable (${err.status}), using cached config.`
+            );
+          } else {
+            printWarning("Server unreachable, using cached config.");
+          }
+          console.log(`  ${pc14.dim("Config may be stale. Retry when connected.")}`);
+          return;
+        }
+        if (!serverResponse.valid) {
+          printWarning("Server returned invalid config. Keeping current config.");
+          return;
+        }
+        await mkdir11(join23(targetDir, ".flydocs"), { recursive: true });
+        const configWithHash = applyConfigHash(serverResponse.config);
+        await writeConfig(targetDir, configWithHash);
+        changes.push("Updated .flydocs/config.json");
+        const serverTemplateVersion = serverResponse.templates.version;
+        if (serverTemplateVersion > currentTemplateVersion) {
+          try {
+            const templatesResponse = await fetchTemplates(
+              apiKey,
+              currentTemplateVersion
+            );
+            if (templatesResponse.templates.length > 0) {
+              const templatesDir = join23(
+                targetDir,
+                ".claude",
+                "skills",
+                "flydocs-workflow",
+                "templates"
+              );
+              await mkdir11(templatesDir, { recursive: true });
+              for (const template of templatesResponse.templates) {
+                const filename = `${template.type}.md`;
+                const subdir = template.category === "issue" ? "issues" : template.category === "pr" ? "pr" : template.category === "comment" ? "." : ".";
+                const templateDir = join23(templatesDir, subdir);
+                await mkdir11(templateDir, { recursive: true });
+                await writeFile13(
+                  join23(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/cleanup.ts
+var cleanup_exports = {};
+__export(cleanup_exports, {
+  default: () => cleanup_default
+});
+import { defineCommand as defineCommand10 } from "citty";
+import pc15 from "picocolors";
+import { join as join24 } from "path";
+import { readFile as readFile15, writeFile as writeFile14, rm as rm6 } from "fs/promises";
+async function scanArtifacts(targetDir) {
+  const actions = [];
+  const localMePath = join24(targetDir, ".flydocs", "me.json");
+  if (await pathExists(localMePath) && await pathExists(globalMePath())) {
+    actions.push({
+      description: "Remove .flydocs/me.json (migrated to ~/.flydocs/me.json)",
+      path: localMePath,
+      type: "file"
+    });
+  }
+  const validationCachePath = join24(
+    targetDir,
+    ".flydocs",
+    "validation-cache.json"
+  );
+  if (await pathExists(validationCachePath)) {
+    actions.push({
+      description: "Remove .flydocs/validation-cache.json (replaced by configVersion)",
+      path: validationCachePath,
+      type: "file"
+    });
+  }
+  const hasGlobalCreds = await pathExists(credentialsPath());
+  for (const envFile of [".env", ".env.local"]) {
+    const envPath = join24(targetDir, envFile);
+    if (!await pathExists(envPath)) continue;
+    const content = await readFile15(envPath, "utf-8");
+    const lines = content.split("\n");
+    for (const line of lines) {
+      const trimmed = line.trim();
+      if (hasGlobalCreds && trimmed.startsWith("FLYDOCS_API_KEY=")) {
+        actions.push({
+          description: `Remove FLYDOCS_API_KEY from ${envFile} (migrated to ~/.flydocs/credentials)`,
+          path: envPath,
+          type: "line"
+        });
+      }
+      if (trimmed.startsWith("FLYDOCS_RELAY_URL=")) {
+        actions.push({
+          description: `Remove FLYDOCS_RELAY_URL from ${envFile}`,
+          path: envPath,
+          type: "line"
+        });
+      }
+    }
+  }
+  try {
+    const config = await readAnyConfig(targetDir);
+    const rawContent = await readFile15(
+      join24(targetDir, ".flydocs", "config.json"),
+      "utf-8"
+    );
+    const raw = JSON.parse(rawContent);
+    const ghostFields = ["provider", "statusMapping"];
+    for (const field of ghostFields) {
+      if (field in raw) {
+        actions.push({
+          description: `Remove ghost field "${field}" from config.json`,
+          path: join24(targetDir, ".flydocs", "config.json"),
+          type: "field"
+        });
+      }
+    }
+    if (isConfigV2(config)) {
+      const v1OnlyFields = [
+        "workspaceId",
+        "issueLabels",
+        "workspace",
+        "onboardComplete",
+        "sourceRepo",
+        "designSystem",
+        "aiLabor"
+      ];
+      for (const field of v1OnlyFields) {
+        if (field in raw) {
+          actions.push({
+            description: `Remove v1 field "${field}" from config.json (server-owned in v2)`,
+            path: join24(targetDir, ".flydocs", "config.json"),
+            type: "field"
+          });
+        }
+      }
+    }
+  } catch {
+  }
+  return actions;
+}
+async function executeCleanup(targetDir, actions) {
+  const fileRemovals = actions.filter((a) => a.type === "file");
+  const lineRemovals = actions.filter((a) => a.type === "line");
+  const fieldRemovals = actions.filter((a) => a.type === "field");
+  for (const action of fileRemovals) {
+    await rm6(action.path, { force: true });
+  }
+  const envFiles = /* @__PURE__ */ new Map();
+  for (const action of lineRemovals) {
+    if (!envFiles.has(action.path)) {
+      const content = await readFile15(action.path, "utf-8");
+      envFiles.set(action.path, content.split("\n"));
+    }
+  }
+  for (const [envPath, lines] of envFiles) {
+    const filtered = lines.filter((line) => {
+      const trimmed = line.trim();
+      return !trimmed.startsWith("FLYDOCS_API_KEY=") && !trimmed.startsWith("FLYDOCS_RELAY_URL=");
+    });
+    const hasContent = filtered.some(
+      (l) => l.trim().length > 0 && !l.trim().startsWith("#")
+    );
+    if (!hasContent) {
+      await rm6(envPath, { force: true });
+    } else {
+      await writeFile14(envPath, filtered.join("\n"), "utf-8");
+    }
+  }
+  if (fieldRemovals.length > 0) {
+    const configPath = join24(targetDir, ".flydocs", "config.json");
+    const content = await readFile15(configPath, "utf-8");
+    const config = JSON.parse(content);
+    for (const action of fieldRemovals) {
+      const match = action.description.match(/"(\w+)"/);
+      if (match) {
+        delete config[match[1]];
+      }
+    }
+    await writeFile14(
+      configPath,
+      JSON.stringify(config, null, 2) + "\n",
+      "utf-8"
+    );
+  }
+}
+var cleanup_default;
+var init_cleanup = __esm({
+  "src/commands/cleanup.ts"() {
+    "use strict";
+    init_ui();
+    init_fs_ops();
+    init_config();
+    init_types();
+    init_global_config();
+    cleanup_default = defineCommand10({
+      meta: {
+        name: "cleanup",
+        description: "Remove legacy v1 artifacts after migration (dry-run by default)"
+      },
+      args: {
+        confirm: {
+          type: "boolean",
+          description: "Actually remove artifacts (default: dry-run only)",
+          default: false
+        },
+        path: {
+          type: "string",
+          description: "Path to project directory"
+        }
+      },
+      async run({ args }) {
+        const targetDir = args.path ?? process.cwd();
+        console.log();
+        console.log(`  ${pc15.bold("FlyDocs Cleanup")}`);
+        console.log();
+        const hasConfig = await pathExists(
+          join24(targetDir, ".flydocs", "config.json")
+        );
+        if (!hasConfig) {
+          printError("No .flydocs/config.json found. Run flydocs init first.");
+          process.exit(1);
+        }
+        const hasGlobalCreds = await pathExists(credentialsPath());
+        if (!hasGlobalCreds) {
+          printWarning(
+            "No global credentials found. Run flydocs init to set up credentials before cleanup."
+          );
+        }
+        const actions = await scanArtifacts(targetDir);
+        if (actions.length === 0) {
+          printStatus("No legacy artifacts found. Already clean.");
+          console.log();
+          return;
+        }
+        const mode = args.confirm ? "Removing" : "Would remove";
+        printInfo(`${mode} ${actions.length} legacy artifact(s):`);
+        console.log();
+        for (const action of actions) {
+          const icon = args.confirm ? pc15.red("-") : pc15.yellow("?");
+          console.log(`  ${icon} ${action.description}`);
+        }
+        console.log();
+        if (!args.confirm) {
+          printInfo(
+            `Dry-run complete. Run ${pc15.cyan("flydocs cleanup --confirm")} to remove.`
+          );
+          console.log();
+          return;
+        }
+        await executeCleanup(targetDir, actions);
+        printCompletionBox("Cleanup Complete", [
+          `${pc15.green("+")} Removed ${actions.length} legacy artifact(s)`
+        ]);
         console.log();
       }
     });
@@ -3855,15 +4984,15 @@ var upgrade_exports = {};
 __export(upgrade_exports, {
   default: () => upgrade_default
 });
-import { defineCommand as defineCommand7 } from "citty";
-import pc12 from "picocolors";
+import { defineCommand as defineCommand11 } from "citty";
+import pc16 from "picocolors";
 var upgrade_default;
 var init_upgrade = __esm({
   "src/commands/upgrade.ts"() {
     "use strict";
     init_config();
     init_fs_ops();
-    upgrade_default = defineCommand7({
+    upgrade_default = defineCommand11({
       meta: {
         name: "upgrade",
         description: "Learn about FlyDocs Cloud tier and upgrade from local"
@@ -3892,34 +5021,34 @@ var init_upgrade = __esm({
         console.log();
         if (currentTier === "cloud") {
           console.log(
-            `  ${pc12.green("\u2713")} You're already on the ${pc12.bold("cloud")} tier.`
+            `  ${pc16.green("\u2713")} You're already on the ${pc16.bold("cloud")} tier.`
           );
           console.log();
           console.log(`  Your issues sync with your provider via the relay API.`);
           console.log(
-            `  Run ${pc12.cyan("flydocs connect")} to update your connection settings.`
+            `  Run ${pc16.cyan("flydocs connect")} to update your connection settings.`
           );
           console.log();
           return;
         }
-        console.log(`  ${pc12.bold("FlyDocs Cloud Tier")}`);
+        console.log(`  ${pc16.bold("FlyDocs Cloud Tier")}`);
         console.log();
-        console.log(`  You're currently on the ${pc12.yellow("local")} tier.`);
+        console.log(`  You're currently on the ${pc16.yellow("local")} tier.`);
         console.log(`  Upgrade to cloud for:`);
         console.log();
-        console.log(`    ${pc12.cyan("\u2192")} Issue sync with Linear, Jira, and more`);
-        console.log(`    ${pc12.cyan("\u2192")} Project milestones and cycle management`);
-        console.log(`    ${pc12.cyan("\u2192")} Team assignment and priority tracking`);
-        console.log(`    ${pc12.cyan("\u2192")} Project health updates and dashboards`);
-        console.log(`    ${pc12.cyan("\u2192")} Cross-project issue linking`);
+        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();
-        console.log(`  ${pc12.bold("How to upgrade:")}`);
+        console.log(`  ${pc16.bold("How to upgrade:")}`);
         console.log();
-        console.log(`    Option 1: Run ${pc12.cyan("/flydocs-upgrade")} in your IDE`);
+        console.log(`    Option 1: Run ${pc16.cyan("/flydocs-upgrade")} in your IDE`);
         console.log(`              Guided migration with issue transfer`);
         console.log();
         console.log(
-          `    Option 2: Run ${pc12.cyan("flydocs connect")} from terminal`
+          `    Option 2: Run ${pc16.cyan("flydocs connect")} from terminal`
         );
         console.log(`              Quick tier swap (no issue migration)`);
         console.log();
@@ -3933,23 +5062,23 @@ var self_update_exports = {};
 __export(self_update_exports, {
   default: () => self_update_default
 });
-import { defineCommand as defineCommand8 } from "citty";
+import { defineCommand as defineCommand12 } from "citty";
 import { execSync } from "child_process";
-import pc13 from "picocolors";
+import pc17 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 = defineCommand8({
+    self_update_default = defineCommand12({
       meta: {
         name: "self-update",
         description: "Update FlyDocs CLI to the latest version"
       },
       async run() {
         console.log();
-        console.log(`  Updating ${pc13.cyan(PACKAGE_NAME)}...`);
+        console.log(`  Updating ${pc17.cyan(PACKAGE_NAME)}...`);
         console.log();
         try {
           execSync(`npm install -g ${PACKAGE_NAME}@beta`, {
@@ -3974,15 +5103,15 @@ var telemetry_exports = {};
 __export(telemetry_exports, {
   default: () => telemetry_default
 });
-import { defineCommand as defineCommand9 } from "citty";
-import pc14 from "picocolors";
+import { defineCommand as defineCommand13 } from "citty";
+import pc18 from "picocolors";
 var enable, disable, status, telemetry_default;
 var init_telemetry2 = __esm({
   "src/commands/telemetry.ts"() {
     "use strict";
     init_telemetry();
     init_ui();
-    enable = defineCommand9({
+    enable = defineCommand13({
       meta: {
         name: "enable",
         description: "Enable anonymous usage analytics"
@@ -3997,7 +5126,7 @@ var init_telemetry2 = __esm({
         }
       }
     });
-    disable = defineCommand9({
+    disable = defineCommand13({
       meta: {
         name: "disable",
         description: "Disable anonymous usage analytics"
@@ -4015,7 +5144,7 @@ var init_telemetry2 = __esm({
         }
       }
     });
-    status = defineCommand9({
+    status = defineCommand13({
       meta: {
         name: "status",
         description: "Show current telemetry status"
@@ -4023,37 +5152,37 @@ var init_telemetry2 = __esm({
       async run() {
         const info = await getStatus();
         console.log();
-        console.log(pc14.bold("Telemetry Status"));
+        console.log(pc18.bold("Telemetry Status"));
         console.log();
         const effectivelyEnabled = info.enabled && !info.envOverride;
         console.log(
-          `  Enabled:        ${effectivelyEnabled ? pc14.green("yes") : pc14.yellow("no")}`
+          `  Enabled:        ${effectivelyEnabled ? pc18.green("yes") : pc18.yellow("no")}`
         );
         if (info.envOverride) {
           console.log(
-            `  Env override:   ${pc14.yellow("FLYDOCS_TELEMETRY=0 (disabled via env)")}`
+            `  Env override:   ${pc18.yellow("FLYDOCS_TELEMETRY=0 (disabled via env)")}`
           );
         }
         if (info.anonymousId) {
-          console.log(`  Anonymous ID:   ${pc14.dim(info.anonymousId)}`);
+          console.log(`  Anonymous ID:   ${pc18.dim(info.anonymousId)}`);
         } else {
           console.log(
-            `  Anonymous ID:   ${pc14.dim("(not yet created \u2014 generated on first run)")}`
+            `  Anonymous ID:   ${pc18.dim("(not yet created \u2014 generated on first run)")}`
           );
         }
         console.log();
         console.log(
-          pc14.dim(
+          pc18.dim(
             "  FlyDocs collects anonymous usage analytics to improve the CLI."
           )
         );
         console.log(
-          pc14.dim("  No personal data, file contents, or code is ever collected.")
+          pc18.dim("  No personal data, file contents, or code is ever collected.")
         );
         console.log();
       }
     });
-    telemetry_default = defineCommand9({
+    telemetry_default = defineCommand13({
       meta: {
         name: "telemetry",
         description: "Manage anonymous usage analytics (enable, disable, status)"
@@ -4069,14 +5198,18 @@ var init_telemetry2 = __esm({
 
 // src/cli.ts
 init_constants();
-import { defineCommand as defineCommand10, runMain } from "citty";
+import { defineCommand as defineCommand14, runMain } from "citty";
 var SUB_COMMANDS = /* @__PURE__ */ new Set([
   "install",
+  "init",
   "update",
   "uninstall",
   "setup",
   "skills",
   "connect",
+  "auth",
+  "sync",
+  "cleanup",
   "upgrade",
   "self-update",
   "telemetry"
@@ -4089,7 +5222,7 @@ var firstPositional = userArgs.find((a) => !a.startsWith("-"));
 if (!hasMetaFlag && (!firstPositional || !SUB_COMMANDS.has(firstPositional))) {
   process.argv.splice(2, 0, "install");
 }
-var main = defineCommand10({
+var main = defineCommand14({
   meta: {
     name: CLI_NAME,
     version: CLI_VERSION,
@@ -4097,11 +5230,15 @@ var main = defineCommand10({
   },
   subCommands: {
     install: () => Promise.resolve().then(() => (init_install(), install_exports)).then((m) => m.default),
+    init: () => Promise.resolve().then(() => (init_init(), init_exports)).then((m) => m.default),
     update: () => Promise.resolve().then(() => (init_update(), update_exports)).then((m) => m.default),
     uninstall: () => Promise.resolve().then(() => (init_uninstall(), uninstall_exports)).then((m) => m.default),
     setup: () => Promise.resolve().then(() => (init_setup(), setup_exports)).then((m) => m.default),
     skills: () => Promise.resolve().then(() => (init_skills2(), skills_exports)).then((m) => m.default),
     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),
+    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),
     telemetry: () => Promise.resolve().then(() => (init_telemetry2(), telemetry_exports)).then((m) => m.default)