@flydocs/cli 0.6.0-alpha.3 → 0.6.0-alpha.30

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.3";
+    CLI_VERSION = "0.6.0-alpha.30";
     CLI_NAME = "flydocs";
     PACKAGE_NAME = "@flydocs/cli";
     POSTHOG_API_KEY = "phc_v1MSJTQDFkMS90CBh3mxIz3v8bYCCnKU6v1ir6bz0Xn";
@@ -50,6 +50,7 @@ async function ensureDirectories(targetDir, tier) {
     "flydocs/knowledge/decisions",
     "flydocs/knowledge/notes",
     "flydocs/knowledge/product",
+    "flydocs/knowledge/templates",
     "flydocs/design-system"
   ];
   if (tier === "local") {
@@ -135,8 +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;
@@ -267,12 +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";
@@ -292,12 +351,13 @@ function extractPreservedValues(config) {
   return {
     tier: config.tier,
     setupComplete: config.setupComplete ?? false,
-    providerTeamId: config.provider?.teamId ?? null,
+    workspaceId: config.workspaceId ?? null,
+    configVersion: config.configVersion,
     workspace: config.workspace ?? {},
     issueLabels: config.issueLabels ?? {},
-    statusMapping: config.statusMapping ?? {},
     detectedStack: config.detectedStack ?? {},
     skills: config.skills ?? {},
+    topology: config.topology,
     designSystem: config.designSystem ?? null,
     aiLabor: config.aiLabor ?? {}
   };
@@ -311,11 +371,9 @@ async function mergeConfig(templateDir, version, tierFlag, preserved) {
   config.version = version;
   config.tier = tierFlag ?? preserved.tier;
   config.setupComplete = preserved.setupComplete;
-  if (preserved.providerTeamId !== null) {
-    if (!config.provider) {
-      config.provider = { type: "linear", teamId: null };
-    }
-    config.provider.teamId = preserved.providerTeamId;
+  config.workspaceId = preserved.workspaceId;
+  if (preserved.configVersion !== void 0) {
+    config.configVersion = preserved.configVersion;
   }
   if (Object.keys(preserved.workspace).length > 0) {
     config.workspace = preserved.workspace;
@@ -323,15 +381,15 @@ async function mergeConfig(templateDir, version, tierFlag, preserved) {
   if (Object.keys(preserved.issueLabels).length > 0) {
     config.issueLabels = preserved.issueLabels;
   }
-  if (Object.keys(preserved.statusMapping).length > 0) {
-    config.statusMapping = preserved.statusMapping;
-  }
   if (Object.keys(preserved.detectedStack).length > 0) {
     config.detectedStack = preserved.detectedStack;
   }
   if (Object.keys(preserved.skills).length > 0) {
     config.skills = preserved.skills;
   }
+  if (preserved.topology !== void 0) {
+    config.topology = preserved.topology;
+  }
   if (preserved.designSystem !== null) {
     config.designSystem = preserved.designSystem;
   }
@@ -343,137 +401,80 @@ async function mergeConfig(templateDir, version, tierFlag, preserved) {
 var init_config = __esm({
   "src/lib/config.ts"() {
     "use strict";
+    init_types();
+    init_config_integrity();
   }
 });
 
 // src/lib/skills.ts
 import { join as join4 } from "path";
-async function installOwnedSkills(templateDir, targetDir, tier) {
+async function installOwnedSkills(templateDir, targetDir, _tier) {
   const skillsDir = join4(targetDir, ".claude", "skills");
   const templateSkillsDir = join4(templateDir, ".claude", "skills");
   await replaceDirectory(
-    join4(templateSkillsDir, "flydocs-workflow"),
-    join4(skillsDir, "flydocs-workflow")
-  );
-  const activeMech = MECHANISM_SKILLS[tier];
-  const inactiveMech = tier === "local" ? MECHANISM_SKILLS.cloud : MECHANISM_SKILLS.local;
-  await replaceDirectory(
-    join4(templateSkillsDir, activeMech),
-    join4(skillsDir, activeMech)
+    join4(templateSkillsDir, OWNED_SKILL),
+    join4(skillsDir, OWNED_SKILL)
   );
-  const { rm: rm6 } = await import("fs/promises");
-  const inactivePath = join4(skillsDir, inactiveMech);
-  if (await pathExists(inactivePath)) {
-    await rm6(inactivePath, { recursive: true, force: true });
-  }
-  for (const skill of CORE_SKILLS) {
-    if (skill === "flydocs-workflow") continue;
-    const src = join4(templateSkillsDir, skill);
-    if (await pathExists(src)) {
-      await replaceDirectory(src, join4(skillsDir, skill));
-    }
-  }
-  if (tier === "cloud") {
-    for (const skill of CLOUD_ONLY_SKILLS) {
-      const src = join4(templateSkillsDir, skill);
-      if (await pathExists(src)) {
-        await replaceDirectory(src, join4(skillsDir, skill));
-      }
-    }
-  }
   const readmeSrc = join4(templateSkillsDir, "README.md");
   if (await pathExists(readmeSrc)) {
     await copyFile(readmeSrc, join4(skillsDir, "README.md"));
   }
 }
-async function replaceOwnedSkills(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");
-  for (const skill of CORE_SKILLS) {
-    const src = join4(templateSkillsDir, skill);
-    if (await pathExists(src)) {
-      await replaceDirectory(src, join4(skillsDir, skill));
-    }
-  }
-  for (const skill of CLOUD_ONLY_SKILLS) {
-    const dest = join4(skillsDir, skill);
-    if (tier === "cloud") {
-      const src = join4(templateSkillsDir, skill);
-      if (await pathExists(src)) {
-        await replaceDirectory(src, dest);
-      }
-    } else if (await pathExists(dest)) {
-      await rm6(dest, { recursive: true, force: true });
-    }
-  }
-  const activeMech = MECHANISM_SKILLS[tier];
-  const inactiveMech = tier === "local" ? MECHANISM_SKILLS.cloud : MECHANISM_SKILLS.local;
-  const inactivePath = join4(skillsDir, inactiveMech);
-  if (await pathExists(inactivePath)) {
-    await rm6(inactivePath, { recursive: true, force: true });
-  }
+  const { rm: rm7 } = await import("fs/promises");
   await replaceDirectory(
-    join4(templateSkillsDir, activeMech),
-    join4(skillsDir, activeMech)
+    join4(templateSkillsDir, OWNED_SKILL),
+    join4(skillsDir, OWNED_SKILL)
   );
+  for (const legacy of LEGACY_SKILLS) {
+    const legacyPath = join4(skillsDir, legacy);
+    if (await pathExists(legacyPath)) {
+      await rm7(legacyPath, { recursive: true, force: true });
+    }
+  }
   const readmeSrc = join4(templateSkillsDir, "README.md");
   if (await pathExists(readmeSrc)) {
     await copyFile(readmeSrc, join4(skillsDir, "README.md"));
   }
 }
 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",
     "skills",
-    "flydocs-workflow",
+    OWNED_SKILL,
     "cursor-rule.mdc"
   );
   if (await pathExists(workflowRule)) {
     await copyFile(workflowRule, join4(rulesDir, "flydocs-workflow.mdc"));
   }
-  for (const mech of ["flydocs-local", "flydocs-cloud"]) {
-    const mechRule = join4(
-      targetDir,
-      ".claude",
-      "skills",
-      mech,
-      "cursor-rule.mdc"
-    );
-    if (await pathExists(mechRule)) {
-      await copyFile(mechRule, join4(rulesDir, "flydocs-mechanism.mdc"));
+  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 rm7(legacyRule, { force: true });
     }
   }
-  const context7Rule = join4(
-    targetDir,
-    ".claude",
-    "skills",
-    "flydocs-context7",
-    "cursor-rule.mdc"
-  );
-  if (await pathExists(context7Rule)) {
-    await copyFile(context7Rule, join4(rulesDir, "flydocs-context7.mdc"));
-  }
 }
-var CORE_SKILLS, CLOUD_ONLY_SKILLS, MECHANISM_SKILLS;
+var OWNED_SKILL, LEGACY_SKILLS;
 var init_skills = __esm({
   "src/lib/skills.ts"() {
     "use strict";
     init_fs_ops();
-    CORE_SKILLS = [
-      "flydocs-workflow",
+    OWNED_SKILL = "flydocs-workflow";
+    LEGACY_SKILLS = [
+      "flydocs-cloud",
+      "flydocs-local",
       "flydocs-context-graph",
-      "flydocs-context7"
+      "flydocs-context7",
+      "flydocs-figma",
+      "flydocs-estimates"
     ];
-    CLOUD_ONLY_SKILLS = ["flydocs-figma", "flydocs-estimates"];
-    MECHANISM_SKILLS = {
-      local: "flydocs-local",
-      cloud: "flydocs-cloud"
-    };
   }
 });
 
@@ -715,7 +716,9 @@ import { join as join7 } from "path";
 async function runManifestGeneration(targetDir) {
   const scriptPath = join7(
     targetDir,
-    ".flydocs",
+    ".claude",
+    "skills",
+    "flydocs-workflow",
     "scripts",
     "generate_manifest.py"
   );
@@ -735,7 +738,7 @@ async function runContextGraphBuild(targetDir) {
     targetDir,
     ".claude",
     "skills",
-    "flydocs-context-graph",
+    "flydocs-workflow",
     "scripts",
     "graph_build.py"
   );
@@ -772,8 +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 = {};
@@ -1336,10 +1339,19 @@ async function scanDeprecated(targetDir) {
       found.push(dir);
     }
   }
-  for (const hook of DEPRECATED_HOOKS) {
-    const p = join10(targetDir, ".flydocs", "hooks", hook);
-    if (await pathExists(p)) {
-      found.push(`.flydocs/hooks/${hook}`);
+  const foundFlydocsDirs = /* @__PURE__ */ new Set();
+  for (const dir of DEPRECATED_FLYDOCS_DIRS) {
+    if (await pathExists(join10(targetDir, dir))) {
+      found.push(dir);
+      foundFlydocsDirs.add(dir);
+    }
+  }
+  if (!foundFlydocsDirs.has(".flydocs/hooks")) {
+    for (const hook of DEPRECATED_HOOKS) {
+      const p = join10(targetDir, ".flydocs", "hooks", hook);
+      if (await pathExists(p)) {
+        found.push(`.flydocs/hooks/${hook}`);
+      }
     }
   }
   for (const rule of DEPRECATED_CURSOR_RULES) {
@@ -1424,7 +1436,7 @@ async function promptCleanup(targetDir, paths) {
     printStatus(`Deleted: ${p}`);
   }
 }
-var DEPRECATED_DIRS, DEPRECATED_FILES, DEPRECATED_SKILLS, DEPRECATED_RULES_DIR, DEPRECATED_HOOKS, DEPRECATED_CURSOR_RULES, DEPRECATED_CURSOR_RULE_DIRS, DEPRECATED_COMMANDS;
+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 init_deprecated = __esm({
   "src/lib/deprecated.ts"() {
     "use strict";
@@ -1440,10 +1452,14 @@ var init_deprecated = __esm({
       "figma-mcp"
     ];
     DEPRECATED_RULES_DIR = [".flydocs/rules"];
+    DEPRECATED_FLYDOCS_DIRS = [".flydocs/hooks", ".flydocs/scripts"];
     DEPRECATED_HOOKS = [
       "linear-auto-approve.py",
       "session-end.py",
-      "prefer-scripts.py"
+      "prefer-scripts.py",
+      "auto-approve.py",
+      "post-edit.py",
+      "prompt-submit.py"
     ];
     DEPRECATED_CURSOR_RULES = [
       "designer-agent.mdc",
@@ -1490,8 +1506,9 @@ async function ensureGitignore(targetDir) {
 async function migrateGitignore(targetDir) {
   const gitignorePath = join11(targetDir, ".gitignore");
   if (!await pathExists(gitignorePath)) return;
-  const content = await readFile6(gitignorePath, "utf-8");
-  if (!content.includes("flydocs/context/graph.json")) {
+  let content = await readFile6(gitignorePath, "utf-8");
+  for (const entry of FLYDOCS_GITIGNORE_ENTRIES) {
+    if (content.includes(entry)) continue;
     if (content.includes("# FlyDocs")) {
       const lines = content.split("\n");
       const flyDocsIdx = lines.findIndex((l) => l.trim() === "# FlyDocs");
@@ -1500,37 +1517,69 @@ async function migrateGitignore(targetDir) {
         while (insertIdx < lines.length && lines[insertIdx].trim() !== "" && !lines[insertIdx].startsWith("#")) {
           insertIdx++;
         }
-        lines.splice(insertIdx, 0, "flydocs/context/graph.json");
-        await writeFile4(gitignorePath, lines.join("\n"), "utf-8");
+        lines.splice(insertIdx, 0, entry);
+        content = lines.join("\n");
+        await writeFile4(gitignorePath, content, "utf-8");
       } else {
-        await appendFile(
-          gitignorePath,
-          "\nflydocs/context/graph.json\n",
-          "utf-8"
-        );
+        content += `
+${entry}
+`;
+        await writeFile4(gitignorePath, content, "utf-8");
       }
     } else {
-      await appendFile(
-        gitignorePath,
-        "\nflydocs/context/graph.json\n",
-        "utf-8"
-      );
+      content += `
+${entry}
+`;
+      await writeFile4(gitignorePath, content, "utf-8");
     }
-    printStatus("Added flydocs/context/graph.json to .gitignore");
+    printStatus(`Added ${entry} to .gitignore`);
+  }
+}
+async function ensurePlatformIgnores(targetDir) {
+  for (const filename of PLATFORM_IGNORE_FILES) {
+    const filePath = join11(targetDir, filename);
+    if (!await pathExists(filePath)) continue;
+    const content = await readFile6(filePath, "utf-8");
+    if (content.includes("# FlyDocs")) continue;
+    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}`);
   }
 }
-var FLYDOCS_GITIGNORE_ENTRIES, FULL_GITIGNORE_TEMPLATE;
+var PLATFORM_IGNORE_FILES, FLYDOCS_DEPLOY_EXCLUSIONS, FLYDOCS_GITIGNORE_ENTRIES, FULL_GITIGNORE_TEMPLATE;
 var init_gitignore = __esm({
   "src/lib/gitignore.ts"() {
     "use strict";
     init_fs_ops();
     init_ui();
+    PLATFORM_IGNORE_FILES = [
+      ".gcloudignore",
+      ".dockerignore",
+      ".vercelignore",
+      ".npmignore",
+      ".cfignore",
+      ".ebignore",
+      ".funcignore"
+    ];
+    FLYDOCS_DEPLOY_EXCLUSIONS = [
+      ".flydocs/",
+      ".claude/",
+      ".cursor/",
+      "flydocs/",
+      ".flydocs-workspace.json",
+      "AGENTS.md",
+      ".cursorrules"
+    ];
     FLYDOCS_GITIGNORE_ENTRIES = [
       ".env",
       ".env.local",
       ".flydocs/session.json",
       ".flydocs/logs/",
       ".flydocs/backup-*/",
+      ".flydocs/me.json",
+      ".flydocs/validation-cache.json",
+      ".flydocs/integrity-cache.json",
+      ".flydocs/session/",
       "flydocs/context/graph.json"
     ];
     FULL_GITIGNORE_TEMPLATE = `# Environment
@@ -1542,6 +1591,10 @@ var init_gitignore = __esm({
 .flydocs/session.json
 .flydocs/logs/
 .flydocs/backup-*/
+.flydocs/me.json
+.flydocs/validation-cache.json
+.flydocs/integrity-cache.json
+.flydocs/session/
 flydocs/context/graph.json
 
 # Dependencies
@@ -1887,6 +1940,43 @@ async function validateRelayKey(apiKey) {
   if (!data.valid) return { valid: false };
   return { valid: true, org: data.org ?? "your organization" };
 }
+async function fetchWorkspaces(apiKey) {
+  const baseUrl = process.env.FLYDOCS_RELAY_URL?.replace(/\/$/, "") ?? "https://app.flydocs.ai/api/relay";
+  const response = await fetch(`${baseUrl}/auth/workspaces`, {
+    method: "GET",
+    headers: {
+      Authorization: `Bearer ${apiKey}`
+    },
+    signal: AbortSignal.timeout(15e3)
+  });
+  if (!response.ok) {
+    throw new Error(`Failed to fetch workspaces: ${response.status}`);
+  }
+  const data = await response.json();
+  return data;
+}
+async function fetchMe(apiKey) {
+  const baseUrl = process.env.FLYDOCS_RELAY_URL?.replace(/\/$/, "") ?? "https://app.flydocs.ai/api/relay";
+  const response = await fetch(`${baseUrl}/auth/me`, {
+    method: "GET",
+    headers: {
+      Authorization: `Bearer ${apiKey}`
+    },
+    signal: AbortSignal.timeout(15e3)
+  });
+  if (!response.ok) {
+    throw new Error(`Failed to fetch user identity: ${response.status}`);
+  }
+  const data = await response.json();
+  return {
+    displayName: data.displayName ?? null,
+    email: data.email ?? null,
+    providerId: data.providerId ?? null,
+    provider: data.provider ?? null,
+    providerIdentities: data.providerIdentities ?? [],
+    preferences: data.preferences ?? {}
+  };
+}
 async function validateLinearKey(apiKey) {
   const response = await fetch("https://api.linear.app/graphql", {
     method: "POST",
@@ -1934,6 +2024,36 @@ var init_api_key = __esm({
   }
 });
 
+// src/lib/integrity.ts
+import { readFile as readFile11, writeFile as writeFile8 } from "fs/promises";
+import { join as join15 } from "path";
+async function generateIntegrity(targetDir, version) {
+  const manifestPath = join15(targetDir, ".flydocs", "manifest.json");
+  if (!await pathExists(manifestPath)) return;
+  const manifest = JSON.parse(await readFile11(manifestPath, "utf-8"));
+  const ownership = manifest.ownership;
+  if (!ownership) return;
+  const ownedDirs = ownership.owned_directories?.paths ?? [];
+  const ownedFiles = ownership.owned_files?.paths ?? [];
+  const integrity = {
+    generatedAt: (/* @__PURE__ */ new Date()).toISOString(),
+    version,
+    ownedFiles,
+    ownedDirectories: ownedDirs
+  };
+  await writeFile8(
+    join15(targetDir, ".flydocs", "integrity.json"),
+    JSON.stringify(integrity, null, 2) + "\n",
+    "utf-8"
+  );
+}
+var init_integrity = __esm({
+  "src/lib/integrity.ts"() {
+    "use strict";
+    init_fs_ops();
+  }
+});
+
 // src/commands/install.ts
 var install_exports = {};
 __export(install_exports, {
@@ -1941,8 +2061,8 @@ __export(install_exports, {
 });
 import { defineCommand } from "citty";
 import { resolve as resolve2 } from "path";
-import { join as join15 } from "path";
-import { mkdir as mkdir7 } from "fs/promises";
+import { join as join16 } from "path";
+import { mkdir as mkdir7, writeFile as writeFile9 } from "fs/promises";
 import { confirm as confirm2, select, text, isCancel as isCancel3, cancel as cancel2 } from "@clack/prompts";
 import pc6 from "picocolors";
 var install_default;
@@ -1963,6 +2083,7 @@ var init_install = __esm({
     init_update_check();
     init_telemetry();
     init_api_key();
+    init_integrity();
     install_default = defineCommand({
       meta: {
         name: "install",
@@ -2024,7 +2145,7 @@ var init_install = __esm({
             process.exit(1);
           }
           tier = args.tier;
-        } else if (await pathExists(join15(targetDir, ".flydocs", "config.json"))) {
+        } else if (await pathExists(join16(targetDir, ".flydocs", "config.json"))) {
           try {
             const existing = await readConfig(targetDir);
             if (existing.tier) {
@@ -2046,7 +2167,7 @@ var init_install = __esm({
                 {
                   value: "cloud",
                   label: "Cloud (managed)",
-                  hint: "Sync with Linear \u2014 run flydocs connect after install"
+                  hint: "Sync with Linear, Jira, and more"
                 }
               ]
             });
@@ -2073,6 +2194,9 @@ var init_install = __esm({
         }
         printInfo(`Tier: ${tier}`);
         await capture("install_tier_selected", { tier });
+        let selectedWorkspaceId = null;
+        let selectedWorkspaceName = null;
+        let apiKey = null;
         if (tier === "cloud") {
           console.log();
           console.log(`  ${pc6.bold("Connect to FlyDocs Cloud")}`);
@@ -2096,7 +2220,7 @@ var init_install = __esm({
             cancel2("Installation cancelled.");
             process.exit(0);
           }
-          const apiKey = keyInput.trim();
+          apiKey = keyInput.trim();
           printInfo("Validating API key...");
           try {
             const result = await validateRelayKey(apiKey);
@@ -2114,12 +2238,78 @@ var init_install = __esm({
           }
           const envFile = await storeEnvKey(targetDir, "FLYDOCS_API_KEY", apiKey);
           printStatus(`API key stored in ${pc6.dim(envFile)}`);
+          console.log();
+          printInfo("Fetching workspaces...");
+          try {
+            const workspaces = await fetchWorkspaces(apiKey);
+            if (workspaces.length === 0) {
+              printError(
+                "No workspaces found. Create a workspace in the FlyDocs dashboard first, then re-run install."
+              );
+              process.exit(1);
+            }
+            if (workspaces.length === 1) {
+              selectedWorkspaceId = workspaces[0].id;
+              selectedWorkspaceName = workspaces[0].name;
+              printStatus(
+                `Workspace: ${pc6.bold(selectedWorkspaceName)} (auto-selected)`
+              );
+            } else {
+              const workspaceChoice = await select({
+                message: "Select a workspace",
+                options: workspaces.map((ws) => ({
+                  value: ws.id,
+                  label: `${ws.name} (${ws.provider.type})`,
+                  hint: ws.team.name
+                }))
+              });
+              if (isCancel3(workspaceChoice)) {
+                cancel2("Installation cancelled.");
+                process.exit(0);
+              }
+              selectedWorkspaceId = workspaceChoice;
+              const chosen = workspaces.find((ws) => ws.id === selectedWorkspaceId);
+              selectedWorkspaceName = chosen?.name ?? "Unknown";
+              printStatus(`Workspace: ${pc6.bold(selectedWorkspaceName)}`);
+            }
+          } catch {
+            printError(
+              "Could not fetch workspaces. Check your network and try again."
+            );
+            process.exit(1);
+          }
         }
         let skipConfigOverwrite = false;
-        if (!await pathExists(join15(targetDir, ".git"))) {
+        if (!await pathExists(join16(targetDir, ".git"))) {
           printWarning("No git repository detected. Run git init when ready.");
         }
         await ensureDirectories(targetDir, tier);
+        if (tier === "cloud" && apiKey) {
+          try {
+            const me = await fetchMe(apiKey);
+            const meData = {
+              displayName: me.displayName,
+              email: me.email,
+              providerId: me.providerId,
+              provider: me.provider,
+              providerIdentities: me.providerIdentities,
+              preferences: me.preferences
+            };
+            const mePath = join16(targetDir, ".flydocs", "me.json");
+            await writeFile9(
+              mePath,
+              JSON.stringify(meData, null, 2) + "\n",
+              "utf-8"
+            );
+            if (me.displayName) {
+              printStatus(`Identity: ${pc6.bold(me.displayName)}`);
+            }
+          } catch {
+            printWarning(
+              "Could not fetch user identity. Run /flydocs-setup to configure later."
+            );
+          }
+        }
         const existingFiles = await detectExistingConfigs(targetDir);
         if (existingFiles.length > 0) {
           console.log();
@@ -2168,33 +2358,34 @@ var init_install = __esm({
         }
         console.log("Installing framework files...");
         await replaceDirectory(
-          join15(templateDir, ".flydocs", "templates"),
-          join15(targetDir, ".flydocs", "templates")
-        );
-        await replaceDirectory(
-          join15(templateDir, ".flydocs", "hooks"),
-          join15(targetDir, ".flydocs", "hooks")
+          join16(templateDir, ".flydocs", "templates"),
+          join16(targetDir, ".flydocs", "templates")
         );
         await replaceDirectory(
-          join15(templateDir, ".flydocs", "scripts"),
-          join15(targetDir, ".flydocs", "scripts")
+          join16(templateDir, ".claude", "hooks"),
+          join16(targetDir, ".claude", "hooks")
         );
         await copyFile(
-          join15(templateDir, ".flydocs", "version"),
-          join15(targetDir, ".flydocs", "version")
+          join16(templateDir, ".flydocs", "version"),
+          join16(targetDir, ".flydocs", "version")
         );
-        const manifestSrc = join15(templateDir, "manifest.json");
+        const manifestSrc = join16(templateDir, "manifest.json");
         if (await pathExists(manifestSrc)) {
-          await copyFile(manifestSrc, join15(targetDir, ".flydocs", "manifest.json"));
+          await copyFile(manifestSrc, join16(targetDir, ".flydocs", "manifest.json"));
         }
-        const changelogSrc = join15(templateDir, "CHANGELOG.md");
+        const changelogSrc = join16(templateDir, "CHANGELOG.md");
         if (await pathExists(changelogSrc)) {
-          await copyFile(changelogSrc, join15(targetDir, ".flydocs", "CHANGELOG.md"));
+          await copyFile(changelogSrc, join16(targetDir, ".flydocs", "CHANGELOG.md"));
         }
-        printStatus(".flydocs/templates, hooks, version, manifest, changelog");
-        const configPath = join15(targetDir, ".flydocs", "config.json");
+        printStatus(
+          ".flydocs/templates, .claude/hooks, version, manifest, changelog"
+        );
+        const configPath = join16(targetDir, ".flydocs", "config.json");
         if (!await pathExists(configPath)) {
           const config = await createFreshConfig(templateDir, version, tier);
+          if (selectedWorkspaceId) {
+            config.workspaceId = selectedWorkspaceId;
+          }
           await writeConfig(targetDir, config);
           printStatus(`.flydocs/config.json (new, tier: ${tier})`);
         } else if (args.tier) {
@@ -2202,15 +2393,34 @@ var init_install = __esm({
             const existing = await readConfig(targetDir);
             existing.version = version;
             existing.tier = tier;
+            if (selectedWorkspaceId) {
+              existing.workspaceId = selectedWorkspaceId;
+            }
             await writeConfig(targetDir, existing);
             printStatus(`.flydocs/config.json (tier updated: ${tier})`);
           } catch {
             const config = await createFreshConfig(templateDir, version, tier);
+            if (selectedWorkspaceId) {
+              config.workspaceId = selectedWorkspaceId;
+            }
             await writeConfig(targetDir, config);
             printStatus(`.flydocs/config.json (recreated, tier: ${tier})`);
           }
         } else {
-          printWarning(".flydocs/config.json exists, preserving");
+          if (selectedWorkspaceId) {
+            try {
+              const existing = await readConfig(targetDir);
+              existing.workspaceId = selectedWorkspaceId;
+              await writeConfig(targetDir, existing);
+              printWarning(
+                ".flydocs/config.json exists, preserving (workspace updated)"
+              );
+            } catch {
+              printWarning(".flydocs/config.json exists, preserving");
+            }
+          } else {
+            printWarning(".flydocs/config.json exists, preserving");
+          }
         }
         console.log();
         console.log(`Installing skills (tier: ${tier})...`);
@@ -2246,20 +2456,20 @@ var init_install = __esm({
         }
         await capture("install_agents_chosen", { install_agents: installAgents });
         if (installAgents) {
-          const claudeAgentsSrc = join15(templateDir, ".claude", "agents");
+          const claudeAgentsSrc = join16(templateDir, ".claude", "agents");
           if (await pathExists(claudeAgentsSrc)) {
-            await mkdir7(join15(targetDir, ".claude", "agents"), { recursive: true });
+            await mkdir7(join16(targetDir, ".claude", "agents"), { recursive: true });
             await copyDirectoryContents(
               claudeAgentsSrc,
-              join15(targetDir, ".claude", "agents")
+              join16(targetDir, ".claude", "agents")
             );
           }
-          const cursorAgentsSrc = join15(templateDir, ".cursor", "agents");
+          const cursorAgentsSrc = join16(templateDir, ".cursor", "agents");
           if (await pathExists(cursorAgentsSrc)) {
-            await mkdir7(join15(targetDir, ".cursor", "agents"), { recursive: true });
+            await mkdir7(join16(targetDir, ".cursor", "agents"), { recursive: true });
             await copyDirectoryContents(
               cursorAgentsSrc,
-              join15(targetDir, ".cursor", "agents")
+              join16(targetDir, ".cursor", "agents")
             );
           }
           printStatus("Sub-agents installed (.claude/agents, .cursor/agents)");
@@ -2269,30 +2479,30 @@ var init_install = __esm({
         console.log();
         console.log("Installing commands and settings...");
         await copyDirectoryContents(
-          join15(templateDir, ".claude", "commands"),
-          join15(targetDir, ".claude", "commands")
+          join16(templateDir, ".claude", "commands"),
+          join16(targetDir, ".claude", "commands")
         );
         if (!skipConfigOverwrite) {
           await copyFile(
-            join15(templateDir, ".claude", "CLAUDE.md"),
-            join15(targetDir, ".claude", "CLAUDE.md")
+            join16(templateDir, ".claude", "CLAUDE.md"),
+            join16(targetDir, ".claude", "CLAUDE.md")
           );
           await copyFile(
-            join15(templateDir, ".claude", "settings.json"),
-            join15(targetDir, ".claude", "settings.json")
+            join16(templateDir, ".claude", "settings.json"),
+            join16(targetDir, ".claude", "settings.json")
           );
           printStatus(".claude/ (commands, CLAUDE.md, settings)");
         } else {
           printStatus(".claude/ (commands only \u2014 existing config preserved)");
         }
         await copyDirectoryContents(
-          join15(templateDir, ".claude", "commands"),
-          join15(targetDir, ".cursor", "commands")
+          join16(templateDir, ".claude", "commands"),
+          join16(targetDir, ".cursor", "commands")
         );
         if (!skipConfigOverwrite) {
           await copyFile(
-            join15(templateDir, ".cursor", "hooks.json"),
-            join15(targetDir, ".cursor", "hooks.json")
+            join16(templateDir, ".cursor", "hooks.json"),
+            join16(targetDir, ".cursor", "hooks.json")
           );
           printStatus(".cursor/ (commands, hooks)");
         } else {
@@ -2302,8 +2512,8 @@ var init_install = __esm({
         printStatus(".cursor/rules/");
         if (!skipConfigOverwrite) {
           await copyFile(
-            join15(templateDir, "AGENTS.md"),
-            join15(targetDir, "AGENTS.md")
+            join16(templateDir, "AGENTS.md"),
+            join16(targetDir, "AGENTS.md")
           );
           printStatus("AGENTS.md");
         } else {
@@ -2311,44 +2521,46 @@ var init_install = __esm({
         }
         await runManifestGeneration(targetDir);
         await runContextGraphBuild(targetDir);
+        await generateIntegrity(targetDir, version);
+        printStatus("Install integrity recorded");
         console.log();
         console.log("Installing project templates...");
         const userFiles = [
           {
-            src: join15(templateDir, "flydocs", "context", "project.md"),
-            dest: join15(targetDir, "flydocs", "context", "project.md"),
+            src: join16(templateDir, "flydocs", "context", "project.md"),
+            dest: join16(targetDir, "flydocs", "context", "project.md"),
             label: "flydocs/context/project.md"
           },
           {
-            src: join15(templateDir, "flydocs", "knowledge", "INDEX.md"),
-            dest: join15(targetDir, "flydocs", "knowledge", "INDEX.md"),
+            src: join16(templateDir, "flydocs", "knowledge", "INDEX.md"),
+            dest: join16(targetDir, "flydocs", "knowledge", "INDEX.md"),
             label: "flydocs/knowledge/INDEX.md"
           },
           {
-            src: join15(templateDir, "flydocs", "knowledge", "README.md"),
-            dest: join15(targetDir, "flydocs", "knowledge", "README.md"),
+            src: join16(templateDir, "flydocs", "knowledge", "README.md"),
+            dest: join16(targetDir, "flydocs", "knowledge", "README.md"),
             label: "flydocs/knowledge/README.md"
           },
           {
-            src: join15(
+            src: join16(
               templateDir,
               "flydocs",
               "knowledge",
               "product",
               "personas.md"
             ),
-            dest: join15(targetDir, "flydocs", "knowledge", "product", "personas.md"),
+            dest: join16(targetDir, "flydocs", "knowledge", "product", "personas.md"),
             label: "flydocs/knowledge/product/personas.md"
           },
           {
-            src: join15(
+            src: join16(
               templateDir,
               "flydocs",
               "knowledge",
               "product",
               "user-flows.md"
             ),
-            dest: join15(
+            dest: join16(
               targetDir,
               "flydocs",
               "knowledge",
@@ -2358,18 +2570,57 @@ var init_install = __esm({
             label: "flydocs/knowledge/product/user-flows.md"
           },
           {
-            src: join15(templateDir, "flydocs", "design-system", "README.md"),
-            dest: join15(targetDir, "flydocs", "design-system", "README.md"),
+            src: join16(
+              templateDir,
+              "flydocs",
+              "knowledge",
+              "templates",
+              "decision.md"
+            ),
+            dest: join16(
+              targetDir,
+              "flydocs",
+              "knowledge",
+              "templates",
+              "decision.md"
+            ),
+            label: "flydocs/knowledge/templates/decision.md"
+          },
+          {
+            src: join16(
+              templateDir,
+              "flydocs",
+              "knowledge",
+              "templates",
+              "feature.md"
+            ),
+            dest: join16(
+              targetDir,
+              "flydocs",
+              "knowledge",
+              "templates",
+              "feature.md"
+            ),
+            label: "flydocs/knowledge/templates/feature.md"
+          },
+          {
+            src: join16(templateDir, "flydocs", "knowledge", "templates", "note.md"),
+            dest: join16(targetDir, "flydocs", "knowledge", "templates", "note.md"),
+            label: "flydocs/knowledge/templates/note.md"
+          },
+          {
+            src: join16(templateDir, "flydocs", "design-system", "README.md"),
+            dest: join16(targetDir, "flydocs", "design-system", "README.md"),
             label: "flydocs/design-system/README.md"
           },
           {
-            src: join15(
+            src: join16(
               templateDir,
               "flydocs",
               "design-system",
               "component-patterns.md"
             ),
-            dest: join15(
+            dest: join16(
               targetDir,
               "flydocs",
               "design-system",
@@ -2378,13 +2629,13 @@ var init_install = __esm({
             label: "flydocs/design-system/component-patterns.md"
           },
           {
-            src: join15(templateDir, "flydocs", "design-system", "token-mapping.md"),
-            dest: join15(targetDir, "flydocs", "design-system", "token-mapping.md"),
+            src: join16(templateDir, "flydocs", "design-system", "token-mapping.md"),
+            dest: join16(targetDir, "flydocs", "design-system", "token-mapping.md"),
             label: "flydocs/design-system/token-mapping.md"
           },
           {
-            src: join15(templateDir, "flydocs", "README.md"),
-            dest: join15(targetDir, "flydocs", "README.md"),
+            src: join16(templateDir, "flydocs", "README.md"),
+            dest: join16(targetDir, "flydocs", "README.md"),
             label: "flydocs/README.md"
           }
         ];
@@ -2398,12 +2649,13 @@ var init_install = __esm({
             }
           }
         }
-        const envExampleSrc = join15(templateDir, ".env.example");
+        const envExampleSrc = join16(templateDir, ".env.example");
         if (await pathExists(envExampleSrc)) {
-          await copyFile(envExampleSrc, join15(targetDir, ".env.example"));
+          await copyFile(envExampleSrc, join16(targetDir, ".env.example"));
           printStatus(".env.example");
         }
         await ensureGitignore(targetDir);
+        await ensurePlatformIgnores(targetDir);
         console.log();
         console.log("Detecting project stack...");
         const stack = await detectStack(targetDir);
@@ -2572,60 +2824,1142 @@ var init_install = __esm({
   }
 });
 
-// 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 join16 } from "path";
-import { mkdir as mkdir8, cp as cp2, readFile as readFile11, readdir as readdir3, 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";
-var update_default;
-var init_update = __esm({
-  "src/commands/update.ts"() {
+// 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}=(.+)$`, "m"));
+      if (match) return match[1].trim();
+    } catch {
+      continue;
+    }
+  }
+  return null;
+}
+var init_global_config = __esm({
+  "src/lib/global-config.ts"() {
     "use strict";
-    init_template();
-    init_version();
     init_fs_ops();
     init_ui();
-    init_config();
-    init_skills();
-    init_stack();
-    init_community_skills();
-    init_deprecated();
-    init_gitignore();
-    init_post_install();
-    init_update_check();
-    init_telemetry();
-    update_default = defineCommand2({
-      meta: {
-        name: "update",
-        description: "Update an existing FlyDocs installation"
-      },
-      args: {
-        path: {
-          type: "string",
-          description: "Update the specified project directory"
-        },
-        here: {
-          type: "boolean",
-          description: "Update in the current directory",
-          default: false
-        },
-        tier: {
-          type: "string",
-          description: "Change tier: 'local' (free) or 'cloud' (managed)"
-        },
-        force: {
-          type: "boolean",
-          description: "Force update even if versions match",
-          default: false
-        },
-        "local-source": {
-          type: "boolean",
-          description: "Force use of local template/ directory",
+  }
+});
+
+// src/lib/relay-client.ts
+function resolveRelayUrl() {
+  return process.env.FLYDOCS_RELAY_URL?.replace(/\/$/, "") ?? DEFAULT_RELAY_URL;
+}
+function headers(apiKey, workspaceId) {
+  const h = {
+    Authorization: `Bearer ${apiKey}`,
+    "Content-Type": "application/json",
+    Accept: "application/json"
+  };
+  if (workspaceId) h["X-Workspace"] = workspaceId;
+  return h;
+}
+async function fetchConfigV2(apiKey, options = {}) {
+  const baseUrl = resolveRelayUrl();
+  const params = new URLSearchParams({ format: "2" });
+  if (options.includeContext) params.set("includeContext", "true");
+  const response = await fetch(`${baseUrl}/config/generate?${params}`, {
+    method: "GET",
+    headers: headers(apiKey, options.workspaceId),
+    signal: AbortSignal.timeout(3e4)
+  });
+  if (!response.ok) {
+    const body = await response.text().catch(() => "");
+    throw new RelayError(
+      `config/generate failed (${response.status})`,
+      response.status,
+      body
+    );
+  }
+  return await response.json();
+}
+async function fetchTemplates(apiKey, sinceVersion, workspaceId) {
+  const baseUrl = resolveRelayUrl();
+  const response = await fetch(`${baseUrl}/templates?since=${sinceVersion}`, {
+    method: "GET",
+    headers: headers(apiKey, workspaceId),
+    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/commands/cleanup.ts
+var cleanup_exports = {};
+__export(cleanup_exports, {
+  default: () => cleanup_default,
+  executeCleanup: () => executeCleanup,
+  scanArtifacts: () => scanArtifacts
+});
+import { defineCommand as defineCommand2 } from "citty";
+import pc7 from "picocolors";
+import { join as join18 } from "path";
+import { readFile as readFile13, writeFile as writeFile11, rm as rm4 } from "fs/promises";
+async function scanArtifacts(targetDir) {
+  const actions = [];
+  const localMePath = join18(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 = join18(
+    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 = join18(targetDir, envFile);
+    if (!await pathExists(envPath)) continue;
+    const content = await readFile13(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 ${envFile}`,
+          path: envPath,
+          type: "line"
+        });
+      }
+    }
+  }
+  try {
+    const config = await readAnyConfig(targetDir);
+    const rawContent = await readFile13(
+      join18(targetDir, ".flydocs", "config.json"),
+      "utf-8"
+    );
+    const raw = JSON.parse(rawContent);
+    const ghostFields = ["provider", "statusMapping"];
+    for (const field of ghostFields) {
+      if (field in raw) {
+        actions.push({
+          description: `Remove ghost field "${field}" from config.json`,
+          path: join18(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: join18(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 rm4(action.path, { force: true });
+  }
+  const envFiles = /* @__PURE__ */ new Map();
+  for (const action of lineRemovals) {
+    if (!envFiles.has(action.path)) {
+      const content = await readFile13(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 rm4(envPath, { force: true });
+    } else {
+      await writeFile11(envPath, filtered.join("\n"), "utf-8");
+    }
+  }
+  if (fieldRemovals.length > 0) {
+    const configPath = join18(targetDir, ".flydocs", "config.json");
+    const content = await readFile13(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 writeFile11(
+      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 = defineCommand2({
+      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(`  ${pc7.bold("FlyDocs Cleanup")}`);
+        console.log();
+        const hasConfig = await pathExists(
+          join18(targetDir, ".flydocs", "config.json")
+        );
+        if (!hasConfig) {
+          printError("No .flydocs/config.json found. Run flydocs init first.");
+          process.exit(1);
+        }
+        const hasGlobalCreds = await pathExists(credentialsPath());
+        if (!hasGlobalCreds) {
+          printWarning(
+            "No global credentials found. Run flydocs init to set up credentials before cleanup."
+          );
+        }
+        const actions = await scanArtifacts(targetDir);
+        if (actions.length === 0) {
+          printStatus("No legacy artifacts found. Already clean.");
+          console.log();
+          return;
+        }
+        const mode = args.confirm ? "Removing" : "Would remove";
+        printInfo(`${mode} ${actions.length} legacy artifact(s):`);
+        console.log();
+        for (const action of actions) {
+          const icon = args.confirm ? pc7.red("-") : pc7.yellow("?");
+          console.log(`  ${icon} ${action.description}`);
+        }
+        console.log();
+        if (!args.confirm) {
+          printInfo(
+            `Dry-run complete. Run ${pc7.cyan("flydocs cleanup --confirm")} to remove.`
+          );
+          console.log();
+          return;
+        }
+        await executeCleanup(targetDir, actions);
+        printCompletionBox("Cleanup Complete", [
+          `${pc7.green("+")} Removed ${actions.length} legacy artifact(s)`
+        ]);
+        console.log();
+      }
+    });
+  }
+});
+
+// src/lib/workspace.ts
+import { readFile as readFile14, writeFile as writeFile12, readdir as readdir4, stat as stat2 } from "fs/promises";
+import { join as join19, dirname as dirname3, relative, resolve as resolve3 } from "path";
+async function readWorkspaceFile(dir) {
+  const filePath = join19(dir, WORKSPACE_FILENAME);
+  if (!await pathExists(filePath)) return null;
+  const content = await readFile14(filePath, "utf-8");
+  const parsed = JSON.parse(content);
+  validateWorkspaceFile(parsed);
+  return parsed;
+}
+async function writeWorkspaceFile(dir, workspace) {
+  const filePath = join19(dir, WORKSPACE_FILENAME);
+  const content = JSON.stringify(workspace, null, 2) + "\n";
+  await writeFile12(filePath, content, "utf-8");
+}
+async function detectSiblingRepos(parentDir) {
+  const repos = {};
+  const entries = await readdir4(parentDir);
+  for (const entry of entries) {
+    if (entry.startsWith(".")) continue;
+    const entryPath = join19(parentDir, entry);
+    const entryStat = await stat2(entryPath).catch(() => null);
+    if (!entryStat?.isDirectory()) continue;
+    const hasGit = await pathExists(join19(entryPath, ".git"));
+    const hasFlydocs = await pathExists(
+      join19(entryPath, ".flydocs", "config.json")
+    );
+    if (hasGit || hasFlydocs) {
+      repos[entry] = { path: `./${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 = join19(repoDir, "flydocs", "context", "service.json");
+    if (!await pathExists(serviceJsonPath)) continue;
+    try {
+      const content = await readFile14(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 defineCommand3 } from "citty";
+import { text as text2, confirm as confirm3, select as select2, isCancel as isCancel4, cancel as cancel3 } from "@clack/prompts";
+import pc8 from "picocolors";
+import { join as join20 } from "path";
+import { mkdir as mkdir9, writeFile as writeFile13 } from "fs/promises";
+import { execFile } from "child_process";
+import { promisify } from "util";
+async function resolveAndValidateKey(keyArg, targetDir) {
+  let resolved = await resolveApiKey(keyArg, targetDir);
+  if (!resolved) {
+    console.log(
+      `  ${pc8.dim("Get your API key (fdk_...) from your FlyDocs dashboard")}`
+    );
+    console.log();
+    const keyInput = await text2({
+      message: "Enter your API key",
+      placeholder: "fdk_...",
+      validate(value) {
+        if (!value.trim()) return "API key is required";
+        if (detectKeyType(value.trim()) !== "relay") {
+          return "Key must start with fdk_ (FlyDocs API key)";
+        }
+        return void 0;
+      }
+    });
+    if (isCancel4(keyInput)) {
+      cancel3("Init cancelled.");
+      process.exit(0);
+    }
+    resolved = { key: keyInput.trim(), source: "prompt" };
+  } else {
+    printInfo(`Using key from ${resolved.source}`);
+  }
+  const apiKey = resolved.key;
+  printInfo("Validating API key...");
+  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 ${pc8.bold(result.org)}`);
+  } catch {
+    printError(
+      "Could not reach FlyDocs API. Check your network and try again."
+    );
+    console.log(
+      `  ${pc8.dim("flydocs init requires server access. For offline use, run flydocs install instead.")}`
+    );
+    process.exit(1);
+  }
+  const workspaces = await fetchWorkspaces(apiKey);
+  let workspaceId;
+  if (workspaces.length === 0) {
+    printError("No workspaces found. Create one at app.flydocs.ai first.");
+    process.exit(1);
+  } else if (workspaces.length === 1) {
+    workspaceId = workspaces[0].id;
+    printStatus(`Workspace: ${pc8.bold(workspaces[0].name)}`);
+  } else {
+    const choice = await select2({
+      message: "Select workspace",
+      options: workspaces.map((ws) => ({
+        value: ws.id,
+        label: ws.name
+      }))
+    });
+    if (isCancel4(choice)) {
+      cancel3("Init cancelled.");
+      process.exit(0);
+    }
+    workspaceId = choice;
+  }
+  await writeGlobalCredential({
+    apiKey,
+    workspaceId,
+    createdAt: (/* @__PURE__ */ new Date()).toISOString(),
+    lastValidated: (/* @__PURE__ */ new Date()).toISOString()
+  });
+  await checkCredentialPermissions();
+  return { apiKey, workspaceId };
+}
+async function pullServerConfig(apiKey, targetDir, workspaceId, forceIncludeContext = false) {
+  printInfo("Pulling config from server...");
+  const isFirstInit = forceIncludeContext || !await pathExists(join20(targetDir, ".flydocs", "config.json"));
+  try {
+    const response = await fetchConfigV2(apiKey, {
+      includeContext: isFirstInit,
+      workspaceId
+    });
+    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(
+          `  ${pc8.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(join20(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 = join20(targetDir, "flydocs", "context");
+    await mkdir9(contextDir, { recursive: true });
+    const projectMdPath = join20(contextDir, "project.md");
+    if (!await pathExists(projectMdPath)) {
+      await writeFile13(projectMdPath, serverResponse.context.projectMd, "utf-8");
+      actions.push("Wrote flydocs/context/project.md");
+    } else {
+      skipped.push("flydocs/context/project.md (already exists)");
+    }
+    const serviceJsonPath = join20(contextDir, "service.json");
+    if (serverResponse.context.serviceJson && !await pathExists(serviceJsonPath)) {
+      await writeFile13(
+        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");
+  const artifacts = await scanArtifacts(targetDir);
+  if (artifacts.length > 0) {
+    await executeCleanup(targetDir, artifacts);
+    actions.push(`Cleaned ${artifacts.length} legacy artifact(s)`);
+  }
+  return { actions, skipped };
+}
+async function checkGitFreshness(repoDir) {
+  const hasGit = await pathExists(join20(repoDir, ".git"));
+  if (!hasGit) return;
+  try {
+    await execFileAsync("git", ["-C", repoDir, "fetch", "--quiet"], {
+      timeout: 15e3
+    });
+    const { stdout } = await execFileAsync(
+      "git",
+      ["-C", repoDir, "rev-list", "--count", "HEAD..@{upstream}"],
+      { timeout: 5e3 }
+    );
+    const behind = parseInt(stdout.trim(), 10);
+    if (behind <= 0) return;
+    printWarning(`Repo is ${behind} commit(s) behind remote.`);
+    const shouldPull = await confirm3({
+      message: "Pull latest before init?"
+    });
+    if (isCancel4(shouldPull) || !shouldPull) {
+      printInfo("Continuing without pulling.");
+      return;
+    }
+    await execFileAsync("git", ["-C", repoDir, "pull", "--ff-only"], {
+      timeout: 3e4
+    });
+    printStatus("Pulled latest from remote.");
+  } catch {
+  }
+}
+async function isEmptyOrNonRepo(dir) {
+  const hasGit = await pathExists(join20(dir, ".git"));
+  if (hasGit) return false;
+  const siblings = await detectSiblingRepos(dir);
+  if (Object.keys(siblings).length >= 2) return false;
+  return true;
+}
+function repoShortName(fullName) {
+  return fullName.includes("/") ? fullName.split("/").pop() : fullName;
+}
+async function runCloneAndInit(targetDir, keyArg, repos, apiKey, workspaceId) {
+  if (repos.length === 1) {
+    const repo = repos[0];
+    const shortName = repoShortName(repo.name);
+    printInfo(`Workspace has 1 repo: ${pc8.bold(shortName)}`);
+    const shouldClone = await confirm3({
+      message: `Clone ${shortName} and initialize?`
+    });
+    if (isCancel4(shouldClone) || !shouldClone) {
+      cancel3("Init cancelled.");
+      process.exit(0);
+    }
+    const cloneDir = join20(targetDir, shortName);
+    printInfo(`Cloning ${shortName}...`);
+    await execFileAsync("git", ["clone", repo.cloneUrl, cloneDir], {
+      timeout: 6e4
+    });
+    printStatus(`Cloned ${shortName}`);
+    const serverResponse = await pullServerConfig(
+      apiKey,
+      cloneDir,
+      workspaceId,
+      true
+      // always include context on fresh clone
+    );
+    const { actions, skipped } = await initSingleRepo(
+      cloneDir,
+      apiKey,
+      serverResponse
+    );
+    actions.unshift("Stored credential globally (~/.flydocs/credentials)");
+    actions.unshift(`Cloned ${shortName}`);
+    printInitReport(
+      actions,
+      skipped,
+      serverResponse.warnings,
+      !!serverResponse.context
+    );
+  } else {
+    const repoNames = repos.map((r) => repoShortName(r.name));
+    printInfo(`Workspace has ${repos.length} repos:`);
+    for (const name of repoNames) {
+      console.log(`    ${pc8.cyan(name)}`);
+    }
+    console.log();
+    const shouldClone = await confirm3({
+      message: `Clone and initialize all ${repos.length} repos?`
+    });
+    if (isCancel4(shouldClone) || !shouldClone) {
+      cancel3("Init cancelled.");
+      process.exit(0);
+    }
+    const allActions = [
+      "Stored credential globally (~/.flydocs/credentials)"
+    ];
+    const allSkipped = [];
+    let allWarnings = [];
+    let firstResponse;
+    for (let i = 0; i < repos.length; i++) {
+      const repo = repos[i];
+      const shortName = repoNames[i];
+      const cloneDir = join20(targetDir, shortName);
+      console.log();
+      if (await pathExists(join20(cloneDir, ".git"))) {
+        printInfo(`${pc8.bold(shortName)} already cloned, initializing...`);
+        await checkGitFreshness(cloneDir);
+      } else {
+        printInfo(`Cloning ${pc8.bold(shortName)}...`);
+        await execFileAsync("git", ["clone", repo.cloneUrl, cloneDir], {
+          timeout: 6e4
+        });
+        allActions.push(`Cloned ${shortName}`);
+      }
+      const serverResponse = await pullServerConfig(
+        apiKey,
+        cloneDir,
+        workspaceId,
+        true
+        // always include context on fresh clone
+      );
+      if (!firstResponse) firstResponse = serverResponse;
+      const { actions, skipped } = await initSingleRepo(
+        cloneDir,
+        apiKey,
+        serverResponse
+      );
+      for (const action of actions) {
+        allActions.push(`[${shortName}] ${action}`);
+      }
+      for (const skip of skipped) {
+        allSkipped.push(`[${shortName}] ${skip}`);
+      }
+      allWarnings = [...allWarnings, ...serverResponse.warnings];
+      printStatus(`${shortName} initialized`);
+    }
+    if (firstResponse) {
+      const repoEntries = {};
+      for (const name of repoNames) {
+        repoEntries[name] = { path: `./${name}` };
+      }
+      const workspaceFile = buildWorkspaceFile(
+        firstResponse.workspaceId,
+        repoEntries
+      );
+      await writeWorkspaceFile(targetDir, workspaceFile);
+      allActions.push(`.flydocs-workspace.json (${repos.length} repos)`);
+      const contextDir = join20(targetDir, "flydocs", "context");
+      const workspaceMdPath = join20(contextDir, "workspace.md");
+      if (!await pathExists(workspaceMdPath)) {
+        await mkdir9(contextDir, { recursive: true });
+        const content = firstResponse.context?.workspaceMd ?? await generateWorkspaceMd(targetDir, workspaceFile);
+        await writeFile13(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,
+      !!firstResponse?.context
+    );
+  }
+}
+async function isParentDirectory(dir) {
+  const hasGit = await pathExists(join20(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(`    ${pc8.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 = join20(parentDir, repoNames[0]);
+  const { apiKey, workspaceId } = await resolveAndValidateKey(
+    keyArg,
+    firstRepoDir
+  );
+  const allActions = [
+    "Stored credential globally (~/.flydocs/credentials)"
+  ];
+  const allSkipped = [];
+  let allWarnings = [];
+  let firstResponse;
+  for (const repoName of repoNames) {
+    const repoDir = join20(parentDir, repoName);
+    console.log();
+    printInfo(`Initializing ${pc8.bold(repoName)}...`);
+    await checkGitFreshness(repoDir);
+    const serverResponse = await pullServerConfig(apiKey, repoDir, workspaceId);
+    if (!firstResponse) firstResponse = serverResponse;
+    const { actions, skipped } = await initSingleRepo(
+      repoDir,
+      apiKey,
+      serverResponse
+    );
+    for (const action of actions) {
+      allActions.push(`[${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 (${repoNames.length} repos)`);
+    }
+    const contextDir = join20(parentDir, "flydocs", "context");
+    const workspaceMdPath = join20(contextDir, "workspace.md");
+    if (await pathExists(workspaceMdPath)) {
+      allSkipped.push("flydocs/context/workspace.md (already exists)");
+    } else {
+      await mkdir9(contextDir, { recursive: true });
+      const workspaceJson = await readWorkspaceFile(parentDir) ?? buildWorkspaceFile(firstResponse.workspaceId, repos);
+      const content = firstResponse.context?.workspaceMd ?? await generateWorkspaceMd(parentDir, workspaceJson);
+      await writeFile13(workspaceMdPath, content, "utf-8");
+      const source = firstResponse.context?.workspaceMd ? "from server" : "generated locally";
+      allActions.push(`Wrote flydocs/context/workspace.md (${source})`);
+    }
+  }
+  console.log();
+  printInitReport(
+    allActions,
+    allSkipped,
+    allWarnings,
+    !!firstResponse?.context
+  );
+}
+function printInitReport(actions, skipped, warnings, hasContext) {
+  console.log();
+  const lines = [];
+  for (const action of actions) {
+    lines.push(`${pc8.green("+")} ${action}`);
+  }
+  for (const skip of skipped) {
+    lines.push(`${pc8.dim("-")} ${skip}`);
+  }
+  if (!hasContext) {
+    lines.push("");
+    lines.push(
+      `${pc8.yellow("!")} No generated context yet. An admin can generate it from the portal.`
+    );
+  }
+  if (warnings.length > 0) {
+    lines.push("");
+    for (const warning of warnings) {
+      lines.push(`${pc8.yellow("!")} ${warning}`);
+    }
+  }
+  printCompletionBox("FlyDocs Initialized", lines);
+  console.log();
+  console.log(`  Next steps:`);
+  console.log(
+    `    ${pc8.cyan("flydocs sync")}       Pull latest config and templates`
+  );
+  console.log(
+    `    ${pc8.cyan("cursor .")} ${pc8.dim("or")} ${pc8.cyan("code .")}   Open your IDE, then use ${pc8.bold("/start-session")}`
+  );
+  console.log();
+}
+var execFileAsync, 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_cleanup();
+    init_workspace();
+    execFileAsync = promisify(execFile);
+    init_default = defineCommand3({
+      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(`  ${pc8.bold("FlyDocs Init")}`);
+        console.log();
+        if (await isParentDirectory(targetDir)) {
+          await runMultiRepoInit(targetDir, args.key);
+          return;
+        }
+        if (await isEmptyOrNonRepo(targetDir)) {
+          const { apiKey: apiKey2, workspaceId: workspaceId2 } = await resolveAndValidateKey(
+            args.key,
+            targetDir
+          );
+          const preflightResponse = await pullServerConfig(
+            apiKey2,
+            targetDir,
+            workspaceId2
+          );
+          if (preflightResponse.repos && preflightResponse.repos.length > 0) {
+            await runCloneAndInit(
+              targetDir,
+              args.key,
+              preflightResponse.repos,
+              apiKey2,
+              workspaceId2
+            );
+            return;
+          }
+        }
+        await checkGitFreshness(targetDir);
+        const { apiKey, workspaceId } = await resolveAndValidateKey(
+          args.key,
+          targetDir
+        );
+        const serverResponse = await pullServerConfig(
+          apiKey,
+          targetDir,
+          workspaceId,
+          true
+          // init always requests context
+        );
+        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 = join20(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,
+          !!serverResponse.context
+        );
+      }
+    });
+  }
+});
+
+// src/commands/update.ts
+var update_exports = {};
+__export(update_exports, {
+  default: () => update_default
+});
+import { defineCommand as defineCommand4 } from "citty";
+import { resolve as resolve4, join as join21 } from "path";
+import { mkdir as mkdir10, cp as cp2, readFile as readFile15, readdir as readdir5, rm as rm5 } from "fs/promises";
+import { select as select3, text as text3, confirm as confirm4, isCancel as isCancel5, cancel as cancel4 } from "@clack/prompts";
+import pc9 from "picocolors";
+var update_default;
+var init_update = __esm({
+  "src/commands/update.ts"() {
+    "use strict";
+    init_template();
+    init_version();
+    init_fs_ops();
+    init_ui();
+    init_config();
+    init_skills();
+    init_stack();
+    init_community_skills();
+    init_deprecated();
+    init_gitignore();
+    init_post_install();
+    init_update_check();
+    init_telemetry();
+    init_integrity();
+    update_default = defineCommand4({
+      meta: {
+        name: "update",
+        description: "Update an existing FlyDocs installation"
+      },
+      args: {
+        path: {
+          type: "string",
+          description: "Update the specified project directory"
+        },
+        here: {
+          type: "boolean",
+          description: "Update in the current directory",
+          default: false
+        },
+        tier: {
+          type: "string",
+          description: "Change tier: 'local' (free) or 'cloud' (managed)"
+        },
+        force: {
+          type: "boolean",
+          description: "Force update even if versions match",
+          default: false
+        },
+        "local-source": {
+          type: "boolean",
+          description: "Force use of local template/ directory",
           default: false
         },
         yes: {
@@ -2644,11 +3978,11 @@ 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 {
-          const choice = await select2({
+          const choice = await select3({
             message: "Which project would you like to update?",
             options: [
               {
@@ -2661,21 +3995,21 @@ 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 ?? "~")
             );
           }
@@ -2684,11 +4018,11 @@ 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(join16(targetDir, ".flydocs", "version"));
+        const hasVersion = await pathExists(join21(targetDir, ".flydocs", "version"));
         const hasConfig = await pathExists(
-          join16(targetDir, ".flydocs", "config.json")
+          join21(targetDir, ".flydocs", "config.json")
         );
         if (!hasVersion && !hasConfig) {
           printError(`Not a FlyDocs project: ${targetDir}`);
@@ -2699,8 +4033,8 @@ var init_update = __esm({
         console.log();
         let currentVersion = "0.1.0";
         if (hasVersion) {
-          const vContent = await readFile11(
-            join16(targetDir, ".flydocs", "version"),
+          const vContent = await readFile15(
+            join21(targetDir, ".flydocs", "version"),
             "utf-8"
           );
           currentVersion = vContent.trim();
@@ -2719,10 +4053,10 @@ var init_update = __esm({
           printWarning(
             `Project version (${currentVersion}) is newer than installer (${version})`
           );
-          const shouldContinue = await confirm3({
+          const shouldContinue = await confirm4({
             message: "Continue anyway?"
           });
-          if (isCancel4(shouldContinue) || !shouldContinue) {
+          if (isCancel5(shouldContinue) || !shouldContinue) {
             process.exit(0);
           }
         }
@@ -2734,10 +4068,10 @@ var init_update = __esm({
         });
         console.log(`Updating: v${currentVersion} \u2192 v${version}`);
         console.log();
-        const changelogPath = join16(templateDir, "CHANGELOG.md");
+        const changelogPath = join21(templateDir, "CHANGELOG.md");
         const whatsNew = await getWhatsNew(changelogPath, currentVersion, version);
         if (whatsNew.length > 0) {
-          console.log(pc7.cyan("What's new:"));
+          console.log(pc9.cyan("What's new:"));
           console.log();
           for (const entry of whatsNew) {
             console.log(`  ${entry}`);
@@ -2746,36 +4080,37 @@ var init_update = __esm({
         }
         const now = /* @__PURE__ */ new Date();
         const ts = `${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")}${String(now.getSeconds()).padStart(2, "0")}`;
-        const backupDir = join16(targetDir, ".flydocs", `backup-${ts}`);
-        await mkdir8(backupDir, { recursive: true });
+        const backupDir = join21(targetDir, ".flydocs", `backup-${ts}`);
+        await mkdir10(backupDir, { recursive: true });
         if (hasConfig) {
           await cp2(
-            join16(targetDir, ".flydocs", "config.json"),
-            join16(backupDir, "config.json")
+            join21(targetDir, ".flydocs", "config.json"),
+            join21(backupDir, "config.json")
           );
           printStatus(`Config backed up to .flydocs/backup-${ts}/`);
         }
         try {
-          const flydocsDir = join16(targetDir, ".flydocs");
-          const entries = await readdir3(flydocsDir);
+          const flydocsDir = join21(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(join16(flydocsDir, old), { recursive: true, force: true });
+              await rm5(join21(flydocsDir, old), { recursive: true, force: true });
             }
           }
         } catch {
         }
         let preserved = {
-          tier: "cloud",
+          tier: "local",
           setupComplete: false,
-          providerTeamId: null,
+          workspaceId: null,
+          configVersion: void 0,
           workspace: {},
           issueLabels: {},
-          statusMapping: {},
           detectedStack: {},
           skills: {},
+          topology: void 0,
           designSystem: null,
           aiLabor: {}
         };
@@ -2797,22 +4132,20 @@ var init_update = __esm({
         } else {
           effectiveTier = preserved.tier;
         }
+        await ensureDirectories(targetDir, effectiveTier);
         console.log("Replacing framework directories...");
         await replaceDirectory(
-          join16(templateDir, ".flydocs", "templates"),
-          join16(targetDir, ".flydocs", "templates")
-        );
-        await replaceDirectory(
-          join16(templateDir, ".flydocs", "hooks"),
-          join16(targetDir, ".flydocs", "hooks")
+          join21(templateDir, ".flydocs", "templates"),
+          join21(targetDir, ".flydocs", "templates")
         );
+        printStatus(".flydocs/templates");
         await replaceDirectory(
-          join16(templateDir, ".flydocs", "scripts"),
-          join16(targetDir, ".flydocs", "scripts")
+          join21(templateDir, ".claude", "hooks"),
+          join21(targetDir, ".claude", "hooks")
         );
-        printStatus(".flydocs/templates, hooks, scripts");
+        printStatus(".claude/hooks");
         const hasExistingAgents = await pathExists(
-          join16(targetDir, ".claude", "agents")
+          join21(targetDir, ".claude", "agents")
         );
         let installAgents;
         if (args.yes) {
@@ -2821,7 +4154,7 @@ var init_update = __esm({
           installAgents = true;
         } else {
           console.log();
-          console.log(`  ${pc7.bold(pc7.yellow("Sub-Agents (Recommended)"))}`);
+          console.log(`  ${pc9.bold(pc9.yellow("Sub-Agents (Recommended)"))}`);
           console.log();
           console.log(
             "  Sub-agents are specialized roles (PM, implementation, review,"
@@ -2833,31 +4166,31 @@ 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 = join16(templateDir, ".claude", "agents");
+          const claudeAgentsSrc = join21(templateDir, ".claude", "agents");
           if (await pathExists(claudeAgentsSrc)) {
-            await mkdir8(join16(targetDir, ".claude", "agents"), { recursive: true });
+            await mkdir10(join21(targetDir, ".claude", "agents"), { recursive: true });
             await copyDirectoryContents(
               claudeAgentsSrc,
-              join16(targetDir, ".claude", "agents")
+              join21(targetDir, ".claude", "agents")
             );
           }
-          const cursorAgentsSrc = join16(templateDir, ".cursor", "agents");
+          const cursorAgentsSrc = join21(templateDir, ".cursor", "agents");
           if (await pathExists(cursorAgentsSrc)) {
-            await mkdir8(join16(targetDir, ".cursor", "agents"), { recursive: true });
+            await mkdir10(join21(targetDir, ".cursor", "agents"), { recursive: true });
             await copyDirectoryContents(
               cursorAgentsSrc,
-              join16(targetDir, ".cursor", "agents")
+              join21(targetDir, ".cursor", "agents")
             );
           }
           printStatus(
@@ -2871,46 +4204,62 @@ var init_update = __esm({
         console.log();
         console.log("Replacing framework files...");
         await copyFile(
-          join16(templateDir, ".claude", "CLAUDE.md"),
-          join16(targetDir, ".claude", "CLAUDE.md")
+          join21(templateDir, ".claude", "CLAUDE.md"),
+          join21(targetDir, ".claude", "CLAUDE.md")
         );
         await copyFile(
-          join16(templateDir, ".claude", "settings.json"),
-          join16(targetDir, ".claude", "settings.json")
+          join21(templateDir, ".claude", "settings.json"),
+          join21(targetDir, ".claude", "settings.json")
         );
         printStatus(".claude/CLAUDE.md, settings.json");
         await copyDirectoryContents(
-          join16(templateDir, ".claude", "commands"),
-          join16(targetDir, ".claude", "commands")
+          join21(templateDir, ".claude", "commands"),
+          join21(targetDir, ".claude", "commands")
         );
         await copyDirectoryContents(
-          join16(templateDir, ".claude", "commands"),
-          join16(targetDir, ".cursor", "commands")
+          join21(templateDir, ".claude", "commands"),
+          join21(targetDir, ".cursor", "commands")
         );
         printStatus(".claude/commands, .cursor/commands");
-        const skillsReadmeSrc = join16(templateDir, ".claude", "skills", "README.md");
+        const skillsReadmeSrc = join21(templateDir, ".claude", "skills", "README.md");
         if (await pathExists(skillsReadmeSrc)) {
           await copyFile(
             skillsReadmeSrc,
-            join16(targetDir, ".claude", "skills", "README.md")
+            join21(targetDir, ".claude", "skills", "README.md")
           );
         }
         printStatus(".claude/skills/README.md");
         await copyFile(
-          join16(templateDir, ".cursor", "hooks.json"),
-          join16(targetDir, ".cursor", "hooks.json")
+          join21(templateDir, ".cursor", "hooks.json"),
+          join21(targetDir, ".cursor", "hooks.json")
         );
         printStatus(".cursor/hooks.json");
         await copyFile(
-          join16(templateDir, "AGENTS.md"),
-          join16(targetDir, "AGENTS.md")
+          join21(templateDir, "AGENTS.md"),
+          join21(targetDir, "AGENTS.md")
         );
         printStatus("AGENTS.md");
-        const envExampleSrc = join16(templateDir, ".env.example");
+        const envExampleSrc = join21(templateDir, ".env.example");
         if (await pathExists(envExampleSrc)) {
-          await copyFile(envExampleSrc, join16(targetDir, ".env.example"));
+          await copyFile(envExampleSrc, join21(targetDir, ".env.example"));
           printStatus(".env.example");
         }
+        const knowledgeTemplatesDir = join21(
+          targetDir,
+          "flydocs",
+          "knowledge",
+          "templates"
+        );
+        if (!await pathExists(knowledgeTemplatesDir)) {
+          await mkdir10(knowledgeTemplatesDir, { recursive: true });
+        }
+        for (const tmpl of ["decision.md", "feature.md", "note.md"]) {
+          const src = join21(templateDir, "flydocs", "knowledge", "templates", tmpl);
+          const dest = join21(knowledgeTemplatesDir, tmpl);
+          if (await pathExists(src) && !await pathExists(dest)) {
+            await copyFile(src, dest);
+          }
+        }
         await runManifestGeneration(targetDir);
         await runContextGraphBuild(targetDir);
         console.log();
@@ -2933,20 +4282,22 @@ var init_update = __esm({
           printWarning("Config merge failed \u2014 config.json preserved as-is");
         }
         await copyFile(
-          join16(templateDir, ".flydocs", "version"),
-          join16(targetDir, ".flydocs", "version")
+          join21(templateDir, ".flydocs", "version"),
+          join21(targetDir, ".flydocs", "version")
         );
         printStatus(`.flydocs/version \u2192 ${version}`);
-        const clSrc = join16(templateDir, "CHANGELOG.md");
+        const clSrc = join21(templateDir, "CHANGELOG.md");
         if (await pathExists(clSrc)) {
-          await copyFile(clSrc, join16(targetDir, ".flydocs", "CHANGELOG.md"));
+          await copyFile(clSrc, join21(targetDir, ".flydocs", "CHANGELOG.md"));
           printStatus(".flydocs/CHANGELOG.md");
         }
-        const mfSrc = join16(templateDir, "manifest.json");
+        const mfSrc = join21(templateDir, "manifest.json");
         if (await pathExists(mfSrc)) {
-          await copyFile(mfSrc, join16(targetDir, ".flydocs", "manifest.json"));
+          await copyFile(mfSrc, join21(targetDir, ".flydocs", "manifest.json"));
           printStatus(".flydocs/manifest.json");
         }
+        await generateIntegrity(targetDir, version);
+        printStatus("Install integrity recorded");
         console.log();
         console.log("Detecting project stack...");
         const stack = await detectStack(targetDir);
@@ -2963,6 +4314,7 @@ var init_update = __esm({
           printInfo("No framework detected in package.json");
         }
         await migrateGitignore(targetDir);
+        await ensurePlatformIgnores(targetDir);
         console.log();
         console.log("Checking for deprecated files...");
         await handleLegacyContext(targetDir);
@@ -3003,22 +4355,22 @@ var uninstall_exports = {};
 __export(uninstall_exports, {
   default: () => uninstall_default
 });
-import { defineCommand as defineCommand3 } from "citty";
-import { resolve as resolve4, join as join17 } from "path";
-import { readdir as readdir4, 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 defineCommand5 } from "citty";
+import { resolve as resolve5, join as join22 } from "path";
+import { readdir as readdir6, rm as rm6, rename as rename2 } from "fs/promises";
+import { confirm as confirm5, select as select4, isCancel as isCancel6, cancel as cancel5 } from "@clack/prompts";
+import pc10 from "picocolors";
 async function removeOwnedSkills(targetDir) {
-  const skillsDir = join17(targetDir, ".claude", "skills");
+  const skillsDir = join22(targetDir, ".claude", "skills");
   const removed = [];
   if (!await pathExists(skillsDir)) {
     return removed;
   }
   try {
-    const entries = await readdir4(skillsDir);
+    const entries = await readdir6(skillsDir);
     for (const entry of entries) {
       if (entry.startsWith(OWNED_SKILL_PREFIX)) {
-        await rm5(join17(skillsDir, entry), { recursive: true, force: true });
+        await rm6(join22(skillsDir, entry), { recursive: true, force: true });
         removed.push(`.claude/skills/${entry}`);
       }
     }
@@ -3027,16 +4379,16 @@ async function removeOwnedSkills(targetDir) {
   return removed;
 }
 async function removeOwnedCursorRules(targetDir) {
-  const rulesDir = join17(targetDir, ".cursor", "rules");
+  const rulesDir = join22(targetDir, ".cursor", "rules");
   const removed = [];
   if (!await pathExists(rulesDir)) {
     return removed;
   }
   try {
-    const entries = await readdir4(rulesDir);
+    const entries = await readdir6(rulesDir);
     for (const entry of entries) {
       if (entry.startsWith(OWNED_RULE_PREFIX) && entry.endsWith(".mdc")) {
-        await rm5(join17(rulesDir, entry), { force: true });
+        await rm6(join22(rulesDir, entry), { force: true });
         removed.push(`.cursor/rules/${entry}`);
       }
     }
@@ -3046,7 +4398,7 @@ async function removeOwnedCursorRules(targetDir) {
 }
 async function isEmptyDir(dirPath) {
   try {
-    const entries = await readdir4(dirPath);
+    const entries = await readdir6(dirPath);
     return entries.length === 0;
   } catch {
     return false;
@@ -3055,9 +4407,9 @@ async function isEmptyDir(dirPath) {
 async function cleanupEmptyParents(targetDir, dirs) {
   const cleaned = [];
   for (const dir of dirs) {
-    const fullPath = join17(targetDir, dir);
+    const fullPath = join22(targetDir, dir);
     if (await pathExists(fullPath) && await isEmptyDir(fullPath)) {
-      await rm5(fullPath, { recursive: true, force: true });
+      await rm6(fullPath, { recursive: true, force: true });
       cleaned.push(dir);
     }
   }
@@ -3076,16 +4428,18 @@ var init_uninstall = __esm({
       [".claude/settings.json", "file"],
       [".claude/agents", "dir"],
       [".claude/commands", "dir"],
+      [".claude/hooks", "dir"],
       [".claude/skills/README.md", "file"],
       [".cursor/hooks.json", "file"],
       [".cursor/agents", "dir"],
+      [".cursor/commands", "dir"],
       [".flydocs", "dir"],
       ["AGENTS.md", "file"],
       [".env.example", "file"]
     ];
     OWNED_SKILL_PREFIX = "flydocs-";
     OWNED_RULE_PREFIX = "flydocs-";
-    uninstall_default = defineCommand3({
+    uninstall_default = defineCommand5({
       meta: {
         name: "uninstall",
         description: "Remove FlyDocs from a project directory"
@@ -3121,7 +4475,7 @@ 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 {
@@ -3131,9 +4485,9 @@ var init_uninstall = __esm({
           printError(`Directory does not exist: ${targetDir}`);
           process.exit(1);
         }
-        targetDir = resolve4(targetDir);
-        const hasFlydocs = await pathExists(join17(targetDir, ".flydocs"));
-        const hasAgentsMd = await pathExists(join17(targetDir, "AGENTS.md"));
+        targetDir = resolve5(targetDir);
+        const hasFlydocs = await pathExists(join22(targetDir, ".flydocs"));
+        const hasAgentsMd = await pathExists(join22(targetDir, "AGENTS.md"));
         if (!hasFlydocs && !hasAgentsMd) {
           printError(`Not a FlyDocs project: ${targetDir}`);
           printInfo("No .flydocs/ directory or AGENTS.md found.");
@@ -3145,12 +4499,12 @@ var init_uninstall = __esm({
         const removeAll = forceAll || args.all;
         const skipPrompts = forceAll || args.yes;
         let contentAction = "preserve";
-        const hasUserContent = await pathExists(join17(targetDir, "flydocs"));
+        const hasUserContent = await pathExists(join22(targetDir, "flydocs"));
         if (hasUserContent) {
           if (removeAll) {
             contentAction = "remove";
           } else if (!skipPrompts) {
-            const choice = await select3({
+            const choice = await select4({
               message: "What should happen to your flydocs/ content (project docs, knowledge base)?",
               options: [
                 {
@@ -3170,8 +4524,8 @@ var init_uninstall = __esm({
                 }
               ]
             });
-            if (isCancel5(choice)) {
-              cancel4("Uninstall cancelled.");
+            if (isCancel6(choice)) {
+              cancel5("Uninstall cancelled.");
               process.exit(0);
             }
             contentAction = choice;
@@ -3179,40 +4533,40 @@ var init_uninstall = __esm({
         }
         if (!skipPrompts) {
           console.log();
-          console.log(pc8.bold("The following will be removed:"));
+          console.log(pc10.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(`    ${pc10.dim(path)}`);
           }
-          console.log(`    ${pc8.dim(".claude/skills/flydocs-*")}`);
-          console.log(`    ${pc8.dim(".cursor/rules/flydocs-*.mdc")}`);
+          console.log(`    ${pc10.dim(".claude/skills/flydocs-*")}`);
+          console.log(`    ${pc10.dim(".cursor/rules/flydocs-*.mdc")}`);
           if (hasUserContent) {
             if (contentAction === "archive") {
               console.log();
               console.log(
-                `  User content: ${pc8.yellow("flydocs/ -> flydocs-archive/")}`
+                `  User content: ${pc10.yellow("flydocs/ -> flydocs-archive/")}`
               );
             } else if (contentAction === "remove") {
               console.log();
-              console.log(`  User content: ${pc8.red("flydocs/ (deleted)")}`);
+              console.log(`  User content: ${pc10.red("flydocs/ (deleted)")}`);
             } else {
               console.log();
-              console.log(`  User content: ${pc8.green("flydocs/ (preserved)")}`);
+              console.log(`  User content: ${pc10.green("flydocs/ (preserved)")}`);
             }
           }
           console.log();
-          console.log(pc8.bold("Preserved:"));
+          console.log(pc10.bold("Preserved:"));
           console.log(
-            `    ${pc8.dim(".claude/skills/ (non-flydocs community skills)")}`
+            `    ${pc10.dim(".claude/skills/ (non-flydocs community skills)")}`
           );
-          console.log(`    ${pc8.dim(".env, .env.local")}`);
+          console.log(`    ${pc10.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);
           }
         }
@@ -3228,16 +4582,16 @@ var init_uninstall = __esm({
         const removedRules = await removeOwnedCursorRules(targetDir);
         result.removed.push(...removedRules);
         for (const [relativePath, type] of ALWAYS_REMOVED) {
-          const fullPath = join17(targetDir, relativePath);
+          const fullPath = join22(targetDir, relativePath);
           if (!await pathExists(fullPath)) {
             result.skipped.push(relativePath);
             continue;
           }
           try {
             if (type === "dir") {
-              await rm5(fullPath, { recursive: true, force: true });
+              await rm6(fullPath, { recursive: true, force: true });
             } else {
-              await rm5(fullPath, { force: true });
+              await rm6(fullPath, { force: true });
             }
             result.removed.push(relativePath);
           } catch {
@@ -3246,16 +4600,16 @@ var init_uninstall = __esm({
           }
         }
         if (hasUserContent) {
-          const flydocsPath = join17(targetDir, "flydocs");
+          const flydocsPath = join22(targetDir, "flydocs");
           if (contentAction === "archive") {
-            const archivePath = join17(targetDir, "flydocs-archive");
+            const archivePath = join22(targetDir, "flydocs-archive");
             if (await pathExists(archivePath)) {
-              await rm5(archivePath, { recursive: true, force: true });
+              await rm6(archivePath, { recursive: true, force: true });
             }
             await rename2(flydocsPath, archivePath);
             result.archived.push("flydocs/ -> flydocs-archive/");
           } else if (contentAction === "remove") {
-            await rm5(flydocsPath, { recursive: true, force: true });
+            await rm6(flydocsPath, { recursive: true, force: true });
             result.removed.push("flydocs/");
           }
         }
@@ -3274,17 +4628,17 @@ var init_uninstall = __esm({
           result.restored = originals.map((f) => f.relativePath);
         }
         console.log();
-        console.log(pc8.bold("Uninstall Summary"));
+        console.log(pc10.bold("Uninstall Summary"));
         console.log();
         if (result.removed.length > 0) {
-          console.log(`  ${pc8.green("Removed")} (${result.removed.length}):`);
+          console.log(`  ${pc10.green("Removed")} (${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(`  ${pc10.yellow("Archived")} (${result.archived.length}):`);
           for (const item of result.archived) {
             printInfo(item);
           }
@@ -3292,7 +4646,7 @@ var init_uninstall = __esm({
         if (result.restored.length > 0) {
           console.log();
           console.log(
-            `  ${pc8.green("Restored")} (${result.restored.length} pre-FlyDocs original(s)):`
+            `  ${pc10.green("Restored")} (${result.restored.length} pre-FlyDocs original(s)):`
           );
           for (const item of result.restored) {
             printInfo(item);
@@ -3301,16 +4655,16 @@ var init_uninstall = __esm({
         if (result.skipped.length > 0) {
           console.log();
           console.log(
-            `  ${pc8.dim("Skipped")} (${result.skipped.length} \u2014 not found):`
+            `  ${pc10.dim("Skipped")} (${result.skipped.length} \u2014 not found):`
           );
           for (const item of result.skipped) {
-            console.log(`  ${pc8.dim(item)}`);
+            console.log(`  ${pc10.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: ${pc10.cyan("npx @flydocs/cli install --here")}`);
         console.log();
       }
     });
@@ -3322,28 +4676,28 @@ var setup_exports = {};
 __export(setup_exports, {
   default: () => setup_default
 });
-import { defineCommand as defineCommand4 } from "citty";
-import pc9 from "picocolors";
+import { defineCommand as defineCommand6 } from "citty";
+import pc11 from "picocolors";
 var setup_default;
 var init_setup = __esm({
   "src/commands/setup.ts"() {
     "use strict";
-    setup_default = defineCommand4({
+    setup_default = defineCommand6({
       meta: {
         name: "setup",
         description: "Configure FlyDocs settings for this project"
       },
       run() {
         console.log();
-        console.log(`  ${pc9.bold("FlyDocs Setup")}`);
+        console.log(`  ${pc11.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`
+          `  ${pc11.cyan("Claude Code:")}  Type ${pc11.bold("/flydocs-setup")} in chat`
         );
         console.log(
-          `  ${pc9.cyan("Cursor:")}      Type ${pc9.bold("/flydocs-setup")} in chat`
+          `  ${pc11.cyan("Cursor:")}      Type ${pc11.bold("/flydocs-setup")} in chat`
         );
         console.log();
         console.log(`  This configures your project context, detects your stack,`);
@@ -3359,14 +4713,14 @@ var skills_exports = {};
 __export(skills_exports, {
   default: () => skills_default
 });
-import { defineCommand as defineCommand5 } from "citty";
-import pc10 from "picocolors";
+import { defineCommand as defineCommand7 } from "citty";
+import pc12 from "picocolors";
 var list, search, add, remove, skills_default;
 var init_skills2 = __esm({
   "src/commands/skills.ts"() {
     "use strict";
     init_skill_manager();
-    list = defineCommand5({
+    list = defineCommand7({
       meta: {
         name: "list",
         description: "List installed skills"
@@ -3382,26 +4736,26 @@ var init_skills2 = __esm({
         console.log(`${total} skill(s) installed:`);
         if (result.platform.length > 0) {
           console.log();
-          console.log(pc10.bold("Platform"));
+          console.log(pc12.bold("Platform"));
           for (const skill of result.platform) {
             console.log(
-              `  ${skill.name} ${pc10.dim(`(${skill.triggers} triggers)`)}`
+              `  ${skill.name} ${pc12.dim(`(${skill.triggers} triggers)`)}`
             );
           }
         }
         if (result.community.length > 0) {
           console.log();
-          console.log(pc10.bold("Community"));
+          console.log(pc12.bold("Community"));
           for (const skill of result.community) {
             console.log(
-              `  ${skill.name} ${pc10.dim(`(${skill.triggers} triggers)`)}`
+              `  ${skill.name} ${pc12.dim(`(${skill.triggers} triggers)`)}`
             );
           }
         }
         console.log();
       }
     });
-    search = defineCommand5({
+    search = defineCommand7({
       meta: {
         name: "search",
         description: "Search community skills"
@@ -3417,24 +4771,24 @@ 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: ${pc12.cyan("https://skills.sh/")}`);
           return;
         }
         console.log();
         console.log(`${results.length} skill(s) matching "${args.keyword}":`);
         console.log();
         for (const skill of results) {
-          console.log(`  ${pc10.bold(skill.name)}`);
+          console.log(`  ${pc12.bold(skill.name)}`);
           console.log(`  ${skill.description}`);
-          console.log(`  ${pc10.dim(skill.repo)}`);
+          console.log(`  ${pc12.dim(skill.repo)}`);
           if (skill.tags.length > 0) {
-            console.log(`  ${pc10.dim(skill.tags.join(", "))}`);
+            console.log(`  ${pc12.dim(skill.tags.join(", "))}`);
           }
           console.log();
         }
       }
     });
-    add = defineCommand5({
+    add = defineCommand7({
       meta: {
         name: "add",
         description: "Install a community skill"
@@ -3450,7 +4804,7 @@ var init_skills2 = __esm({
         await addSkill(process.cwd(), args.source);
       }
     });
-    remove = defineCommand5({
+    remove = defineCommand7({
       meta: {
         name: "remove",
         description: "Remove an installed community skill"
@@ -3466,7 +4820,7 @@ var init_skills2 = __esm({
         await removeSkill(process.cwd(), args.name);
       }
     });
-    skills_default = defineCommand5({
+    skills_default = defineCommand7({
       meta: {
         name: "skills",
         description: "Manage FlyDocs skills (list, search, add, remove)"
@@ -3486,10 +4840,10 @@ 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 join18 } from "path";
+import { defineCommand as defineCommand8 } from "citty";
+import { text as text4, confirm as confirm6, isCancel as isCancel7, cancel as cancel6 } from "@clack/prompts";
+import pc13 from "picocolors";
+import { join as join23 } from "path";
 var connect_default;
 var init_connect = __esm({
   "src/commands/connect.ts"() {
@@ -3499,7 +4853,7 @@ var init_connect = __esm({
     init_template();
     init_ui();
     init_api_key();
-    connect_default = defineCommand6({
+    connect_default = defineCommand8({
       meta: {
         name: "connect",
         description: "Connect FlyDocs to a cloud provider"
@@ -3519,16 +4873,16 @@ var init_connect = __esm({
         },
         key: {
           type: "string",
-          description: "API key (fdk_ for relay, lin_api_ for direct Linear)"
+          description: "FlyDocs API key (fdk_...)"
         }
       },
       async run({ args }) {
         const targetDir = args.path ?? process.cwd();
-        const configPath = join18(targetDir, ".flydocs", "config.json");
+        const configPath = join23(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 ${pc13.cyan("flydocs")} first to install FlyDocs in this project.`
           );
           process.exit(1);
         }
@@ -3536,46 +4890,45 @@ 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(`  ${pc13.bold("Connect to FlyDocs Cloud")}`);
         console.log();
         console.log(
-          `  ${pc11.dim("FlyDocs API key (fdk_...): Get from your FlyDocs dashboard")}`
-        );
-        console.log(
-          `  ${pc11.dim("Linear API key (lin_api_...): Get from Linear \u2192 Settings \u2192 API")}`
+          `  ${pc13.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_... or lin_api_...",
+            placeholder: "fdk_...",
             validate(value) {
               if (!value.trim()) return "API key is required";
               const type = detectKeyType(value.trim());
               if (type === "unknown")
-                return "Key must start with fdk_ (FlyDocs) or lin_api_ (Linear)";
+                return "Key must start with fdk_ (FlyDocs API key)";
               return void 0;
             }
           });
-          if (isCancel6(keyInput)) {
-            cancel5("Connection cancelled.");
+          if (isCancel7(keyInput)) {
+            cancel6("Connection cancelled.");
             process.exit(0);
           }
           apiKey = keyInput.trim();
         }
         const keyType = detectKeyType(apiKey);
         if (keyType === "unknown") {
-          printError("Unrecognized key format. Expected fdk_ or lin_api_ prefix.");
+          printError(
+            "Unrecognized key format. Expected fdk_ prefix (FlyDocs API key)."
+          );
           process.exit(1);
         }
         printInfo("Validating API key...");
@@ -3587,7 +4940,7 @@ 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 ${pc13.bold(result.org)}`);
           } catch {
             printError(
               "Could not reach relay API. Check your network and try again."
@@ -3595,7 +4948,7 @@ 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 ${pc13.dim(envFile)}`);
         } else {
           try {
             const result = await validateLinearKey(apiKey);
@@ -3605,7 +4958,7 @@ var init_connect = __esm({
               process.exit(1);
             }
             printStatus(
-              `Authenticated as ${pc11.bold(result.name)} (${result.email})`
+              `Authenticated as ${pc13.bold(result.name)} (${result.email})`
             );
           } catch {
             printError("Invalid API key or network error.");
@@ -3613,47 +4966,274 @@ 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 ${pc13.dim(envFile)}`);
         }
         const wasLocal = config.tier === "local";
         config.tier = "cloud";
-        config.provider = config.provider ?? { type: "linear", teamId: null };
-        config.provider.type = "linear";
+        const configRecord = config;
+        delete configRecord.statusMapping;
+        delete configRecord.provider;
         await writeConfig(targetDir, config);
         printStatus("Config updated to cloud tier");
         if (wasLocal) {
-          try {
-            const templateDir = await resolveTemplatePath(
-              args["local-source"] || void 0
-            );
-            const templateSkillsDir = join18(templateDir, ".claude", "skills");
-            const skillsDir = join18(targetDir, ".claude", "skills");
-            await replaceDirectory(
-              join18(templateSkillsDir, "flydocs-cloud"),
-              join18(skillsDir, "flydocs-cloud")
-            );
-            const { rm: rm6 } = await import("fs/promises");
-            const localSkillDir = join18(skillsDir, "flydocs-local");
-            if (await pathExists(localSkillDir)) {
-              await rm6(localSkillDir, { recursive: true, force: true });
-            }
-            printStatus("Cloud mechanism skill installed");
-          } catch {
-            printInfo(
-              "Could not swap mechanism skills automatically. Run flydocs update to complete."
-            );
-          }
+          printInfo(
+            "Tier changed to cloud. Run flydocs update to refresh skill scripts."
+          );
         }
         console.log();
         console.log(
-          `  ${pc11.bold("Connected!")} Your project is now on the cloud tier.`
+          `  ${pc13.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 ${pc13.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 ${pc13.cyan("/start-session")} to begin working`);
+        console.log();
+      }
+    });
+  }
+});
+
+// src/commands/auth.ts
+var auth_exports = {};
+__export(auth_exports, {
+  default: () => auth_default
+});
+import { defineCommand as defineCommand9 } from "citty";
+import { text as text5, confirm as confirm7, isCancel as isCancel8, cancel as cancel7 } from "@clack/prompts";
+import pc14 from "picocolors";
+var auth_default;
+var init_auth = __esm({
+  "src/commands/auth.ts"() {
+    "use strict";
+    init_ui();
+    init_api_key();
+    init_global_config();
+    auth_default = defineCommand9({
+      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(`  ${pc14.bold("FlyDocs Authentication")}`);
+        console.log();
+        let apiKey = args.key ?? "";
+        const existing = await readGlobalCredential();
+        if (existing?.apiKey && !apiKey) {
+          printInfo(
+            `Existing key found: ${pc14.dim(existing.apiKey.slice(0, 8) + "...")}`
+          );
+          const replace = await confirm7({
+            message: "Replace with a new key?"
+          });
+          if (isCancel8(replace) || !replace) {
+            console.log(`  No changes made.`);
+            return;
+          }
+        }
+        if (!apiKey) {
+          console.log(
+            `  ${pc14.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 ${pc14.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 ${pc14.dim(credentialsPath())}`);
+        await checkCredentialPermissions();
+        console.log();
+        console.log(`  ${pc14.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 defineCommand10 } from "citty";
+import pc15 from "picocolors";
+import { join as join24 } from "path";
+import { mkdir as mkdir11, writeFile as writeFile14 } from "fs/promises";
+var sync_default;
+var init_sync = __esm({
+  "src/commands/sync.ts"() {
+    "use strict";
+    init_ui();
+    init_global_config();
+    init_config();
+    init_config_integrity();
+    init_fs_ops();
+    init_types();
+    init_relay_client();
+    sync_default = defineCommand10({
+      meta: {
+        name: "sync",
+        description: "Pull latest config and templates from server"
+      },
+      args: {
+        path: {
+          type: "string",
+          description: "Path to project directory"
+        }
+      },
+      async run({ args }) {
+        const targetDir = args.path ?? process.cwd();
+        const changes = [];
+        console.log();
+        printInfo("Syncing with server...");
+        const resolved = await resolveApiKey(void 0, targetDir);
+        if (!resolved) {
+          printError(
+            "No API key found. Run `flydocs auth` or `flydocs init` first."
+          );
+          process.exit(1);
+        }
+        const apiKey = resolved.key;
+        const cred = await readGlobalCredential();
+        const workspaceId = cred?.workspaceId;
+        if (!workspaceId) {
+          printError(
+            "No workspace ID found. Run `flydocs init` to set up your workspace."
+          );
+          process.exit(1);
+        }
+        let currentTemplateVersion = 0;
+        try {
+          const currentConfig = await readAnyConfig(targetDir);
+          if (isConfigV2(currentConfig)) {
+            currentTemplateVersion = currentConfig.configVersion ?? 0;
+          }
+        } catch {
+        }
+        let serverResponse;
+        try {
+          serverResponse = await fetchConfigV2(apiKey, { workspaceId });
+        } catch (err) {
+          if (err instanceof RelayError) {
+            printWarning(
+              `Server unavailable (${err.status}), using cached config.`
+            );
+          } else {
+            printWarning("Server unreachable, using cached config.");
+          }
+          console.log(`  ${pc15.dim("Config may be stale. Retry when connected.")}`);
+          return;
+        }
+        if (!serverResponse.valid) {
+          printWarning("Server returned invalid config. Keeping current config.");
+          return;
+        }
+        await mkdir11(join24(targetDir, ".flydocs"), { recursive: true });
+        const configWithHash = applyConfigHash(serverResponse.config);
+        await writeConfig(targetDir, configWithHash);
+        changes.push("Updated .flydocs/config.json");
+        const serverTemplateVersion = serverResponse.templates.version;
+        if (serverTemplateVersion > currentTemplateVersion) {
+          try {
+            const templatesResponse = await fetchTemplates(
+              apiKey,
+              currentTemplateVersion,
+              workspaceId
+            );
+            if (templatesResponse.templates.length > 0) {
+              const templatesDir = join24(
+                targetDir,
+                ".claude",
+                "skills",
+                "flydocs-workflow",
+                "templates"
+              );
+              await mkdir11(templatesDir, { recursive: true });
+              for (const template of templatesResponse.templates) {
+                const filename = `${template.type}.md`;
+                const subdir = template.category === "issue" ? "issues" : template.category === "pr" ? "pr" : template.category === "comment" ? "." : ".";
+                const templateDir = join24(templatesDir, subdir);
+                await mkdir11(templateDir, { recursive: true });
+                await writeFile14(
+                  join24(templateDir, filename),
+                  template.content,
+                  "utf-8"
+                );
+              }
+              changes.push(
+                `Updated ${templatesResponse.templates.length} templates (v${currentTemplateVersion} \u2192 v${serverTemplateVersion})`
+              );
+            }
+          } catch (err) {
+            if (err instanceof RelayError) {
+              printWarning("Could not fetch templates. Will retry on next sync.");
+            } else {
+              printWarning("Template sync failed. Will retry on next sync.");
+            }
+          }
+        }
+        if (changes.length === 0) {
+          printStatus("Already up to date.");
+        } else {
+          for (const change of changes) {
+            printStatus(change);
+          }
+        }
         console.log();
       }
     });
@@ -3665,15 +5245,15 @@ 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"
@@ -3702,38 +5282,34 @@ 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(
-            `  Your issues sync with Linear via the cloud mechanism skill.`
-          );
-          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 coming soon)`
-        );
-        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();
@@ -3747,23 +5323,23 @@ 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`, {
@@ -3788,15 +5364,15 @@ 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"
@@ -3811,7 +5387,7 @@ var init_telemetry2 = __esm({
         }
       }
     });
-    disable = defineCommand9({
+    disable = defineCommand13({
       meta: {
         name: "disable",
         description: "Disable anonymous usage analytics"
@@ -3829,7 +5405,7 @@ var init_telemetry2 = __esm({
         }
       }
     });
-    status = defineCommand9({
+    status = defineCommand13({
       meta: {
         name: "status",
         description: "Show current telemetry status"
@@ -3837,37 +5413,37 @@ 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)"
@@ -3883,14 +5459,18 @@ 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"
@@ -3903,7 +5483,7 @@ 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,
@@ -3911,11 +5491,15 @@ 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)