@flydocs/cli 0.6.0-alpha.2 → 0.6.0-alpha.20

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.2";
+    CLI_VERSION = "0.6.0-alpha.20";
     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(text3) {
-  return `\x1B[38;2;55;45;70m${text3}\x1B[0m`;
+function shadow(text4) {
+  return `\x1B[38;2;55;45;70m${text4}\x1B[0m`;
 }
 function renderBannerBlock() {
   const height = BANNER_ROWS.length;
@@ -292,12 +293,13 @@ 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 +313,9 @@ 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 +323,15 @@ 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;
   }
@@ -348,75 +348,32 @@ var init_config = __esm({
 
 // 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")
+    join4(templateSkillsDir, OWNED_SKILL),
+    join4(skillsDir, OWNED_SKILL)
   );
-  const activeMech = MECHANISM_SKILLS[tier];
-  const inactiveMech = tier === "local" ? MECHANISM_SKILLS.cloud : MECHANISM_SKILLS.local;
-  await replaceDirectory(
-    join4(templateSkillsDir, activeMech),
-    join4(skillsDir, activeMech)
-  );
-  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 });
-  }
   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 rm6(legacyPath, { recursive: true, force: true });
+    }
+  }
   const readmeSrc = join4(templateSkillsDir, "README.md");
   if (await pathExists(readmeSrc)) {
     await copyFile(readmeSrc, join4(skillsDir, "README.md"));
@@ -430,50 +387,34 @@ async function copyCursorRules(targetDir) {
     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: rm6 } = await import("fs/promises");
+  for (const legacy of ["flydocs-mechanism.mdc", "flydocs-context7.mdc"]) {
+    const legacyRule = join4(rulesDir, legacy);
+    if (await pathExists(legacyRule)) {
+      await rm6(legacyRule, { force: true });
     }
   }
-  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"
-    };
   }
 });
 
@@ -485,6 +426,18 @@ import {
   writeFile as writeFile2
 } from "fs/promises";
 import { join as join5, dirname as dirname2 } from "path";
+async function detectExistingConfigs(targetDir) {
+  const existing = [];
+  const backupDir = join5(targetDir, BACKUP_ORIGINALS_DIR);
+  for (const relativePath of RESTORABLE_FILES) {
+    const filePath = join5(targetDir, relativePath);
+    const backupPath = join5(backupDir, relativePath);
+    if (await pathExists(filePath) && !await pathExists(backupPath)) {
+      existing.push(relativePath);
+    }
+  }
+  return existing;
+}
 async function backupOriginals(targetDir, files = RESTORABLE_FILES) {
   const backedUp = [];
   const backupDir = join5(targetDir, BACKUP_ORIGINALS_DIR);
@@ -703,7 +656,9 @@ import { join as join7 } from "path";
 async function runManifestGeneration(targetDir) {
   const scriptPath = join7(
     targetDir,
-    ".flydocs",
+    ".claude",
+    "skills",
+    "flydocs-workflow",
     "scripts",
     "generate_manifest.py"
   );
@@ -723,7 +678,7 @@ async function runContextGraphBuild(targetDir) {
     targetDir,
     ".claude",
     "skills",
-    "flydocs-context-graph",
+    "flydocs-workflow",
     "scripts",
     "graph_build.py"
   );
@@ -760,8 +715,8 @@ function flushFrontmatterValue(mode, lines) {
       return lines.join("\n").trim();
   }
 }
-function parseFrontmatter(text3) {
-  const match = text3.match(/^---\s*\n([\s\S]*?)\n---/);
+function parseFrontmatter(text4) {
+  const match = text4.match(/^---\s*\n([\s\S]*?)\n---/);
   if (!match) return null;
   const block = match[1];
   const result = {};
@@ -947,7 +902,8 @@ function searchCatalog(keyword) {
     return searchable.includes(lower);
   });
 }
-async function addSkill(targetDir, source) {
+async function addSkill(targetDir, source, options) {
+  const quiet = options?.quiet ?? false;
   if (isPlatformSkill(source)) {
     printError(`Cannot install platform skill '${source}'.`);
     console.log("  Platform skills (flydocs-*) are managed by the installer.");
@@ -965,11 +921,13 @@ async function addSkill(targetDir, source) {
     console.log(`  Remove first: flydocs skills remove ${skillName}`);
     return;
   }
-  console.log();
-  console.log(
-    `${pc3.blue("->")} Installing ${pc3.cyan(skillName)} from ${repo}...`
-  );
-  console.log();
+  if (!quiet) {
+    console.log();
+    console.log(
+      `${pc3.blue("->")} Installing ${pc3.cyan(skillName)} from ${repo}...`
+    );
+    console.log();
+  }
   let success;
   try {
     success = await downloadSkillTree(repo, skillName, skillsDir);
@@ -1003,19 +961,23 @@ async function addSkill(targetDir, source) {
     );
     return;
   }
-  if (!fm["triggers"]) {
+  if (!fm["triggers"] && !quiet) {
     printWarning(
       "SKILL.md has no triggers -- skill won't appear in manifest index."
     );
   }
-  printStatus("Downloaded skill files");
+  if (!quiet) {
+    printStatus("Downloaded skill files");
+  }
   const cursorRuleSrc = join8(skillsDir, "cursor-rule.mdc");
   if (await pathExists(cursorRuleSrc)) {
     const cursorRulesDir = join8(targetDir, ".cursor", "rules");
     await mkdir3(cursorRulesDir, { recursive: true });
     const cursorRuleDest = join8(cursorRulesDir, `${skillName}.mdc`);
     await copyFile(cursorRuleSrc, cursorRuleDest);
-    printStatus("Installed cursor rule");
+    if (!quiet) {
+      printStatus("Installed cursor rule");
+    }
   }
   const config = await readConfig(targetDir);
   const installed = config.skills?.installed ?? [];
@@ -1027,12 +989,16 @@ async function addSkill(targetDir, source) {
     }
     config.skills.installed = installed;
     await writeConfig(targetDir, config);
-    printStatus("Updated config.json");
+    if (!quiet) {
+      printStatus("Updated config.json");
+    }
   }
   await runManifestGeneration(targetDir);
-  console.log();
-  printStatus(`Installed ${pc3.cyan(skillName)}`);
-  console.log();
+  if (!quiet) {
+    console.log();
+    printStatus(`Installed ${pc3.cyan(skillName)}`);
+    console.log();
+  }
 }
 async function removeSkill(targetDir, name) {
   if (isPlatformSkill(name)) {
@@ -1187,7 +1153,8 @@ async function promptCommunitySkills(targetDir, stack, autoYes) {
   let successCount = 0;
   for (const skill of selected) {
     try {
-      await addSkill(targetDir, `${skill.repo}:${skill.name}`);
+      await addSkill(targetDir, `${skill.repo}:${skill.name}`, { quiet: true });
+      printStatus(`Installed ${pc4.cyan(skill.name)}`);
       successCount++;
     } catch {
       printError(`${skill.name} (failed)`);
@@ -1312,10 +1279,19 @@ 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) {
@@ -1400,7 +1376,7 @@ 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";
@@ -1416,10 +1392,14 @@ 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",
@@ -1466,8 +1446,9 @@ 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");
@@ -1476,23 +1457,22 @@ 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`);
   }
 }
 var FLYDOCS_GITIGNORE_ENTRIES, FULL_GITIGNORE_TEMPLATE;
@@ -1507,6 +1487,10 @@ 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"
     ];
     FULL_GITIGNORE_TEMPLATE = `# Environment
@@ -1518,6 +1502,10 @@ 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
@@ -1840,6 +1828,143 @@ var init_telemetry = __esm({
   }
 });
 
+// src/lib/api-key.ts
+import { readFile as readFile10, writeFile as writeFile7, appendFile as appendFile2 } from "fs/promises";
+import { join as join14 } from "path";
+function detectKeyType(key) {
+  if (key.startsWith("fdk_")) return "relay";
+  if (key.startsWith("lin_api_")) return "direct";
+  return "unknown";
+}
+async function validateRelayKey(apiKey) {
+  const baseUrl = process.env.FLYDOCS_RELAY_URL?.replace(/\/$/, "") ?? "https://app.flydocs.ai/api/relay";
+  const response = await fetch(`${baseUrl}/auth/validate`, {
+    method: "POST",
+    headers: {
+      Authorization: `Bearer ${apiKey}`,
+      "Content-Type": "application/json"
+    },
+    signal: AbortSignal.timeout(15e3)
+  });
+  if (!response.ok) return { valid: false };
+  const data = await response.json();
+  if (!data.valid) return { valid: false };
+  return { valid: true, org: data.org ?? "your organization" };
+}
+async function fetchWorkspaces(apiKey) {
+  const baseUrl = process.env.FLYDOCS_RELAY_URL?.replace(/\/$/, "") ?? "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: ${response.status}`);
+  }
+  const data = await response.json();
+  return {
+    displayName: data.displayName ?? null,
+    email: data.email ?? null,
+    providerId: data.providerId ?? null,
+    provider: data.provider ?? null,
+    providerIdentities: data.providerIdentities ?? [],
+    preferences: data.preferences ?? {}
+  };
+}
+async function validateLinearKey(apiKey) {
+  const response = await fetch("https://api.linear.app/graphql", {
+    method: "POST",
+    headers: {
+      Authorization: apiKey,
+      "Content-Type": "application/json"
+    },
+    body: JSON.stringify({ query: "{ viewer { id name email } }" }),
+    signal: AbortSignal.timeout(15e3)
+  });
+  if (!response.ok) return { valid: false };
+  const data = await response.json();
+  if (!data.data?.viewer) return { valid: false };
+  return {
+    valid: true,
+    name: data.data.viewer.name,
+    email: data.data.viewer.email
+  };
+}
+async function storeEnvKey(targetDir, envVarName, value) {
+  const envPath = join14(targetDir, ".env");
+  const envLocalPath = join14(targetDir, ".env.local");
+  const targetEnvPath = await pathExists(envLocalPath) ? envLocalPath : envPath;
+  const pattern = new RegExp(`${envVarName}=.*`);
+  if (await pathExists(targetEnvPath)) {
+    const envContent = await readFile10(targetEnvPath, "utf-8");
+    if (pattern.test(envContent)) {
+      const updated = envContent.replace(pattern, `${envVarName}=${value}`);
+      await writeFile7(targetEnvPath, updated, "utf-8");
+    } else {
+      await appendFile2(targetEnvPath, `
+${envVarName}=${value}
+`);
+    }
+  } else {
+    await writeFile7(targetEnvPath, `${envVarName}=${value}
+`, "utf-8");
+  }
+  return targetEnvPath === envLocalPath ? ".env.local" : ".env";
+}
+var init_api_key = __esm({
+  "src/lib/api-key.ts"() {
+    "use strict";
+    init_fs_ops();
+  }
+});
+
+// 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, {
@@ -1847,9 +1972,9 @@ __export(install_exports, {
 });
 import { defineCommand } from "citty";
 import { resolve as resolve2 } from "path";
-import { join as join14 } from "path";
-import { mkdir as mkdir7 } from "fs/promises";
-import { confirm as confirm2, select, isCancel as isCancel3, cancel as cancel2 } from "@clack/prompts";
+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;
 var init_install = __esm({
@@ -1868,6 +1993,8 @@ var init_install = __esm({
     init_post_install();
     init_update_check();
     init_telemetry();
+    init_api_key();
+    init_integrity();
     install_default = defineCommand({
       meta: {
         name: "install",
@@ -1929,7 +2056,7 @@ var init_install = __esm({
             process.exit(1);
           }
           tier = args.tier;
-        } else if (await pathExists(join14(targetDir, ".flydocs", "config.json"))) {
+        } else if (await pathExists(join16(targetDir, ".flydocs", "config.json"))) {
           try {
             const existing = await readConfig(targetDir);
             if (existing.tier) {
@@ -1951,7 +2078,7 @@ 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"
                 }
               ]
             });
@@ -1978,48 +2105,198 @@ var init_install = __esm({
         }
         printInfo(`Tier: ${tier}`);
         await capture("install_tier_selected", { tier });
-        if (!await pathExists(join14(targetDir, ".git"))) {
+        let selectedWorkspaceId = null;
+        let selectedWorkspaceName = null;
+        let apiKey = null;
+        if (tier === "cloud") {
+          console.log();
+          console.log(`  ${pc6.bold("Connect to FlyDocs Cloud")}`);
+          console.log();
+          console.log(
+            `  ${pc6.dim("Get your API key from your FlyDocs dashboard (fdk_...)")}`
+          );
+          console.log();
+          const keyInput = await text({
+            message: "Enter your FlyDocs API key",
+            placeholder: "fdk_...",
+            validate(value) {
+              if (!value.trim()) return "API key is required";
+              const type = detectKeyType(value.trim());
+              if (type !== "relay")
+                return "Cloud tier requires a FlyDocs API key (fdk_...)";
+              return void 0;
+            }
+          });
+          if (isCancel3(keyInput)) {
+            cancel2("Installation cancelled.");
+            process.exit(0);
+          }
+          apiKey = keyInput.trim();
+          printInfo("Validating API key...");
+          try {
+            const result = await validateRelayKey(apiKey);
+            if (!result.valid) {
+              printError("Invalid API key or relay API unreachable.");
+              console.log(`  Check your key and try again.`);
+              process.exit(1);
+            }
+            printStatus(`Connected to ${pc6.bold(result.org)}`);
+          } catch {
+            printError(
+              "Could not reach relay API. Check your network and try again."
+            );
+            process.exit(1);
+          }
+          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(join16(targetDir, ".git"))) {
           printWarning("No git repository detected. Run git init when ready.");
         }
         await ensureDirectories(targetDir, tier);
-        const backedUp = await backupOriginals(targetDir);
-        if (backedUp.length > 0) {
-          printStatus(
-            `Backed up ${backedUp.length} existing config file(s) to .flydocs/backup-originals/`
+        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();
+          printWarning(
+            `Found ${existingFiles.length} existing config file(s) that FlyDocs will overwrite:`
           );
-          for (const f of backedUp) {
-            printInfo(`  ${f}`);
+          for (const f of existingFiles) {
+            console.log(`    ${pc6.dim(f)}`);
+          }
+          console.log();
+          if (!args.yes) {
+            const overwriteChoice = await select({
+              message: "How should FlyDocs handle these files?",
+              options: [
+                {
+                  value: "backup",
+                  label: "Overwrite (backed up)",
+                  hint: "Files are saved to .flydocs/backup-originals/ and restored on uninstall"
+                },
+                {
+                  value: "skip",
+                  label: "Skip overwriting",
+                  hint: "Keep your existing files \u2014 FlyDocs config may be incomplete"
+                }
+              ]
+            });
+            if (isCancel3(overwriteChoice)) {
+              cancel2("Installation cancelled.");
+              process.exit(0);
+            }
+            if (overwriteChoice === "skip") {
+              printInfo(
+                "Keeping existing files. Run /flydocs-setup to merge your config manually."
+              );
+              skipConfigOverwrite = true;
+            }
+          }
+          if (!skipConfigOverwrite) {
+            const backedUp = await backupOriginals(targetDir);
+            if (backedUp.length > 0) {
+              printStatus(
+                `Backed up ${backedUp.length} file(s) to .flydocs/backup-originals/`
+              );
+            }
           }
         }
         console.log("Installing framework files...");
         await replaceDirectory(
-          join14(templateDir, ".flydocs", "templates"),
-          join14(targetDir, ".flydocs", "templates")
-        );
-        await replaceDirectory(
-          join14(templateDir, ".flydocs", "hooks"),
-          join14(targetDir, ".flydocs", "hooks")
+          join16(templateDir, ".flydocs", "templates"),
+          join16(targetDir, ".flydocs", "templates")
         );
         await replaceDirectory(
-          join14(templateDir, ".flydocs", "scripts"),
-          join14(targetDir, ".flydocs", "scripts")
+          join16(templateDir, ".claude", "hooks"),
+          join16(targetDir, ".claude", "hooks")
         );
         await copyFile(
-          join14(templateDir, ".flydocs", "version"),
-          join14(targetDir, ".flydocs", "version")
+          join16(templateDir, ".flydocs", "version"),
+          join16(targetDir, ".flydocs", "version")
         );
-        const manifestSrc = join14(templateDir, "manifest.json");
+        const manifestSrc = join16(templateDir, "manifest.json");
         if (await pathExists(manifestSrc)) {
-          await copyFile(manifestSrc, join14(targetDir, ".flydocs", "manifest.json"));
+          await copyFile(manifestSrc, join16(targetDir, ".flydocs", "manifest.json"));
         }
-        const changelogSrc = join14(templateDir, "CHANGELOG.md");
+        const changelogSrc = join16(templateDir, "CHANGELOG.md");
         if (await pathExists(changelogSrc)) {
-          await copyFile(changelogSrc, join14(targetDir, ".flydocs", "CHANGELOG.md"));
+          await copyFile(changelogSrc, join16(targetDir, ".flydocs", "CHANGELOG.md"));
         }
-        printStatus(".flydocs/templates, hooks, version, manifest, changelog");
-        const configPath = join14(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) {
@@ -2027,15 +2304,34 @@ 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})...`);
@@ -2071,20 +2367,20 @@ var init_install = __esm({
         }
         await capture("install_agents_chosen", { install_agents: installAgents });
         if (installAgents) {
-          const claudeAgentsSrc = join14(templateDir, ".claude", "agents");
+          const claudeAgentsSrc = join16(templateDir, ".claude", "agents");
           if (await pathExists(claudeAgentsSrc)) {
-            await mkdir7(join14(targetDir, ".claude", "agents"), { recursive: true });
+            await mkdir7(join16(targetDir, ".claude", "agents"), { recursive: true });
             await copyDirectoryContents(
               claudeAgentsSrc,
-              join14(targetDir, ".claude", "agents")
+              join16(targetDir, ".claude", "agents")
             );
           }
-          const cursorAgentsSrc = join14(templateDir, ".cursor", "agents");
+          const cursorAgentsSrc = join16(templateDir, ".cursor", "agents");
           if (await pathExists(cursorAgentsSrc)) {
-            await mkdir7(join14(targetDir, ".cursor", "agents"), { recursive: true });
+            await mkdir7(join16(targetDir, ".cursor", "agents"), { recursive: true });
             await copyDirectoryContents(
               cursorAgentsSrc,
-              join14(targetDir, ".cursor", "agents")
+              join16(targetDir, ".cursor", "agents")
             );
           }
           printStatus("Sub-agents installed (.claude/agents, .cursor/agents)");
@@ -2094,74 +2390,88 @@ var init_install = __esm({
         console.log();
         console.log("Installing commands and settings...");
         await copyDirectoryContents(
-          join14(templateDir, ".claude", "commands"),
-          join14(targetDir, ".claude", "commands")
-        );
-        await copyFile(
-          join14(templateDir, ".claude", "CLAUDE.md"),
-          join14(targetDir, ".claude", "CLAUDE.md")
+          join16(templateDir, ".claude", "commands"),
+          join16(targetDir, ".claude", "commands")
         );
-        await copyFile(
-          join14(templateDir, ".claude", "settings.json"),
-          join14(targetDir, ".claude", "settings.json")
-        );
-        printStatus(".claude/ (commands, CLAUDE.md, settings)");
+        if (!skipConfigOverwrite) {
+          await copyFile(
+            join16(templateDir, ".claude", "CLAUDE.md"),
+            join16(targetDir, ".claude", "CLAUDE.md")
+          );
+          await copyFile(
+            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(
-          join14(templateDir, ".claude", "commands"),
-          join14(targetDir, ".cursor", "commands")
+          join16(templateDir, ".claude", "commands"),
+          join16(targetDir, ".cursor", "commands")
         );
-        await copyFile(
-          join14(templateDir, ".cursor", "hooks.json"),
-          join14(targetDir, ".cursor", "hooks.json")
-        );
-        printStatus(".cursor/ (commands, hooks)");
+        if (!skipConfigOverwrite) {
+          await copyFile(
+            join16(templateDir, ".cursor", "hooks.json"),
+            join16(targetDir, ".cursor", "hooks.json")
+          );
+          printStatus(".cursor/ (commands, hooks)");
+        } else {
+          printStatus(".cursor/ (commands only \u2014 existing hooks preserved)");
+        }
         await copyCursorRules(targetDir);
         printStatus(".cursor/rules/");
-        await copyFile(
-          join14(templateDir, "AGENTS.md"),
-          join14(targetDir, "AGENTS.md")
-        );
-        printStatus("AGENTS.md");
+        if (!skipConfigOverwrite) {
+          await copyFile(
+            join16(templateDir, "AGENTS.md"),
+            join16(targetDir, "AGENTS.md")
+          );
+          printStatus("AGENTS.md");
+        } else {
+          printInfo("AGENTS.md preserved (existing)");
+        }
         await runManifestGeneration(targetDir);
         await runContextGraphBuild(targetDir);
+        await generateIntegrity(targetDir, version);
+        printStatus("Install integrity recorded");
         console.log();
         console.log("Installing project templates...");
         const userFiles = [
           {
-            src: join14(templateDir, "flydocs", "context", "project.md"),
-            dest: join14(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: join14(templateDir, "flydocs", "knowledge", "INDEX.md"),
-            dest: join14(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: join14(templateDir, "flydocs", "knowledge", "README.md"),
-            dest: join14(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: join14(
+            src: join16(
               templateDir,
               "flydocs",
               "knowledge",
               "product",
               "personas.md"
             ),
-            dest: join14(targetDir, "flydocs", "knowledge", "product", "personas.md"),
+            dest: join16(targetDir, "flydocs", "knowledge", "product", "personas.md"),
             label: "flydocs/knowledge/product/personas.md"
           },
           {
-            src: join14(
+            src: join16(
               templateDir,
               "flydocs",
               "knowledge",
               "product",
               "user-flows.md"
             ),
-            dest: join14(
+            dest: join16(
               targetDir,
               "flydocs",
               "knowledge",
@@ -2171,18 +2481,57 @@ var init_install = __esm({
             label: "flydocs/knowledge/product/user-flows.md"
           },
           {
-            src: join14(templateDir, "flydocs", "design-system", "README.md"),
-            dest: join14(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: join14(
+            src: join16(
               templateDir,
               "flydocs",
               "design-system",
               "component-patterns.md"
             ),
-            dest: join14(
+            dest: join16(
               targetDir,
               "flydocs",
               "design-system",
@@ -2191,13 +2540,13 @@ var init_install = __esm({
             label: "flydocs/design-system/component-patterns.md"
           },
           {
-            src: join14(templateDir, "flydocs", "design-system", "token-mapping.md"),
-            dest: join14(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: join14(templateDir, "flydocs", "README.md"),
-            dest: join14(targetDir, "flydocs", "README.md"),
+            src: join16(templateDir, "flydocs", "README.md"),
+            dest: join16(targetDir, "flydocs", "README.md"),
             label: "flydocs/README.md"
           }
         ];
@@ -2211,9 +2560,9 @@ var init_install = __esm({
             }
           }
         }
-        const envExampleSrc = join14(templateDir, ".env.example");
+        const envExampleSrc = join16(templateDir, ".env.example");
         if (await pathExists(envExampleSrc)) {
-          await copyFile(envExampleSrc, join14(targetDir, ".env.example"));
+          await copyFile(envExampleSrc, join16(targetDir, ".env.example"));
           printStatus(".env.example");
         }
         await ensureGitignore(targetDir);
@@ -2253,9 +2602,8 @@ var init_install = __esm({
           `Version: ${version}`,
           "",
           "Next steps:",
-          "  1. Run flydocs connect to set up your API key",
-          "  2. Run /flydocs-setup to configure your workspace",
-          "  3. Start working with /start-session",
+          "  1. Run /flydocs-setup to configure your workspace",
+          "  2. Start working with /start-session",
           "",
           "Docs: https://www.flydocs.ai/docs"
         ];
@@ -2392,9 +2740,9 @@ __export(update_exports, {
   default: () => update_default
 });
 import { defineCommand as defineCommand2 } from "citty";
-import { resolve as resolve3, join as join15 } from "path";
-import { mkdir as mkdir8, cp as cp2, readFile as readFile10, readdir as readdir3, rm as rm4 } from "fs/promises";
-import { select as select2, text, confirm as confirm3, isCancel as isCancel4, cancel as cancel3 } from "@clack/prompts";
+import { resolve as resolve3, join as join17 } from "path";
+import { mkdir as mkdir8, cp as cp2, readFile as readFile12, readdir as readdir4, rm as rm4 } from "fs/promises";
+import { select as select2, text as text2, confirm as confirm3, isCancel as isCancel4, cancel as cancel3 } from "@clack/prompts";
 import pc7 from "picocolors";
 var update_default;
 var init_update = __esm({
@@ -2413,6 +2761,7 @@ var init_update = __esm({
     init_post_install();
     init_update_check();
     init_telemetry();
+    init_integrity();
     update_default = defineCommand2({
       meta: {
         name: "update",
@@ -2482,7 +2831,7 @@ var init_update = __esm({
           if (choice === "cwd") {
             targetDir = process.cwd();
           } else {
-            const enteredPath = await text({
+            const enteredPath = await text2({
               message: "Enter project path:"
             });
             if (isCancel4(enteredPath)) {
@@ -2500,9 +2849,9 @@ var init_update = __esm({
         }
         targetDir = resolve3(targetDir);
         process.chdir(targetDir);
-        const hasVersion = await pathExists(join15(targetDir, ".flydocs", "version"));
+        const hasVersion = await pathExists(join17(targetDir, ".flydocs", "version"));
         const hasConfig = await pathExists(
-          join15(targetDir, ".flydocs", "config.json")
+          join17(targetDir, ".flydocs", "config.json")
         );
         if (!hasVersion && !hasConfig) {
           printError(`Not a FlyDocs project: ${targetDir}`);
@@ -2513,8 +2862,8 @@ var init_update = __esm({
         console.log();
         let currentVersion = "0.1.0";
         if (hasVersion) {
-          const vContent = await readFile10(
-            join15(targetDir, ".flydocs", "version"),
+          const vContent = await readFile12(
+            join17(targetDir, ".flydocs", "version"),
             "utf-8"
           );
           currentVersion = vContent.trim();
@@ -2548,7 +2897,7 @@ var init_update = __esm({
         });
         console.log(`Updating: v${currentVersion} \u2192 v${version}`);
         console.log();
-        const changelogPath = join15(templateDir, "CHANGELOG.md");
+        const changelogPath = join17(templateDir, "CHANGELOG.md");
         const whatsNew = await getWhatsNew(changelogPath, currentVersion, version);
         if (whatsNew.length > 0) {
           console.log(pc7.cyan("What's new:"));
@@ -2560,36 +2909,37 @@ var init_update = __esm({
         }
         const now = /* @__PURE__ */ new Date();
         const ts = `${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")}${String(now.getSeconds()).padStart(2, "0")}`;
-        const backupDir = join15(targetDir, ".flydocs", `backup-${ts}`);
+        const backupDir = join17(targetDir, ".flydocs", `backup-${ts}`);
         await mkdir8(backupDir, { recursive: true });
         if (hasConfig) {
           await cp2(
-            join15(targetDir, ".flydocs", "config.json"),
-            join15(backupDir, "config.json")
+            join17(targetDir, ".flydocs", "config.json"),
+            join17(backupDir, "config.json")
           );
           printStatus(`Config backed up to .flydocs/backup-${ts}/`);
         }
         try {
-          const flydocsDir = join15(targetDir, ".flydocs");
-          const entries = await readdir3(flydocsDir);
+          const flydocsDir = join17(targetDir, ".flydocs");
+          const entries = await readdir4(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(join15(flydocsDir, old), { recursive: true, force: true });
+              await rm4(join17(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: {}
         };
@@ -2611,22 +2961,20 @@ var init_update = __esm({
         } else {
           effectiveTier = preserved.tier;
         }
+        await ensureDirectories(targetDir, effectiveTier);
         console.log("Replacing framework directories...");
         await replaceDirectory(
-          join15(templateDir, ".flydocs", "templates"),
-          join15(targetDir, ".flydocs", "templates")
+          join17(templateDir, ".flydocs", "templates"),
+          join17(targetDir, ".flydocs", "templates")
         );
+        printStatus(".flydocs/templates");
         await replaceDirectory(
-          join15(templateDir, ".flydocs", "hooks"),
-          join15(targetDir, ".flydocs", "hooks")
+          join17(templateDir, ".claude", "hooks"),
+          join17(targetDir, ".claude", "hooks")
         );
-        await replaceDirectory(
-          join15(templateDir, ".flydocs", "scripts"),
-          join15(targetDir, ".flydocs", "scripts")
-        );
-        printStatus(".flydocs/templates, hooks, scripts");
+        printStatus(".claude/hooks");
         const hasExistingAgents = await pathExists(
-          join15(targetDir, ".claude", "agents")
+          join17(targetDir, ".claude", "agents")
         );
         let installAgents;
         if (args.yes) {
@@ -2658,20 +3006,20 @@ var init_update = __esm({
           }
         }
         if (installAgents) {
-          const claudeAgentsSrc = join15(templateDir, ".claude", "agents");
+          const claudeAgentsSrc = join17(templateDir, ".claude", "agents");
           if (await pathExists(claudeAgentsSrc)) {
-            await mkdir8(join15(targetDir, ".claude", "agents"), { recursive: true });
+            await mkdir8(join17(targetDir, ".claude", "agents"), { recursive: true });
             await copyDirectoryContents(
               claudeAgentsSrc,
-              join15(targetDir, ".claude", "agents")
+              join17(targetDir, ".claude", "agents")
             );
           }
-          const cursorAgentsSrc = join15(templateDir, ".cursor", "agents");
+          const cursorAgentsSrc = join17(templateDir, ".cursor", "agents");
           if (await pathExists(cursorAgentsSrc)) {
-            await mkdir8(join15(targetDir, ".cursor", "agents"), { recursive: true });
+            await mkdir8(join17(targetDir, ".cursor", "agents"), { recursive: true });
             await copyDirectoryContents(
               cursorAgentsSrc,
-              join15(targetDir, ".cursor", "agents")
+              join17(targetDir, ".cursor", "agents")
             );
           }
           printStatus(
@@ -2685,46 +3033,62 @@ var init_update = __esm({
         console.log();
         console.log("Replacing framework files...");
         await copyFile(
-          join15(templateDir, ".claude", "CLAUDE.md"),
-          join15(targetDir, ".claude", "CLAUDE.md")
+          join17(templateDir, ".claude", "CLAUDE.md"),
+          join17(targetDir, ".claude", "CLAUDE.md")
         );
         await copyFile(
-          join15(templateDir, ".claude", "settings.json"),
-          join15(targetDir, ".claude", "settings.json")
+          join17(templateDir, ".claude", "settings.json"),
+          join17(targetDir, ".claude", "settings.json")
         );
         printStatus(".claude/CLAUDE.md, settings.json");
         await copyDirectoryContents(
-          join15(templateDir, ".claude", "commands"),
-          join15(targetDir, ".claude", "commands")
+          join17(templateDir, ".claude", "commands"),
+          join17(targetDir, ".claude", "commands")
         );
         await copyDirectoryContents(
-          join15(templateDir, ".claude", "commands"),
-          join15(targetDir, ".cursor", "commands")
+          join17(templateDir, ".claude", "commands"),
+          join17(targetDir, ".cursor", "commands")
         );
         printStatus(".claude/commands, .cursor/commands");
-        const skillsReadmeSrc = join15(templateDir, ".claude", "skills", "README.md");
+        const skillsReadmeSrc = join17(templateDir, ".claude", "skills", "README.md");
         if (await pathExists(skillsReadmeSrc)) {
           await copyFile(
             skillsReadmeSrc,
-            join15(targetDir, ".claude", "skills", "README.md")
+            join17(targetDir, ".claude", "skills", "README.md")
           );
         }
         printStatus(".claude/skills/README.md");
         await copyFile(
-          join15(templateDir, ".cursor", "hooks.json"),
-          join15(targetDir, ".cursor", "hooks.json")
+          join17(templateDir, ".cursor", "hooks.json"),
+          join17(targetDir, ".cursor", "hooks.json")
         );
         printStatus(".cursor/hooks.json");
         await copyFile(
-          join15(templateDir, "AGENTS.md"),
-          join15(targetDir, "AGENTS.md")
+          join17(templateDir, "AGENTS.md"),
+          join17(targetDir, "AGENTS.md")
         );
         printStatus("AGENTS.md");
-        const envExampleSrc = join15(templateDir, ".env.example");
+        const envExampleSrc = join17(templateDir, ".env.example");
         if (await pathExists(envExampleSrc)) {
-          await copyFile(envExampleSrc, join15(targetDir, ".env.example"));
+          await copyFile(envExampleSrc, join17(targetDir, ".env.example"));
           printStatus(".env.example");
         }
+        const knowledgeTemplatesDir = join17(
+          targetDir,
+          "flydocs",
+          "knowledge",
+          "templates"
+        );
+        if (!await pathExists(knowledgeTemplatesDir)) {
+          await mkdir8(knowledgeTemplatesDir, { recursive: true });
+        }
+        for (const tmpl of ["decision.md", "feature.md", "note.md"]) {
+          const src = join17(templateDir, "flydocs", "knowledge", "templates", tmpl);
+          const dest = join17(knowledgeTemplatesDir, tmpl);
+          if (await pathExists(src) && !await pathExists(dest)) {
+            await copyFile(src, dest);
+          }
+        }
         await runManifestGeneration(targetDir);
         await runContextGraphBuild(targetDir);
         console.log();
@@ -2747,20 +3111,22 @@ var init_update = __esm({
           printWarning("Config merge failed \u2014 config.json preserved as-is");
         }
         await copyFile(
-          join15(templateDir, ".flydocs", "version"),
-          join15(targetDir, ".flydocs", "version")
+          join17(templateDir, ".flydocs", "version"),
+          join17(targetDir, ".flydocs", "version")
         );
         printStatus(`.flydocs/version \u2192 ${version}`);
-        const clSrc = join15(templateDir, "CHANGELOG.md");
+        const clSrc = join17(templateDir, "CHANGELOG.md");
         if (await pathExists(clSrc)) {
-          await copyFile(clSrc, join15(targetDir, ".flydocs", "CHANGELOG.md"));
+          await copyFile(clSrc, join17(targetDir, ".flydocs", "CHANGELOG.md"));
           printStatus(".flydocs/CHANGELOG.md");
         }
-        const mfSrc = join15(templateDir, "manifest.json");
+        const mfSrc = join17(templateDir, "manifest.json");
         if (await pathExists(mfSrc)) {
-          await copyFile(mfSrc, join15(targetDir, ".flydocs", "manifest.json"));
+          await copyFile(mfSrc, join17(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);
@@ -2818,21 +3184,21 @@ __export(uninstall_exports, {
   default: () => uninstall_default
 });
 import { defineCommand as defineCommand3 } from "citty";
-import { resolve as resolve4, join as join16 } from "path";
-import { readdir as readdir4, rm as rm5, rename as rename2 } from "fs/promises";
+import { resolve as resolve4, join as join18 } from "path";
+import { readdir as readdir5, rm as rm5, rename as rename2 } from "fs/promises";
 import { confirm as confirm4, select as select3, isCancel as isCancel5, cancel as cancel4 } from "@clack/prompts";
 import pc8 from "picocolors";
 async function removeOwnedSkills(targetDir) {
-  const skillsDir = join16(targetDir, ".claude", "skills");
+  const skillsDir = join18(targetDir, ".claude", "skills");
   const removed = [];
   if (!await pathExists(skillsDir)) {
     return removed;
   }
   try {
-    const entries = await readdir4(skillsDir);
+    const entries = await readdir5(skillsDir);
     for (const entry of entries) {
       if (entry.startsWith(OWNED_SKILL_PREFIX)) {
-        await rm5(join16(skillsDir, entry), { recursive: true, force: true });
+        await rm5(join18(skillsDir, entry), { recursive: true, force: true });
         removed.push(`.claude/skills/${entry}`);
       }
     }
@@ -2841,16 +3207,16 @@ async function removeOwnedSkills(targetDir) {
   return removed;
 }
 async function removeOwnedCursorRules(targetDir) {
-  const rulesDir = join16(targetDir, ".cursor", "rules");
+  const rulesDir = join18(targetDir, ".cursor", "rules");
   const removed = [];
   if (!await pathExists(rulesDir)) {
     return removed;
   }
   try {
-    const entries = await readdir4(rulesDir);
+    const entries = await readdir5(rulesDir);
     for (const entry of entries) {
       if (entry.startsWith(OWNED_RULE_PREFIX) && entry.endsWith(".mdc")) {
-        await rm5(join16(rulesDir, entry), { force: true });
+        await rm5(join18(rulesDir, entry), { force: true });
         removed.push(`.cursor/rules/${entry}`);
       }
     }
@@ -2860,7 +3226,7 @@ async function removeOwnedCursorRules(targetDir) {
 }
 async function isEmptyDir(dirPath) {
   try {
-    const entries = await readdir4(dirPath);
+    const entries = await readdir5(dirPath);
     return entries.length === 0;
   } catch {
     return false;
@@ -2869,7 +3235,7 @@ async function isEmptyDir(dirPath) {
 async function cleanupEmptyParents(targetDir, dirs) {
   const cleaned = [];
   for (const dir of dirs) {
-    const fullPath = join16(targetDir, dir);
+    const fullPath = join18(targetDir, dir);
     if (await pathExists(fullPath) && await isEmptyDir(fullPath)) {
       await rm5(fullPath, { recursive: true, force: true });
       cleaned.push(dir);
@@ -2890,9 +3256,11 @@ 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"]
@@ -2946,8 +3314,8 @@ var init_uninstall = __esm({
           process.exit(1);
         }
         targetDir = resolve4(targetDir);
-        const hasFlydocs = await pathExists(join16(targetDir, ".flydocs"));
-        const hasAgentsMd = await pathExists(join16(targetDir, "AGENTS.md"));
+        const hasFlydocs = await pathExists(join18(targetDir, ".flydocs"));
+        const hasAgentsMd = await pathExists(join18(targetDir, "AGENTS.md"));
         if (!hasFlydocs && !hasAgentsMd) {
           printError(`Not a FlyDocs project: ${targetDir}`);
           printInfo("No .flydocs/ directory or AGENTS.md found.");
@@ -2959,7 +3327,7 @@ var init_uninstall = __esm({
         const removeAll = forceAll || args.all;
         const skipPrompts = forceAll || args.yes;
         let contentAction = "preserve";
-        const hasUserContent = await pathExists(join16(targetDir, "flydocs"));
+        const hasUserContent = await pathExists(join18(targetDir, "flydocs"));
         if (hasUserContent) {
           if (removeAll) {
             contentAction = "remove";
@@ -3042,7 +3410,7 @@ var init_uninstall = __esm({
         const removedRules = await removeOwnedCursorRules(targetDir);
         result.removed.push(...removedRules);
         for (const [relativePath, type] of ALWAYS_REMOVED) {
-          const fullPath = join16(targetDir, relativePath);
+          const fullPath = join18(targetDir, relativePath);
           if (!await pathExists(fullPath)) {
             result.skipped.push(relativePath);
             continue;
@@ -3060,9 +3428,9 @@ var init_uninstall = __esm({
           }
         }
         if (hasUserContent) {
-          const flydocsPath = join16(targetDir, "flydocs");
+          const flydocsPath = join18(targetDir, "flydocs");
           if (contentAction === "archive") {
-            const archivePath = join16(targetDir, "flydocs-archive");
+            const archivePath = join18(targetDir, "flydocs-archive");
             if (await pathExists(archivePath)) {
               await rm5(archivePath, { recursive: true, force: true });
             }
@@ -3301,70 +3669,9 @@ __export(connect_exports, {
   default: () => connect_default
 });
 import { defineCommand as defineCommand6 } from "citty";
-import { text as text2, confirm as confirm5, isCancel as isCancel6, cancel as cancel5 } from "@clack/prompts";
+import { text as text3, confirm as confirm5, isCancel as isCancel6, cancel as cancel5 } from "@clack/prompts";
 import pc11 from "picocolors";
-import { readFile as readFile11, writeFile as writeFile7, appendFile as appendFile2 } from "fs/promises";
-import { join as join17 } from "path";
-function detectKeyType(key) {
-  if (key.startsWith("fdk_")) return "relay";
-  if (key.startsWith("lin_api_")) return "direct";
-  return "unknown";
-}
-async function validateRelayKey(apiKey) {
-  const baseUrl = process.env.FLYDOCS_RELAY_URL?.replace(/\/$/, "") ?? "https://app.flydocs.ai/api/relay";
-  const response = await fetch(`${baseUrl}/auth/validate`, {
-    method: "POST",
-    headers: {
-      Authorization: `Bearer ${apiKey}`,
-      "Content-Type": "application/json"
-    },
-    signal: AbortSignal.timeout(15e3)
-  });
-  if (!response.ok) return { valid: false };
-  const data = await response.json();
-  if (!data.valid) return { valid: false };
-  return { valid: true, org: data.org ?? "your organization" };
-}
-async function validateLinearKey(apiKey) {
-  const response = await fetch("https://api.linear.app/graphql", {
-    method: "POST",
-    headers: {
-      Authorization: apiKey,
-      "Content-Type": "application/json"
-    },
-    body: JSON.stringify({ query: "{ viewer { id name email } }" }),
-    signal: AbortSignal.timeout(15e3)
-  });
-  if (!response.ok) return { valid: false };
-  const data = await response.json();
-  if (!data.data?.viewer) return { valid: false };
-  return {
-    valid: true,
-    name: data.data.viewer.name,
-    email: data.data.viewer.email
-  };
-}
-async function storeEnvKey(targetDir, envVarName, value) {
-  const envPath = join17(targetDir, ".env");
-  const envLocalPath = join17(targetDir, ".env.local");
-  const targetEnvPath = await pathExists(envLocalPath) ? envLocalPath : envPath;
-  const pattern = new RegExp(`${envVarName}=.*`);
-  if (await pathExists(targetEnvPath)) {
-    const envContent = await readFile11(targetEnvPath, "utf-8");
-    if (pattern.test(envContent)) {
-      const updated = envContent.replace(pattern, `${envVarName}=${value}`);
-      await writeFile7(targetEnvPath, updated, "utf-8");
-    } else {
-      await appendFile2(targetEnvPath, `
-${envVarName}=${value}
-`);
-    }
-  } else {
-    await writeFile7(targetEnvPath, `${envVarName}=${value}
-`, "utf-8");
-  }
-  return targetEnvPath === envLocalPath ? ".env.local" : ".env";
-}
+import { join as join19 } from "path";
 var connect_default;
 var init_connect = __esm({
   "src/commands/connect.ts"() {
@@ -3373,6 +3680,7 @@ var init_connect = __esm({
     init_fs_ops();
     init_template();
     init_ui();
+    init_api_key();
     connect_default = defineCommand6({
       meta: {
         name: "connect",
@@ -3393,12 +3701,12 @@ 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 = join17(targetDir, ".flydocs", "config.json");
+        const configPath = join19(targetDir, ".flydocs", "config.json");
         if (!await pathExists(configPath)) {
           printError("Not a FlyDocs project (.flydocs/config.json not found).");
           console.log(
@@ -3422,22 +3730,19 @@ var init_connect = __esm({
         console.log(`  ${pc11.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")}`
+          `  ${pc11.dim("Get your API key (fdk_...) from your FlyDocs dashboard")}`
         );
         console.log();
         let apiKey = args.key ?? "";
         if (!apiKey) {
-          const keyInput = await text2({
+          const keyInput = await text3({
             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;
             }
           });
@@ -3449,7 +3754,9 @@ var init_connect = __esm({
         }
         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...");
@@ -3491,32 +3798,15 @@ var init_connect = __esm({
         }
         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 = join17(templateDir, ".claude", "skills");
-            const skillsDir = join17(targetDir, ".claude", "skills");
-            await replaceDirectory(
-              join17(templateSkillsDir, "flydocs-cloud"),
-              join17(skillsDir, "flydocs-cloud")
-            );
-            const { rm: rm6 } = await import("fs/promises");
-            const localSkillDir = join17(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(
@@ -3579,9 +3869,7 @@ var init_upgrade = __esm({
             `  ${pc12.green("\u2713")} You're already on the ${pc12.bold("cloud")} tier.`
           );
           console.log();
-          console.log(
-            `  Your issues sync with Linear via the cloud mechanism skill.`
-          );
+          console.log(`  Your issues sync with your provider via the relay API.`);
           console.log(
             `  Run ${pc12.cyan("flydocs connect")} to update your connection settings.`
           );
@@ -3593,9 +3881,7 @@ var init_upgrade = __esm({
         console.log(`  You're currently on the ${pc12.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")} Issue sync with Linear, Jira, and more`);
         console.log(`    ${pc12.cyan("\u2192")} Project milestones and cycle management`);
         console.log(`    ${pc12.cyan("\u2192")} Team assignment and priority tracking`);
         console.log(`    ${pc12.cyan("\u2192")} Project health updates and dashboards`);