@synapsync/cli 0.1.4 → 0.1.6

package/dist/index.js

@@ -28,7 +28,7 @@ var init_version = __esm({
   "src/version.ts"() {
     "use strict";
     init_esm_shims();
-    version = "0.1.4";
+    version = "0.1.6";
   }
 });
 
@@ -70,6 +70,7 @@ var COGNITIVE_FILE_NAMES = {
 };
 var DEFAULT_SYNAPSYNC_DIR = process.env["SYNAPSYNC_DIR"] ?? ".synapsync";
 var CONFIG_FILE_NAME = "synapsync.config.yaml";
+var AGENTS_MD_FILE_NAME = "AGENTS.md";
 var DEFAULT_AGENTS_DIR = process.env["SYNAPSYNC_AGENTS_DIR"] ?? ".agents";
 var DEFAULT_SKILLS_SUBDIR = process.env["SYNAPSYNC_SKILLS_SUBDIR"] ?? "skills";
 var CATEGORIES = [
@@ -718,8 +719,8 @@ function registerInfoCommand(program) {
 
 // src/commands/init.ts
 init_esm_shims();
-import * as fs2 from "fs";
-import * as path3 from "path";
+import * as fs5 from "fs";
+import * as path6 from "path";
 import * as p from "@clack/prompts";
 import pc4 from "picocolors";
 
@@ -822,8 +823,8 @@ function validateConfig(config) {
   }
   return errors;
 }
-function getNestedValue(obj, path17) {
-  const parts = path17.split(".");
+function getNestedValue(obj, path18) {
+  const parts = path18.split(".");
   let current = obj;
   for (const part of parts) {
     if (current === null || current === void 0) {
@@ -836,8 +837,8 @@ function getNestedValue(obj, path17) {
   }
   return current;
 }
-function setNestedValue(obj, path17, value) {
-  const parts = path17.split(".");
+function setNestedValue(obj, path18, value) {
+  const parts = path18.split(".");
   let current = obj;
   for (let i = 0; i < parts.length - 1; i++) {
     const part = parts[i];
@@ -1018,1630 +1019,1861 @@ ${messages}`);
   }
 };
 
-// src/commands/init.ts
-async function executeInitCommand(options = {}) {
-  const projectRoot = process.cwd();
-  const configPath = path3.join(projectRoot, CONFIG_FILE_NAME);
-  const storagePath = path3.join(projectRoot, DEFAULT_SYNAPSYNC_DIR);
-  if (ConfigManager.isProjectInitialized(projectRoot)) {
-    logger.line();
-    logger.warning("Project already initialized.");
-    logger.log(`  ${pc4.dim("Config:")} ${configPath}`);
-    logger.log(`  ${pc4.dim("Storage:")} ${storagePath}`);
-    logger.line();
-    logger.hint("Use /config to view or modify settings.");
-    return null;
+// src/services/agents-md/generator.ts
+init_esm_shims();
+import * as fs4 from "fs";
+import * as path5 from "path";
+
+// src/services/manifest/manager.ts
+init_esm_shims();
+import * as fs2 from "fs";
+import * as path3 from "path";
+
+// src/services/manifest/types.ts
+init_esm_shims();
+var DEFAULT_MANIFEST = {
+  version: "1.0.0",
+  lastUpdated: (/* @__PURE__ */ new Date()).toISOString(),
+  cognitives: {},
+  syncs: {}
+};
+
+// src/services/manifest/manager.ts
+var ManifestManager = class {
+  manifestPath;
+  manifest;
+  constructor(synapSyncDir) {
+    this.manifestPath = path3.join(synapSyncDir, "manifest.json");
+    this.manifest = this.load();
   }
-  if (options.yes === true) {
-    return initializeProject({
-      name: options.name ?? path3.basename(projectRoot),
-      ...options.description !== void 0 && { description: options.description },
-      providers: options.providers ?? ["claude"]
-    });
+  /**
+   * Load manifest from disk
+   */
+  load() {
+    if (!fs2.existsSync(this.manifestPath)) {
+      return { ...DEFAULT_MANIFEST };
+    }
+    try {
+      const content = fs2.readFileSync(this.manifestPath, "utf-8");
+      const parsed = JSON.parse(content);
+      return {
+        version: parsed.version ?? DEFAULT_MANIFEST.version,
+        lastUpdated: parsed.lastUpdated ?? DEFAULT_MANIFEST.lastUpdated,
+        cognitives: parsed.cognitives ?? {},
+        syncs: parsed.syncs ?? {}
+      };
+    } catch {
+      return { ...DEFAULT_MANIFEST };
+    }
   }
-  logger.line();
-  p.intro(pc4.bgCyan(pc4.black(" Initialize SynapSync Project ")));
-  const result = await p.group(
-    {
-      name: () => {
-        const defaultName = path3.basename(projectRoot);
-        return p.text({
-          message: "Project name",
-          placeholder: defaultName,
-          defaultValue: defaultName,
-          validate: (value) => {
-            const finalValue = value.trim() === "" ? defaultName : value;
-            if (!/^[a-z0-9-_]+$/i.test(finalValue)) {
-              return "Project name can only contain letters, numbers, hyphens, and underscores";
-            }
-            return void 0;
-          }
-        });
-      },
-      description: () => p.text({
-        message: "Description (optional)",
-        placeholder: "A brief description of your project"
-      }),
-      providers: () => p.multiselect({
-        message: "Select AI providers to enable",
-        options: SUPPORTED_PROVIDERS.map((provider) => ({
-          value: provider,
-          label: getProviderLabel(provider),
-          hint: getProviderHint(provider)
-        })),
-        initialValues: ["claude"],
-        required: false
-      })
-    },
-    {
-      onCancel: () => {
-        p.cancel("Project initialization cancelled.");
-        return process.exit(0);
-      }
+  /**
+   * Save manifest to disk
+   */
+  save() {
+    this.manifest.lastUpdated = (/* @__PURE__ */ new Date()).toISOString();
+    const content = JSON.stringify(this.manifest, null, 2);
+    fs2.writeFileSync(this.manifestPath, content, "utf-8");
+  }
+  /**
+   * Get the current manifest
+   */
+  getManifest() {
+    return this.manifest;
+  }
+  /**
+   * Get all cognitives from manifest
+   */
+  getCognitives() {
+    return Object.values(this.manifest.cognitives);
+  }
+  /**
+   * Get a specific cognitive by name
+   */
+  getCognitive(name) {
+    return this.manifest.cognitives[name];
+  }
+  /**
+   * Check if a cognitive exists in manifest
+   */
+  hasCognitive(name) {
+    return this.manifest.cognitives[name] !== void 0;
+  }
+  /**
+   * Add a cognitive to manifest
+   */
+  addCognitive(cognitive) {
+    this.manifest.cognitives[cognitive.name] = cognitive;
+  }
+  /**
+   * Update a cognitive in manifest
+   */
+  updateCognitive(name, updates) {
+    const existing = this.manifest.cognitives[name];
+    if (existing !== void 0) {
+      this.manifest.cognitives[name] = { ...existing, ...updates };
     }
-  );
-  if (p.isCancel(result)) {
-    return null;
   }
-  return initializeProject({
-    name: result.name,
-    description: result.description,
-    providers: result.providers
-  });
-}
-function initializeProject(setup) {
-  const projectRoot = process.cwd();
-  const configPath = path3.join(projectRoot, CONFIG_FILE_NAME);
-  const storagePath = path3.join(projectRoot, DEFAULT_SYNAPSYNC_DIR);
-  const s = p.spinner();
-  s.start("Creating project structure...");
-  try {
-    createStorageStructure(storagePath);
-    const configManager = new ConfigManager(projectRoot);
-    configManager.create(setup.name, setup.description);
-    for (const provider of setup.providers) {
-      configManager.set(`sync.providers.${provider}.enabled`, true);
+  /**
+   * Remove a cognitive from manifest
+   */
+  removeCognitive(name) {
+    if (this.manifest.cognitives[name] !== void 0) {
+      delete this.manifest.cognitives[name];
+      return true;
     }
-    configManager.save();
-    createManifest(storagePath);
-    updateGitignore(projectRoot);
-    s.stop("Project structure created!");
-    showSuccessMessage(setup, configPath, storagePath);
-    return {
-      success: true,
-      projectPath: projectRoot,
-      configPath,
-      storagePath
+    return false;
+  }
+  /**
+   * Reconcile manifest with scanned cognitives
+   * Returns what was added, removed, and updated
+   */
+  reconcile(scannedCognitives) {
+    const result = {
+      added: [],
+      removed: [],
+      updated: [],
+      unchanged: 0
     };
-  } catch (error) {
-    s.stop("Failed to create project.");
-    logger.line();
-    if (error instanceof Error) {
-      logger.error(error.message);
+    const scannedMap = /* @__PURE__ */ new Map();
+    for (const cognitive of scannedCognitives) {
+      scannedMap.set(cognitive.name, cognitive);
     }
-    throw error;
-  }
-}
-function createStorageStructure(storagePath) {
-  fs2.mkdirSync(storagePath, { recursive: true });
-  for (const cognitiveType of COGNITIVE_TYPES) {
-    const typePath = path3.join(storagePath, `${cognitiveType}s`);
-    fs2.mkdirSync(typePath, { recursive: true });
-    const gitkeepPath = path3.join(typePath, ".gitkeep");
-    fs2.writeFileSync(gitkeepPath, "");
-  }
-}
-function createManifest(storagePath) {
-  const manifestPath = path3.join(storagePath, "manifest.json");
-  const manifest = {
-    version: "1.0.0",
-    lastUpdated: (/* @__PURE__ */ new Date()).toISOString(),
-    cognitives: {},
-    syncs: {}
-  };
-  fs2.writeFileSync(manifestPath, JSON.stringify(manifest, null, 2));
-}
-function updateGitignore(projectRoot) {
-  const gitignorePath = path3.join(projectRoot, ".gitignore");
-  const synapsyncEntries = `
-# SynapSync
-.synapsync/manifest.json
-*.local.yaml
-`;
-  if (fs2.existsSync(gitignorePath)) {
-    const content = fs2.readFileSync(gitignorePath, "utf-8");
-    if (!content.includes("# SynapSync")) {
-      fs2.appendFileSync(gitignorePath, synapsyncEntries);
+    for (const name of Object.keys(this.manifest.cognitives)) {
+      if (!scannedMap.has(name)) {
+        result.removed.push(name);
+      }
     }
-  } else {
-    fs2.writeFileSync(gitignorePath, synapsyncEntries.trim() + "\n");
+    for (const scanned of scannedCognitives) {
+      const existing = this.manifest.cognitives[scanned.name];
+      if (existing === void 0) {
+        result.added.push(scanned);
+      } else if (scanned.hash !== void 0 && existing.hash !== scanned.hash) {
+        result.updated.push(scanned);
+      } else {
+        result.unchanged++;
+      }
+    }
+    return result;
   }
-}
-function getProviderLabel(provider) {
-  const labels = {
-    claude: "Claude (Anthropic)",
-    openai: "OpenAI (GPT)",
-    gemini: "Gemini (Google)",
-    cursor: "Cursor IDE",
-    windsurf: "Windsurf IDE",
-    copilot: "GitHub Copilot"
-  };
-  return labels[provider];
-}
-function getProviderHint(provider) {
-  const hints = {
-    claude: "Claude Code, Claude Desktop",
-    openai: "ChatGPT, API",
-    gemini: "Google AI Studio",
-    cursor: "AI-first code editor",
-    windsurf: "AI-powered IDE",
-    copilot: "VS Code integration"
-  };
-  return hints[provider];
-}
-function showSuccessMessage(setup, configPath, storagePath) {
-  logger.line();
-  p.note(
-    [
-      `${pc4.dim("Config:")}   ${pc4.cyan(configPath)}`,
-      `${pc4.dim("Storage:")}  ${pc4.cyan(storagePath)}`,
-      "",
-      `${pc4.dim("Providers:")} ${setup.providers.map((p2) => pc4.green(p2)).join(", ") || pc4.dim("none")}`
-    ].join("\n"),
-    `Project "${setup.name}" initialized!`
-  );
-  logger.line();
-  logger.bold("  Next Steps:");
-  logger.line();
-  logger.log(`  ${pc4.cyan("1.")} Connect to providers:`);
-  logger.log(`     ${pc4.dim("$")} synapsync connect claude`);
-  logger.line();
-  logger.log(`  ${pc4.cyan("2.")} Add cognitives:`);
-  logger.log(`     ${pc4.dim("$")} synapsync add code-reviewer`);
-  logger.log(`     ${pc4.dim("$")} synapsync add github:user/my-skill`);
-  logger.line();
-  logger.log(`  ${pc4.cyan("3.")} Sync to providers:`);
-  logger.log(`     ${pc4.dim("$")} synapsync sync`);
-  logger.line();
-  p.outro(pc4.green("Happy syncing!"));
-}
-function registerInitCommand(program) {
-  program.command("init").description("Initialize a new SynapSync project").option("-n, --name <name>", "Project name").option("-d, --description <desc>", "Project description").option("-p, --provider <providers...>", "Enable providers (claude, openai, etc.)").option("-y, --yes", "Skip prompts and use defaults").action(async (options) => {
-    await executeInitCommand({
-      ...options.name !== void 0 && { name: options.name },
-      ...options.description !== void 0 && { description: options.description },
-      ...options.provider !== void 0 && { providers: options.provider },
-      ...options.yes !== void 0 && { yes: options.yes }
-    });
-  });
-}
-
-// src/commands/config.ts
-init_esm_shims();
-import pc5 from "picocolors";
-function executeConfigCommand(args) {
-  const options = parseConfigArgs(args);
-  const configManager = ConfigManager.findConfig();
-  if (configManager === null) {
-    logger.line();
-    logger.error("No SynapSync project found.");
-    logger.hint("Run /init to initialize a project.");
-    return;
+  /**
+   * Apply reconciliation result to manifest
+   */
+  applyReconciliation(result) {
+    for (const name of result.removed) {
+      delete this.manifest.cognitives[name];
+    }
+    for (const cognitive of result.added) {
+      this.manifest.cognitives[cognitive.name] = cognitive;
+    }
+    for (const cognitive of result.updated) {
+      const existing = this.manifest.cognitives[cognitive.name];
+      if (existing !== void 0) {
+        const updated = {
+          ...existing,
+          ...cognitive,
+          // Keep original installation info
+          installedAt: existing.installedAt,
+          source: existing.source
+        };
+        if (existing.sourceUrl !== void 0) {
+          updated.sourceUrl = existing.sourceUrl;
+        }
+        this.manifest.cognitives[cognitive.name] = updated;
+      }
+    }
   }
-  switch (options.action) {
-    case "list":
-      showConfigList(configManager);
-      break;
-    case "get":
-      showConfigValue(configManager, options.key ?? "");
-      break;
-    case "set":
-      setConfigValue(configManager, options.key ?? "", options.value ?? "");
-      break;
+  /**
+   * Get provider sync state
+   */
+  getProviderSync(provider) {
+    return this.manifest.syncs[provider];
   }
-}
-function showConfigList(configManager) {
-  const flatConfig = configManager.flatten();
-  logger.line();
-  logger.bold("  Configuration");
-  logger.line();
-  const groups = {};
-  for (const [key, value] of Object.entries(flatConfig)) {
-    const parts = key.split(".");
-    const group2 = parts[0] ?? "other";
-    groups[group2] ??= {};
-    groups[group2][key] = value;
+  /**
+   * Update provider sync state
+   */
+  setProviderSync(provider, state) {
+    this.manifest.syncs[provider] = state;
   }
-  for (const [group2, values] of Object.entries(groups)) {
-    logger.log(`  ${pc5.cyan(group2)}:`);
-    for (const [key, value] of Object.entries(values)) {
-      const displayKey = key.replace(`${group2}.`, "");
-      const displayValue = formatValue(value);
-      logger.log(`    ${pc5.dim(displayKey.padEnd(30))} ${displayValue}`);
-    }
-    logger.line();
+  /**
+   * Get all synced cognitives for a provider
+   */
+  getSyncedCognitives(provider) {
+    return this.manifest.syncs[provider]?.cognitives ?? [];
   }
-  logger.hint(`Config file: ${configManager.getProjectRoot()}/synapsync.config.yaml`);
-}
-function showConfigValue(configManager, key) {
-  if (key === "") {
-    logger.line();
-    logger.error("Key is required.");
-    logger.hint("Usage: /config get <key>");
-    logger.hint("Example: /config get cli.theme");
-    return;
+  /**
+   * Get cognitive count
+   */
+  getCognitiveCount() {
+    return Object.keys(this.manifest.cognitives).length;
   }
-  const value = configManager.get(key);
-  logger.line();
-  if (value === void 0) {
-    logger.warning(`Key not found: ${pc5.cyan(key)}`);
-    logger.line();
-    logger.hint("Use /config list to see all available keys.");
-  } else {
-    logger.log(`  ${pc5.cyan(key)} = ${formatValue(value)}`);
+  /**
+   * Get cognitives by type
+   */
+  getCognitivesByType(type) {
+    return Object.values(this.manifest.cognitives).filter((c) => c.type === type);
   }
-}
-function setConfigValue(configManager, key, value) {
-  if (key === "") {
-    logger.line();
-    logger.error("Key is required.");
-    logger.hint("Usage: /config set <key> <value>");
-    logger.hint("Example: /config set cli.theme dark");
-    return;
+  /**
+   * Get cognitives by source
+   */
+  getCognitivesBySource(source) {
+    return Object.values(this.manifest.cognitives).filter((c) => c.source === source);
   }
-  if (value === "") {
-    logger.line();
-    logger.error("Value is required.");
-    logger.hint("Usage: /config set <key> <value>");
-    return;
+};
+
+// src/services/scanner/scanner.ts
+init_esm_shims();
+import * as fs3 from "fs";
+import * as path4 from "path";
+import * as crypto from "crypto";
+
+// src/services/scanner/parser.ts
+init_esm_shims();
+function parseFrontmatter(content) {
+  const match = content.match(/^---\n([\s\S]*?)\n---/);
+  if (match?.[1] === void 0) {
+    return {};
   }
-  const existingValue = configManager.get(key);
-  const isNewKey = existingValue === void 0;
-  const parsedValue = parseValue(value);
-  configManager.set(key, parsedValue);
-  configManager.save();
-  logger.line();
-  if (isNewKey) {
-    logger.warning(`Created new key: ${pc5.cyan(key)}`);
+  try {
+    return parseYaml(match[1]);
+  } catch {
+    return {};
   }
-  logger.success(`${pc5.cyan(key)} = ${formatValue(parsedValue)}`);
 }
-function parseConfigArgs(args) {
-  const parts = args.trim().split(/\s+/);
-  const action = (parts[0] ?? "list").toLowerCase();
-  if (action === "" || action === "list") {
-    return { action: "list" };
+function parseYaml(yaml2) {
+  const result = {};
+  const lines = yaml2.split("\n");
+  let currentKey = null;
+  let currentArray = null;
+  for (const line of lines) {
+    if (line.trim() === "" || line.trim().startsWith("#")) {
+      continue;
+    }
+    if (line.match(/^\s+-\s+/)) {
+      const value = line.replace(/^\s+-\s+/, "").trim();
+      if (currentArray !== null) {
+        currentArray.push(cleanValue(value));
+      }
+      continue;
+    }
+    const colonIndex = line.indexOf(":");
+    if (colonIndex > 0) {
+      const key = line.slice(0, colonIndex).trim();
+      const rawValue = line.slice(colonIndex + 1).trim();
+      if (currentKey !== null && currentArray !== null) {
+        setNestedValue2(result, currentKey, currentArray);
+        currentArray = null;
+      }
+      currentKey = key;
+      if (rawValue === "" || rawValue === "|" || rawValue === ">") {
+        currentArray = [];
+      } else if (rawValue.startsWith("[") && rawValue.endsWith("]")) {
+        const arrayContent = rawValue.slice(1, -1);
+        const items = arrayContent.split(",").map((item) => cleanValue(item.trim()));
+        setNestedValue2(result, key, items);
+        currentKey = null;
+      } else {
+        setNestedValue2(result, key, cleanValue(rawValue));
+        currentKey = null;
+      }
+    }
   }
-  if (action === "get") {
-    return {
-      action: "get",
-      key: parts[1] ?? ""
-    };
+  if (currentKey !== null && currentArray !== null) {
+    setNestedValue2(result, currentKey, currentArray);
   }
-  if (action === "set") {
-    return {
-      action: "set",
-      key: parts[1] ?? "",
-      value: parts.slice(2).join(" ")
-    };
+  return result;
+}
+function cleanValue(value) {
+  if (value.startsWith('"') && value.endsWith('"') || value.startsWith("'") && value.endsWith("'")) {
+    return value.slice(1, -1);
   }
-  return {
-    action: "get",
-    key: action
-  };
+  return value;
 }
-function formatValue(value) {
-  if (value === null || value === void 0) {
-    return pc5.dim("(not set)");
-  }
-  if (typeof value === "boolean") {
-    return value ? pc5.green("true") : pc5.red("false");
-  }
-  if (typeof value === "number") {
-    return pc5.yellow(String(value));
-  }
-  if (typeof value === "string") {
-    return pc5.white(`"${value}"`);
-  }
-  if (Array.isArray(value)) {
-    return pc5.dim(`[${value.join(", ")}]`);
-  }
-  return pc5.dim(JSON.stringify(value));
-}
-function parseValue(value) {
-  if (value.toLowerCase() === "true") return true;
-  if (value.toLowerCase() === "false") return false;
-  const num = Number(value);
-  if (!isNaN(num) && value.trim() !== "") return num;
-  return value;
-}
-function registerConfigCommand(program) {
-  const configCmd = program.command("config").description("Manage project configuration");
-  configCmd.command("list").description("Show all configuration values").action(() => {
-    executeConfigCommand("list");
-  });
-  configCmd.command("get <key>").description("Get a configuration value").action((key) => {
-    executeConfigCommand(`get ${key}`);
-  });
-  configCmd.command("set <key> <value>").description("Set a configuration value").action((key, value) => {
-    executeConfigCommand(`set ${key} ${value}`);
-  });
-  configCmd.action(() => {
-    executeConfigCommand("list");
-  });
+function setNestedValue2(obj, key, value) {
+  obj[key] = value;
 }
-
-// src/commands/status.ts
-init_esm_shims();
-import * as fs3 from "fs";
-import * as path4 from "path";
-import pc6 from "picocolors";
-function executeStatusCommand(_args = "") {
-  const status = getProjectStatus();
-  logger.line();
-  if (!status.initialized) {
-    showNotInitialized();
-    return;
+function extractVersion(metadata, content) {
+  if (metadata.version !== void 0) {
+    return metadata.version;
   }
-  showProjectStatus(status);
+  const versionMatch = content.match(/version:\s*['"]?([0-9]+\.[0-9]+\.[0-9]+)['"]?/i);
+  if (versionMatch?.[1] !== void 0) {
+    return versionMatch[1];
+  }
+  return "1.0.0";
 }
-function getProjectStatus() {
-  const configManager = ConfigManager.findConfig();
-  if (configManager === null) {
-    return {
-      initialized: false,
-      cognitives: createEmptyCognitiveCount(),
-      providers: []
-    };
+function extractName(metadata, dirName, content) {
+  if (metadata.name !== void 0) {
+    return metadata.name;
   }
-  const config = configManager.getConfig();
-  const projectRoot = configManager.getProjectRoot();
-  const storagePath = configManager.getSynapSyncDir();
-  const cognitives = countCognitives(storagePath);
-  const providers = getProviderStatuses(config, projectRoot);
-  const lastSync = getLastSyncTime(storagePath);
-  const status = {
-    initialized: true,
-    projectName: config.name,
-    projectRoot,
-    configPath: path4.join(projectRoot, "synapsync.config.yaml"),
-    storagePath,
-    cognitives,
-    providers
-  };
-  if (lastSync !== void 0) {
-    status.lastSync = lastSync;
+  const titleMatch = content.match(/^#\s+(.+)$/m);
+  if (titleMatch?.[1] !== void 0) {
+    return titleMatch[1].toLowerCase().replace(/[^a-z0-9]+/g, "-").replace(/^-|-$/g, "");
   }
-  return status;
+  return dirName;
 }
-function createEmptyCognitiveCount() {
-  const counts = {};
-  for (const type of COGNITIVE_TYPES) {
-    counts[type] = 0;
+
+// src/services/scanner/scanner.ts
+var CognitiveScanner = class {
+  synapSyncDir;
+  constructor(synapSyncDir) {
+    this.synapSyncDir = synapSyncDir;
   }
-  return counts;
-}
-function countCognitives(storagePath) {
-  const counts = createEmptyCognitiveCount();
-  for (const type of COGNITIVE_TYPES) {
-    const typePath = path4.join(storagePath, `${type}s`);
-    if (fs3.existsSync(typePath)) {
-      try {
-        const entries = fs3.readdirSync(typePath, { withFileTypes: true });
-        counts[type] = entries.filter(
-          (e) => e.isDirectory() || e.isSymbolicLink() && !e.name.startsWith(".")
-        ).length;
-      } catch {
-        counts[type] = 0;
+  /**
+   * Scan the filesystem for cognitives
+   */
+  scan(options = {}) {
+    const cognitives = [];
+    const errors = [];
+    const typesToScan = options.types ?? COGNITIVE_TYPES;
+    for (const type of typesToScan) {
+      const typeDir = path4.join(this.synapSyncDir, `${type}s`);
+      if (!fs3.existsSync(typeDir)) {
+        continue;
       }
-    }
-  }
-  return counts;
-}
-function getProviderStatuses(config, projectRoot) {
-  const statuses = [];
-  for (const provider of SUPPORTED_PROVIDERS) {
-    const providerConfig = config.sync?.providers?.[provider];
-    const enabled = providerConfig?.enabled ?? false;
-    const providerPath = path4.join(projectRoot, `.${provider}`);
-    let cognitivesCount = 0;
-    if (fs3.existsSync(providerPath)) {
-      try {
-        const subdirs = ["skills", "agents", "prompts", "workflows", "tools"];
-        for (const subdir of subdirs) {
-          const subdirPath = path4.join(providerPath, subdir);
-          if (fs3.existsSync(subdirPath)) {
-            const entries = fs3.readdirSync(subdirPath);
-            cognitivesCount += entries.filter((e) => !e.startsWith(".")).length;
+      const categories = this.listDirectories(typeDir);
+      for (const category of categories) {
+        if (options.categories !== void 0 && !options.categories.includes(category)) {
+          continue;
+        }
+        const categoryDir = path4.join(typeDir, category);
+        const cognitiveDirs = this.listDirectories(categoryDir);
+        for (const cognitiveDir of cognitiveDirs) {
+          try {
+            const cognitive = this.scanCognitive(
+              path4.join(categoryDir, cognitiveDir),
+              type,
+              category
+            );
+            if (cognitive !== null) {
+              cognitives.push(cognitive);
+            }
+          } catch (error) {
+            errors.push({
+              path: path4.join(categoryDir, cognitiveDir),
+              error: error instanceof Error ? error.message : "Unknown error"
+            });
           }
         }
-      } catch {
       }
     }
-    statuses.push({
-      name: provider,
-      enabled,
-      connected: false,
-      // TODO: Check actual connection status
-      cognitivesCount
-    });
-  }
-  return statuses;
-}
-function getLastSyncTime(storagePath) {
-  const manifestPath = path4.join(storagePath, "manifest.json");
-  if (!fs3.existsSync(manifestPath)) {
-    return void 0;
+    return cognitives;
   }
-  try {
-    const content = fs3.readFileSync(manifestPath, "utf-8");
-    const manifest = JSON.parse(content);
-    return manifest.lastUpdated;
-  } catch {
-    return void 0;
+  /**
+   * Scan a single cognitive directory
+   */
+  scanCognitive(cognitiveDir, type, category) {
+    const filePath = this.findCognitiveFile(cognitiveDir, type);
+    if (filePath === null) {
+      return null;
+    }
+    const content = fs3.readFileSync(filePath, "utf-8");
+    const metadata = parseFrontmatter(content);
+    const dirName = path4.basename(cognitiveDir);
+    const fileName = path4.basename(filePath);
+    const name = extractName(metadata, dirName, content);
+    const version2 = extractVersion(metadata, content);
+    const hash = this.computeHash(content);
+    return {
+      name,
+      type,
+      category: metadata.category ?? category,
+      path: cognitiveDir,
+      filePath,
+      fileName,
+      // Add original filename
+      hash,
+      metadata: {
+        ...metadata,
+        name,
+        version: version2
+      }
+    };
   }
-}
-function showNotInitialized() {
-  logger.bold("  Project Status");
-  logger.line();
-  logger.log(`  ${pc6.red("\u25CF")} ${pc6.dim("Not initialized")}`);
-  logger.line();
-  logger.hint("Run /init to initialize a SynapSync project.");
-}
-function showProjectStatus(status) {
-  logger.bold(`  ${status.projectName ?? "SynapSync Project"}`);
-  logger.line();
-  logger.log(`  ${pc6.green("\u25CF")} ${pc6.dim("Initialized")}`);
-  logger.log(`  ${pc6.dim("Root:")} ${status.projectRoot}`);
-  logger.line();
-  logger.bold("  Cognitives");
-  const totalCognitives = Object.values(status.cognitives).reduce((a, b) => a + b, 0);
-  if (totalCognitives === 0) {
-    logger.log(`  ${pc6.dim("No cognitives installed")}`);
-  } else {
-    for (const type of COGNITIVE_TYPES) {
-      const count = status.cognitives[type];
-      if (count > 0) {
-        const icon = getCognitiveIcon(type);
-        logger.log(`  ${icon} ${pc6.white(count.toString().padStart(3))} ${type}s`);
+  /**
+   * Find the cognitive file in a directory
+   * Checks for legacy fixed filename first, then any file with matching extension
+   */
+  findCognitiveFile(cognitiveDir, type) {
+    const legacyFileName = COGNITIVE_FILE_NAMES[type];
+    const legacyPath = path4.join(cognitiveDir, legacyFileName);
+    if (fs3.existsSync(legacyPath)) {
+      return legacyPath;
+    }
+    const extension = COGNITIVE_FILE_EXTENSIONS[type];
+    if (!fs3.existsSync(cognitiveDir)) {
+      return null;
+    }
+    const files = fs3.readdirSync(cognitiveDir);
+    for (const file of files) {
+      if (file.endsWith(extension) && !file.startsWith(".")) {
+        const fullPath = path4.join(cognitiveDir, file);
+        const stat = fs3.statSync(fullPath);
+        if (stat.isFile()) {
+          return fullPath;
+        }
       }
     }
-    logger.log(`  ${pc6.dim("\u2500\u2500\u2500")}`);
-    logger.log(`  ${pc6.bold(totalCognitives.toString().padStart(5))} total`);
+    return null;
   }
-  logger.line();
-  logger.bold("  Providers");
-  const enabledProviders = status.providers.filter((p2) => p2.enabled);
-  if (enabledProviders.length === 0) {
-    logger.log(`  ${pc6.dim("No providers enabled")}`);
-  } else {
-    for (const provider of enabledProviders) {
-      const icon = provider.cognitivesCount > 0 ? pc6.green("\u25CF") : pc6.yellow("\u25CB");
-      const syncStatus = provider.cognitivesCount > 0 ? pc6.dim(`(${provider.cognitivesCount} synced)`) : pc6.dim("(not synced)");
-      logger.log(`  ${icon} ${pc6.white(provider.name)} ${syncStatus}`);
+  /**
+   * Compare scanned cognitives with manifest and return differences
+   */
+  compare(scanned, manifestCognitives) {
+    const result = {
+      found: scanned,
+      new: [],
+      removed: [],
+      modified: [],
+      unchanged: 0,
+      errors: []
+    };
+    const manifestMap = /* @__PURE__ */ new Map();
+    for (const cognitive of manifestCognitives) {
+      manifestMap.set(cognitive.name, cognitive);
     }
-  }
-  logger.line();
-  if (status.lastSync !== void 0) {
-    const syncDate = new Date(status.lastSync);
-    const relativeTime = getRelativeTime(syncDate);
-    logger.log(`  ${pc6.dim("Last updated:")} ${relativeTime}`);
-    logger.line();
-  }
-  logger.hint("Run /help for available commands.");
-}
-function getCognitiveIcon(type) {
-  const icons = {
-    skill: pc6.blue("\u25C6"),
-    agent: pc6.magenta("\u25C6"),
-    prompt: pc6.yellow("\u25C6"),
-    workflow: pc6.cyan("\u25C6"),
-    tool: pc6.green("\u25C6")
-  };
-  return icons[type];
-}
-function getRelativeTime(date) {
-  const now = /* @__PURE__ */ new Date();
-  const diffMs = now.getTime() - date.getTime();
-  const diffMins = Math.floor(diffMs / 6e4);
-  const diffHours = Math.floor(diffMins / 60);
-  const diffDays = Math.floor(diffHours / 24);
-  if (diffMins < 1) return "just now";
-  if (diffMins < 60) return `${diffMins} minute${diffMins === 1 ? "" : "s"} ago`;
-  if (diffHours < 24) return `${diffHours} hour${diffHours === 1 ? "" : "s"} ago`;
-  if (diffDays < 7) return `${diffDays} day${diffDays === 1 ? "" : "s"} ago`;
-  return date.toLocaleDateString();
-}
-function registerStatusCommand(program) {
-  program.command("status").description("Show project status").action(() => {
-    executeStatusCommand();
-  });
-}
-
-// src/commands/providers.ts
-init_esm_shims();
-import * as fs4 from "fs";
-import * as path5 from "path";
-import pc7 from "picocolors";
-function executeProvidersCommand(args) {
-  const parts = args.trim().split(/\s+/);
-  const subcommand = parts[0]?.toLowerCase() ?? "";
-  const configManager = ConfigManager.findConfig();
-  if (configManager === null) {
-    logger.line();
-    logger.error("No SynapSync project found.");
-    logger.hint("Run /init to initialize a project.");
-    return;
-  }
-  switch (subcommand) {
-    case "":
-    case "list":
-      listProviders(configManager);
-      break;
-    case "enable":
-      enableProvider(configManager, parts[1]);
-      break;
-    case "disable":
-      disableProvider(configManager, parts[1]);
-      break;
-    case "path":
-      setProviderPath(configManager, parts[1], parts[2]);
-      break;
-    default:
-      if (SUPPORTED_PROVIDERS.includes(subcommand)) {
-        showProviderInfo(configManager, subcommand);
+    const scannedMap = /* @__PURE__ */ new Map();
+    for (const cognitive of scanned) {
+      scannedMap.set(cognitive.name, cognitive);
+    }
+    for (const scannedCognitive of scanned) {
+      const manifestCognitive = manifestMap.get(scannedCognitive.name);
+      if (manifestCognitive === void 0) {
+        result.new.push(scannedCognitive);
+      } else if (manifestCognitive.hash !== void 0 && manifestCognitive.hash !== scannedCognitive.hash) {
+        result.modified.push(scannedCognitive);
       } else {
-        logger.line();
-        logger.error(`Unknown subcommand: ${subcommand}`);
-        logger.hint("Usage: /providers [list|enable|disable|path]");
+        result.unchanged++;
       }
+    }
+    for (const manifestCognitive of manifestCognitives) {
+      if (!scannedMap.has(manifestCognitive.name)) {
+        result.removed.push(manifestCognitive.name);
+      }
+    }
+    return result;
   }
-}
-function listProviders(configManager) {
-  const providers = getProvidersInfo(configManager);
-  logger.line();
-  logger.bold("  Providers");
-  logger.line();
-  logger.log(
-    `  ${pc7.dim("Provider".padEnd(12))} ${pc7.dim("Status".padEnd(10))} ${pc7.dim("Path".padEnd(20))} ${pc7.dim("Directory")}`
-  );
-  logger.log(`  ${pc7.dim("\u2500".repeat(60))}`);
-  for (const provider of providers) {
-    const statusIcon = provider.enabled ? pc7.green("\u25CF") : pc7.dim("\u25CB");
-    const statusText = provider.enabled ? pc7.green("enabled") : pc7.dim("disabled");
-    const pathText = pc7.cyan(provider.path);
-    const existsText = provider.exists ? pc7.green("\u2713 exists") : pc7.dim("\u2717 missing");
-    logger.log(
-      `  ${statusIcon} ${pc7.white(provider.name.padEnd(10))} ${statusText.padEnd(19)} ${pathText.padEnd(29)} ${existsText}`
-    );
-  }
-  logger.line();
-  const enabledCount = providers.filter((p2) => p2.enabled).length;
-  logger.log(`  ${pc7.dim("Enabled:")} ${enabledCount} of ${providers.length} providers`);
-  logger.line();
-  logger.hint("Use /providers enable <name> or /providers disable <name>");
-}
-function enableProvider(configManager, providerName) {
-  if (providerName === void 0 || providerName === "") {
-    logger.line();
-    logger.error("Provider name is required.");
-    logger.hint("Usage: /providers enable <provider>");
-    logger.hint(`Available: ${SUPPORTED_PROVIDERS.join(", ")}`);
-    return;
+  /**
+   * Convert a scanned cognitive to a manifest cognitive
+   */
+  toManifestCognitive(scanned) {
+    return {
+      name: scanned.name,
+      type: scanned.type,
+      category: scanned.category,
+      version: scanned.metadata.version ?? "1.0.0",
+      installedAt: (/* @__PURE__ */ new Date()).toISOString(),
+      source: "local",
+      hash: scanned.hash
+    };
   }
-  const provider = providerName.toLowerCase();
-  if (!SUPPORTED_PROVIDERS.includes(provider)) {
-    logger.line();
-    logger.error(`Unknown provider: ${provider}`);
-    logger.hint(`Available: ${SUPPORTED_PROVIDERS.join(", ")}`);
-    return;
+  /**
+   * Compute content hash for change detection
+   */
+  computeHash(content) {
+    return crypto.createHash("sha256").update(content).digest("hex").slice(0, 16);
   }
-  const currentValue = configManager.get(`sync.providers.${provider}.enabled`);
-  if (currentValue === true) {
-    logger.line();
-    logger.info(`Provider '${provider}' is already enabled.`);
-    return;
+  /**
+   * List directories in a path
+   */
+  listDirectories(dirPath) {
+    if (!fs3.existsSync(dirPath)) {
+      return [];
+    }
+    return fs3.readdirSync(dirPath, { withFileTypes: true }).filter((dirent) => dirent.isDirectory()).filter((dirent) => !dirent.name.startsWith(".")).map((dirent) => dirent.name);
   }
-  configManager.set(`sync.providers.${provider}.enabled`, true);
-  const defaultPaths = PROVIDER_PATHS[provider];
-  const currentPaths = configManager.get(`sync.providers.${provider}.paths`);
-  if (currentPaths === void 0) {
-    configManager.set(`sync.providers.${provider}.paths`, defaultPaths);
+  /**
+   * Detect cognitive type from directory contents
+   */
+  detectType(cognitiveDir) {
+    for (const type of COGNITIVE_TYPES) {
+      const fileName = COGNITIVE_FILE_NAMES[type];
+      const filePath = path4.join(cognitiveDir, fileName);
+      if (fs3.existsSync(filePath)) {
+        return type;
+      }
+    }
+    return null;
   }
-  configManager.save();
-  logger.line();
-  logger.success(`Provider '${pc7.cyan(provider)}' enabled`);
-  logger.log(`  ${pc7.dim("Path:")} ${defaultPaths.skill.split("/")[0]}/`);
-  logger.line();
-  logger.hint("Run /sync to synchronize cognitives to this provider.");
-}
-function disableProvider(configManager, providerName) {
-  if (providerName === void 0 || providerName === "") {
-    logger.line();
-    logger.error("Provider name is required.");
-    logger.hint("Usage: /providers disable <provider>");
-    return;
+  /**
+   * Get cognitive count by type
+   */
+  countByType(cognitives) {
+    const counts = {
+      skill: 0,
+      agent: 0,
+      prompt: 0,
+      workflow: 0,
+      tool: 0
+    };
+    for (const cognitive of cognitives) {
+      counts[cognitive.type]++;
+    }
+    return counts;
   }
-  const provider = providerName.toLowerCase();
-  if (!SUPPORTED_PROVIDERS.includes(provider)) {
-    logger.line();
-    logger.error(`Unknown provider: ${provider}`);
-    logger.hint(`Available: ${SUPPORTED_PROVIDERS.join(", ")}`);
-    return;
+};
+
+// src/services/agents-md/generator.ts
+var START_MARKER = "<!-- synapsync:start -->";
+var END_MARKER = "<!-- synapsync:end -->";
+var TYPE_ICONS = {
+  skill: "\u{1F527}",
+  agent: "\u{1F916}",
+  prompt: "\u{1F4AC}",
+  workflow: "\u{1F504}",
+  tool: "\u{1F9F0}"
+};
+var TYPE_LABELS = {
+  skill: "Skills",
+  agent: "Agents",
+  prompt: "Prompts",
+  workflow: "Workflows",
+  tool: "Tools"
+};
+var MAX_DESCRIPTION_LENGTH = 80;
+var AgentsMdGenerator = class {
+  projectRoot;
+  synapSyncDir;
+  scanner;
+  constructor(projectRoot, synapSyncDir) {
+    this.projectRoot = projectRoot;
+    this.synapSyncDir = synapSyncDir;
+    this.scanner = new CognitiveScanner(this.synapSyncDir);
   }
-  const currentValue = configManager.get(`sync.providers.${provider}.enabled`);
-  if (currentValue !== true) {
-    logger.line();
-    logger.info(`Provider '${provider}' is already disabled.`);
-    return;
+  /**
+   * Generate and write the AGENTS.md file from manifest cognitives.
+   */
+  generate(cognitives) {
+    const outputPath = path5.join(this.projectRoot, AGENTS_MD_FILE_NAME);
+    try {
+      const entries = this.buildEntries(cognitives);
+      const managedContent = this.renderManagedSection(entries);
+      this.writeWithMarkers(outputPath, managedContent);
+      return {
+        success: true,
+        filePath: outputPath,
+        cognitiveCount: entries.length
+      };
+    } catch (error) {
+      return {
+        success: false,
+        filePath: outputPath,
+        cognitiveCount: 0,
+        error: error instanceof Error ? error.message : "Unknown error"
+      };
+    }
   }
-  configManager.set(`sync.providers.${provider}.enabled`, false);
-  configManager.save();
-  logger.line();
-  logger.success(`Provider '${pc7.cyan(provider)}' disabled`);
-}
-function setProviderPath(configManager, providerName, newPath) {
-  if (providerName === void 0 || providerName === "") {
-    logger.line();
-    logger.error("Provider name is required.");
-    logger.hint("Usage: /providers path <provider> <path>");
-    return;
-  }
-  if (newPath === void 0 || newPath === "") {
-    logger.line();
-    logger.error("Path is required.");
-    logger.hint("Usage: /providers path <provider> <path>");
-    logger.hint("Example: /providers path claude .claude-code/");
-    return;
-  }
-  const provider = providerName.toLowerCase();
-  if (!SUPPORTED_PROVIDERS.includes(provider)) {
-    logger.line();
-    logger.error(`Unknown provider: ${provider}`);
-    logger.hint(`Available: ${SUPPORTED_PROVIDERS.join(", ")}`);
-    return;
-  }
-  const normalizedPath = newPath.endsWith("/") ? newPath : `${newPath}/`;
-  const cognitiveTypes = ["skill", "agent", "prompt", "workflow", "tool"];
-  for (const type of cognitiveTypes) {
-    configManager.set(`sync.providers.${provider}.paths.${type}`, `${normalizedPath}${type}s`);
-  }
-  configManager.save();
-  logger.line();
-  logger.success(`Updated paths for '${pc7.cyan(provider)}'`);
-  logger.log(`  ${pc7.dim("Base path:")} ${pc7.cyan(normalizedPath)}`);
-  logger.line();
-}
-function showProviderInfo(configManager, provider) {
-  const config = configManager.getConfig();
-  const projectRoot = configManager.getProjectRoot();
-  const providerConfig = config.sync?.providers?.[provider];
-  const enabled = providerConfig?.enabled ?? false;
-  const paths = providerConfig?.paths ?? PROVIDER_PATHS[provider];
-  logger.line();
-  logger.bold(`  ${getProviderDisplayName(provider)}`);
-  logger.line();
-  const statusIcon = enabled ? pc7.green("\u25CF") : pc7.dim("\u25CB");
-  const statusText = enabled ? pc7.green("Enabled") : pc7.dim("Disabled");
-  logger.log(`  ${pc7.dim("Status:")}  ${statusIcon} ${statusText}`);
-  logger.line();
-  logger.log(`  ${pc7.dim("Paths:")}`);
-  const cognitiveTypes = ["skill", "agent", "prompt", "workflow", "tool"];
-  for (const type of cognitiveTypes) {
-    const typePath = paths[type] ?? "";
-    const fullPath = path5.join(projectRoot, typePath);
-    const exists = fs4.existsSync(fullPath);
-    const existsIcon = exists ? pc7.green("\u2713") : pc7.dim("\u2717");
-    logger.log(`    ${pc7.dim(type.padEnd(10))} ${pc7.cyan(typePath)} ${existsIcon}`);
-  }
-  logger.line();
-}
-function getProvidersInfo(configManager) {
-  const config = configManager.getConfig();
-  const projectRoot = configManager.getProjectRoot();
-  const providers = [];
-  for (const provider of SUPPORTED_PROVIDERS) {
-    const providerConfig = config.sync?.providers?.[provider];
-    const enabled = providerConfig?.enabled ?? false;
-    const basePath = providerConfig?.paths?.skill?.split("/")[0] ?? `.${provider}`;
-    const fullPath = path5.join(projectRoot, basePath);
-    const exists = fs4.existsSync(fullPath);
-    providers.push({
-      name: provider,
-      enabled,
-      path: `${basePath}/`,
-      exists
-    });
-  }
-  return providers;
-}
-function getProviderDisplayName(provider) {
-  const names = {
-    claude: "Claude (Anthropic)",
-    openai: "OpenAI (GPT)",
-    gemini: "Gemini (Google)",
-    cursor: "Cursor IDE",
-    windsurf: "Windsurf IDE",
-    copilot: "GitHub Copilot"
-  };
-  return names[provider];
-}
-function registerProvidersCommand(program) {
-  const providersCmd = program.command("providers").description("Manage provider configuration");
-  providersCmd.command("list", { isDefault: true }).description("List all providers and their status").action(() => {
-    executeProvidersCommand("list");
-  });
-  providersCmd.command("enable <provider>").description("Enable a provider").action((provider) => {
-    executeProvidersCommand(`enable ${provider}`);
-  });
-  providersCmd.command("disable <provider>").description("Disable a provider").action((provider) => {
-    executeProvidersCommand(`disable ${provider}`);
-  });
-  providersCmd.command("path <provider> <path>").description("Set custom sync path for a provider").action((provider, newPath) => {
-    executeProvidersCommand(`path ${provider} ${newPath}`);
-  });
-  providersCmd.action(() => {
-    executeProvidersCommand("list");
-  });
-}
-
-// src/commands/search.ts
-init_esm_shims();
-import pc8 from "picocolors";
-
-// src/services/registry/client.ts
-init_esm_shims();
-var RegistryClient = class {
-  baseUrl;
-  indexCache = null;
-  indexCacheTime = 0;
-  cacheTtl;
-  constructor(options = {}) {
-    this.baseUrl = options.baseUrl ?? REGISTRY_BASE_URL;
-    this.cacheTtl = options.cacheTtl ?? 5 * 60 * 1e3;
-  }
-  // ============================================
-  // Index Operations
-  // ============================================
   /**
-   * Fetch the registry index
+   * Generate an empty managed section (used by init).
    */
-  async getIndex(forceRefresh = false) {
-    const now = Date.now();
-    if (!forceRefresh && this.indexCache !== null && now - this.indexCacheTime < this.cacheTtl) {
-      return this.indexCache;
-    }
-    const url = `${this.baseUrl}/${REGISTRY_INDEX_FILE}`;
-    const response = await this.fetch(url);
-    if (!response.ok) {
-      throw new RegistryError(`Failed to fetch registry index: ${response.status} ${response.statusText}`, url);
+  generateEmpty() {
+    const outputPath = path5.join(this.projectRoot, AGENTS_MD_FILE_NAME);
+    try {
+      const managedContent = this.renderEmptySection();
+      this.writeWithMarkers(outputPath, managedContent);
+      return {
+        success: true,
+        filePath: outputPath,
+        cognitiveCount: 0
+      };
+    } catch (error) {
+      return {
+        success: false,
+        filePath: outputPath,
+        cognitiveCount: 0,
+        error: error instanceof Error ? error.message : "Unknown error"
+      };
     }
-    const index = await response.json();
-    this.indexCache = index;
-    this.indexCacheTime = now;
-    return index;
   }
   /**
-   * Get total count of cognitives in registry
+   * Remove the AGENTS.md file entirely (used by purge).
    */
-  async getCount() {
-    const index = await this.getIndex();
-    return index.totalCognitives;
+  remove() {
+    const outputPath = path5.join(this.projectRoot, AGENTS_MD_FILE_NAME);
+    if (fs4.existsSync(outputPath)) {
+      fs4.unlinkSync(outputPath);
+      return true;
+    }
+    return false;
   }
-  // ============================================
-  // Search Operations
-  // ============================================
   /**
-   * Search for cognitives in the registry
+   * Build enriched entries from manifest cognitives.
+   * Scans filesystem for descriptions from frontmatter.
    */
-  async search(query, options = {}) {
-    const index = await this.getIndex();
-    let results = [...index.cognitives];
-    if (query !== void 0 && query.trim() !== "") {
-      const q = query.toLowerCase();
-      results = results.filter(
-        (c) => c.name.toLowerCase().includes(q) || c.description.toLowerCase().includes(q) || c.tags.some((t) => t.toLowerCase().includes(q))
-      );
-    }
-    if (options.type !== void 0) {
-      results = results.filter((c) => c.type === options.type);
-    }
-    if (options.category !== void 0) {
-      results = results.filter((c) => c.category === options.category);
-    }
-    if (options.tag !== void 0) {
-      const tag = options.tag.toLowerCase();
-      results = results.filter((c) => c.tags.some((t) => t.toLowerCase() === tag));
-    }
-    const total = results.length;
-    if (options.limit !== void 0 && options.limit > 0) {
-      results = results.slice(0, options.limit);
+  buildEntries(cognitives) {
+    const scanned = this.scanner.scan();
+    const scannedMap = new Map(scanned.map((s) => [s.name, s]));
+    const entries = [];
+    for (const cognitive of cognitives) {
+      const scannedCognitive = scannedMap.get(cognitive.name);
+      let description = "No description available";
+      let relativePath = "";
+      let fileName = "";
+      if (scannedCognitive !== void 0) {
+        const rawDesc = scannedCognitive.metadata.description;
+        if (typeof rawDesc === "string" && rawDesc.length > 0) {
+          description = rawDesc;
+        } else if (Array.isArray(rawDesc) && rawDesc.length > 0) {
+          description = rawDesc.join(" ");
+        }
+        relativePath = path5.relative(this.projectRoot, scannedCognitive.filePath);
+        fileName = scannedCognitive.fileName ?? path5.basename(scannedCognitive.filePath);
+      } else {
+        const typeDir = `${cognitive.type}s`;
+        const expectedDir = path5.join(this.synapSyncDir, typeDir, cognitive.category, cognitive.name);
+        relativePath = path5.relative(this.projectRoot, expectedDir);
+        fileName = cognitive.name;
+      }
+      entries.push({
+        name: cognitive.name,
+        type: cognitive.type,
+        category: cognitive.category,
+        description: truncateDescription(description),
+        version: cognitive.version,
+        relativePath,
+        fileName
+      });
     }
-    const filters = {};
-    if (options.type !== void 0) filters.type = options.type;
-    if (options.category !== void 0) filters.category = options.category;
-    if (options.tag !== void 0) filters.tag = options.tag;
-    return {
-      cognitives: results,
-      total,
-      ...query !== void 0 ? { query } : {},
-      filters
-    };
+    entries.sort((a, b) => a.name.localeCompare(b.name));
+    return entries;
   }
   /**
-   * Find a cognitive by name
+   * Render the full managed section (between markers).
    */
-  async findByName(name) {
-    const index = await this.getIndex();
-    return index.cognitives.find((c) => c.name === name) ?? null;
+  renderManagedSection(entries) {
+    const lines = [
+      START_MARKER,
+      "# SynapSync Project Cognitives",
+      "",
+      "> Auto-generated by [SynapSync](https://synapsync.github.io/synapsync-cli/). Do not edit this section manually.",
+      ""
+    ];
+    if (entries.length === 0) {
+      lines.push("*No cognitives installed yet. Run `synapsync add <name>` to get started.*");
+    } else {
+      lines.push("## Available Cognitives");
+      lines.push("");
+      for (const type of COGNITIVE_TYPES) {
+        const typeEntries = entries.filter((e) => e.type === type);
+        if (typeEntries.length === 0) continue;
+        lines.push(`### ${TYPE_ICONS[type]} ${TYPE_LABELS[type]}`);
+        lines.push("");
+        lines.push(...this.renderTypeTable(typeEntries));
+        lines.push("");
+      }
+      lines.push("---");
+      lines.push("");
+      lines.push(`*Last updated: ${(/* @__PURE__ */ new Date()).toISOString()} \xB7 ${entries.length} cognitive${entries.length !== 1 ? "s" : ""} installed*`);
+    }
+    lines.push(END_MARKER);
+    return lines.join("\n");
   }
   /**
-   * List all cognitives
+   * Render the empty managed section.
    */
-  async list(options = {}) {
-    const result = await this.search(void 0, options);
-    return result.cognitives;
+  renderEmptySection() {
+    const lines = [
+      START_MARKER,
+      "# SynapSync Project Cognitives",
+      "",
+      "> Auto-generated by [SynapSync](https://synapsync.github.io/synapsync-cli/). Do not edit this section manually.",
+      "",
+      "*No cognitives installed yet. Run `synapsync add <name>` to get started.*",
+      END_MARKER
+    ];
+    return lines.join("\n");
   }
-  // ============================================
-  // Download Operations
-  // ============================================
   /**
-   * Get the manifest for a cognitive
+   * Render a markdown table for a group of entries.
    */
-  async getManifest(cognitiveEntry) {
-    const url = `${this.baseUrl}/${cognitiveEntry.path}/${REGISTRY_MANIFEST_FILE}`;
-    const response = await this.fetch(url);
-    if (!response.ok) {
-      throw new RegistryError(
-        `Failed to fetch manifest for ${cognitiveEntry.name}: ${response.status} ${response.statusText}`,
-        url
-      );
+  renderTypeTable(entries) {
+    const lines = [
+      "| Name | Category | Description | Version | Path |",
+      "|------|----------|-------------|---------|------|"
+    ];
+    for (const entry of entries) {
+      const name = `\`${escapeTableCell(entry.name)}\``;
+      const category = escapeTableCell(entry.category);
+      const description = escapeTableCell(entry.description);
+      const version2 = escapeTableCell(entry.version);
+      const pathLink = `[${escapeTableCell(entry.fileName)}](${entry.relativePath})`;
+      lines.push(`| ${name} | ${category} | ${description} | ${version2} | ${pathLink} |`);
     }
-    return await response.json();
+    return lines;
   }
   /**
-   * Get the content file for a cognitive
+   * Write content within markers, preserving user content outside.
    */
-  async getContent(cognitiveEntry, manifest) {
-    const url = `${this.baseUrl}/${cognitiveEntry.path}/${manifest.file}`;
-    const response = await this.fetch(url);
-    if (!response.ok) {
-      throw new RegistryError(
-        `Failed to fetch content for ${cognitiveEntry.name}: ${response.status} ${response.statusText}`,
-        url
-      );
+  writeWithMarkers(filePath, managedContent) {
+    if (!fs4.existsSync(filePath)) {
+      fs4.writeFileSync(filePath, managedContent + "\n", "utf-8");
+      return;
     }
-    return response.text();
-  }
-  /**
-   * Download a cognitive (manifest + content)
-   */
-  async download(name) {
-    const entry = await this.findByName(name);
-    if (entry === null) {
-      throw new CognitiveNotFoundError(name);
+    const existing = fs4.readFileSync(filePath, "utf-8");
+    const startIdx = existing.indexOf(START_MARKER);
+    const endIdx = existing.indexOf(END_MARKER);
+    if (startIdx !== -1 && endIdx !== -1) {
+      const before = existing.slice(0, startIdx);
+      const after = existing.slice(endIdx + END_MARKER.length);
+      fs4.writeFileSync(filePath, before + managedContent + after, "utf-8");
+    } else if (startIdx !== -1 && endIdx === -1) {
+      const before = existing.slice(0, startIdx);
+      fs4.writeFileSync(filePath, before + managedContent + "\n", "utf-8");
+    } else {
+      const separator = existing.endsWith("\n") ? "\n" : "\n\n";
+      fs4.writeFileSync(filePath, existing + separator + managedContent + "\n", "utf-8");
     }
-    const manifest = await this.getManifest(entry);
-    const content = await this.getContent(entry, manifest);
-    return {
-      manifest,
-      content,
-      path: entry.path
-    };
   }
-  /**
-   * Download additional assets for a cognitive
-   */
-  async downloadAsset(cognitiveEntry, assetPath) {
-    const url = `${this.baseUrl}/${cognitiveEntry.path}/${assetPath}`;
-    const response = await this.fetch(url);
-    if (!response.ok) {
-      throw new RegistryError(
-        `Failed to fetch asset ${assetPath} for ${cognitiveEntry.name}: ${response.status} ${response.statusText}`,
-        url
-      );
-    }
-    return response.text();
-  }
-  // ============================================
-  // Utility Methods
-  // ============================================
-  /**
-   * Check if registry is reachable
-   */
-  async ping() {
-    try {
-      const url = `${this.baseUrl}/${REGISTRY_INDEX_FILE}`;
-      const response = await this.fetch(url, { method: "HEAD" });
-      return response.ok;
-    } catch {
-      return false;
-    }
+};
+function truncateDescription(description) {
+  const text2 = String(description ?? "");
+  if (text2.length <= MAX_DESCRIPTION_LENGTH) {
+    return text2;
   }
-  /**
-   * Clear the cache
-   */
-  clearCache() {
-    this.indexCache = null;
-    this.indexCacheTime = 0;
+  return text2.slice(0, MAX_DESCRIPTION_LENGTH - 3) + "...";
+}
+function escapeTableCell(value) {
+  return String(value ?? "").replace(/\|/g, "\\|");
+}
+function regenerateAgentsMd(projectRoot, synapSyncDir) {
+  const manifest = new ManifestManager(synapSyncDir);
+  const generator = new AgentsMdGenerator(projectRoot, synapSyncDir);
+  return generator.generate(manifest.getCognitives());
+}
+
+// src/commands/init.ts
+async function executeInitCommand(options = {}) {
+  const projectRoot = process.cwd();
+  const configPath = path6.join(projectRoot, CONFIG_FILE_NAME);
+  const storagePath = path6.join(projectRoot, DEFAULT_SYNAPSYNC_DIR);
+  if (ConfigManager.isProjectInitialized(projectRoot)) {
+    logger.line();
+    logger.warning("Project already initialized.");
+    logger.log(`  ${pc4.dim("Config:")} ${configPath}`);
+    logger.log(`  ${pc4.dim("Storage:")} ${storagePath}`);
+    logger.line();
+    logger.hint("Use /config to view or modify settings.");
+    return null;
   }
-  /**
-   * Get the base URL
-   */
-  getBaseUrl() {
-    return this.baseUrl;
+  if (options.yes === true) {
+    return initializeProject({
+      name: options.name ?? path6.basename(projectRoot),
+      ...options.description !== void 0 && { description: options.description },
+      providers: options.providers ?? ["claude"]
+    });
   }
-  // ============================================
-  // Private Methods
-  // ============================================
-  async fetch(url, options) {
-    try {
-      return await fetch(url, {
-        ...options,
-        headers: {
-          "User-Agent": "SynapSync-CLI",
-          ...options?.headers
-        }
-      });
-    } catch (error) {
-      if (error instanceof Error) {
-        throw new RegistryError(`Network error: ${error.message}`, url);
+  logger.line();
+  p.intro(pc4.bgCyan(pc4.black(" Initialize SynapSync Project ")));
+  const result = await p.group(
+    {
+      name: () => {
+        const defaultName = path6.basename(projectRoot);
+        return p.text({
+          message: "Project name",
+          placeholder: defaultName,
+          defaultValue: defaultName,
+          validate: (value) => {
+            const finalValue = value.trim() === "" ? defaultName : value;
+            if (!/^[a-z0-9-_]+$/i.test(finalValue)) {
+              return "Project name can only contain letters, numbers, hyphens, and underscores";
+            }
+            return void 0;
+          }
+        });
+      },
+      description: () => p.text({
+        message: "Description (optional)",
+        placeholder: "A brief description of your project"
+      }),
+      providers: () => p.multiselect({
+        message: "Select AI providers to enable",
+        options: SUPPORTED_PROVIDERS.map((provider) => ({
+          value: provider,
+          label: getProviderLabel(provider),
+          hint: getProviderHint(provider)
+        })),
+        initialValues: ["claude"],
+        required: false
+      })
+    },
+    {
+      onCancel: () => {
+        p.cancel("Project initialization cancelled.");
+        return process.exit(0);
       }
-      throw new RegistryError("Network error", url);
     }
+  );
+  if (p.isCancel(result)) {
+    return null;
   }
-};
-var RegistryError = class extends Error {
-  constructor(message, url) {
-    super(message);
-    this.url = url;
-    this.name = "RegistryError";
-  }
-};
-var CognitiveNotFoundError = class extends Error {
-  constructor(cognitiveName) {
-    super(`Cognitive '${cognitiveName}' not found in registry`);
-    this.cognitiveName = cognitiveName;
-    this.name = "CognitiveNotFoundError";
-  }
-};
-
-// src/commands/search.ts
-async function executeSearchCommand(query, options) {
-  logger.line();
-  const validatedOptions = validateOptions(options);
-  if (validatedOptions === null) {
-    return;
-  }
-  const searchingText = query !== void 0 && query.trim() !== "" ? `Searching for "${query}"...` : "Fetching cognitives from registry...";
-  logger.log(`  ${pc8.dim(searchingText)}`);
+  return initializeProject({
+    name: result.name,
+    description: result.description,
+    providers: result.providers
+  });
+}
+function initializeProject(setup) {
+  const projectRoot = process.cwd();
+  const configPath = path6.join(projectRoot, CONFIG_FILE_NAME);
+  const storagePath = path6.join(projectRoot, DEFAULT_SYNAPSYNC_DIR);
+  const s = p.spinner();
+  s.start("Creating project structure...");
   try {
-    const client = new RegistryClient();
-    const isReachable = await client.ping();
-    if (!isReachable) {
-      logger.line();
-      logger.error("Unable to reach the registry. Check your internet connection.");
-      return;
-    }
-    const searchOpts = {};
-    if (validatedOptions.type !== void 0) searchOpts.type = validatedOptions.type;
-    if (validatedOptions.category !== void 0) searchOpts.category = validatedOptions.category;
-    if (validatedOptions.tag !== void 0) searchOpts.tag = validatedOptions.tag;
-    if (validatedOptions.limit !== void 0) searchOpts.limit = validatedOptions.limit;
-    const result = await client.search(query, searchOpts);
-    process.stdout.write("\x1B[1A\x1B[2K");
-    if (options.json === true) {
-      console.log(JSON.stringify(result, null, 2));
-      return;
+    createStorageStructure(storagePath);
+    const configManager = new ConfigManager(projectRoot);
+    configManager.create(setup.name, setup.description);
+    for (const provider of setup.providers) {
+      configManager.set(`sync.providers.${provider}.enabled`, true);
     }
-    displaySearchResults(result.cognitives, query, result.total);
+    configManager.save();
+    createManifest(storagePath);
+    new AgentsMdGenerator(projectRoot, storagePath).generateEmpty();
+    updateGitignore(projectRoot);
+    s.stop("Project structure created!");
+    showSuccessMessage(setup, configPath, storagePath);
+    return {
+      success: true,
+      projectPath: projectRoot,
+      configPath,
+      storagePath
+    };
   } catch (error) {
+    s.stop("Failed to create project.");
     logger.line();
-    if (error instanceof RegistryError) {
-      logger.error(`Registry error: ${error.message}`);
-    } else if (error instanceof Error) {
-      logger.error(`Search failed: ${error.message}`);
-    } else {
-      logger.error("Search failed with unknown error");
+    if (error instanceof Error) {
+      logger.error(error.message);
     }
+    throw error;
   }
 }
-function validateOptions(options) {
-  const validated = {};
-  if (options.type !== void 0) {
-    if (!COGNITIVE_TYPES.includes(options.type)) {
-      logger.error(`Invalid type: ${options.type}`);
-      logger.hint(`Valid types: ${COGNITIVE_TYPES.join(", ")}`);
-      return null;
-    }
-    validated.type = options.type;
-  }
-  if (options.category !== void 0) {
-    if (!CATEGORIES.includes(options.category)) {
-      logger.error(`Invalid category: ${options.category}`);
-      logger.hint(`Valid categories: ${CATEGORIES.join(", ")}`);
-      return null;
-    }
-    validated.category = options.category;
-  }
-  if (options.tag !== void 0) {
-    validated.tag = options.tag;
-  }
-  if (options.limit !== void 0) {
-    const limit = parseInt(options.limit, 10);
-    if (isNaN(limit) || limit < 1) {
-      logger.error("Limit must be a positive number");
-      return null;
-    }
-    validated.limit = limit;
+function createStorageStructure(storagePath) {
+  fs5.mkdirSync(storagePath, { recursive: true });
+  for (const cognitiveType of COGNITIVE_TYPES) {
+    const typePath = path6.join(storagePath, `${cognitiveType}s`);
+    fs5.mkdirSync(typePath, { recursive: true });
+    const gitkeepPath = path6.join(typePath, ".gitkeep");
+    fs5.writeFileSync(gitkeepPath, "");
   }
-  return validated;
 }
-function displaySearchResults(cognitives, query, total) {
-  if (query !== void 0 && query.trim() !== "") {
-    logger.bold(`  Search Results for "${query}"`);
-  } else {
-    logger.bold("  Registry Cognitives");
-  }
-  logger.line();
-  if (cognitives.length === 0) {
-    logger.log(`  ${pc8.dim("No cognitives found")}`);
-    logger.line();
-    logger.hint("Try a different search query or remove filters.");
-    return;
-  }
-  if (cognitives.length < total) {
-    logger.log(`  ${pc8.dim(`Showing ${cognitives.length} of ${total} results`)}`);
+function createManifest(storagePath) {
+  const manifestPath = path6.join(storagePath, "manifest.json");
+  const manifest = {
+    version: "1.0.0",
+    lastUpdated: (/* @__PURE__ */ new Date()).toISOString(),
+    cognitives: {},
+    syncs: {}
+  };
+  fs5.writeFileSync(manifestPath, JSON.stringify(manifest, null, 2));
+}
+function updateGitignore(projectRoot) {
+  const gitignorePath = path6.join(projectRoot, ".gitignore");
+  const synapsyncEntries = `
+# SynapSync
+.synapsync/manifest.json
+*.local.yaml
+`;
+  if (fs5.existsSync(gitignorePath)) {
+    const content = fs5.readFileSync(gitignorePath, "utf-8");
+    if (!content.includes("# SynapSync")) {
+      fs5.appendFileSync(gitignorePath, synapsyncEntries);
+    }
   } else {
-    logger.log(`  ${pc8.dim(`Found ${total} cognitive${total === 1 ? "" : "s"}`)}`);
+    fs5.writeFileSync(gitignorePath, synapsyncEntries.trim() + "\n");
   }
-  logger.line();
-  for (const cognitive of cognitives) {
-    displayCognitive(cognitive);
-  }
-  logger.line();
-  logger.hint("Run synapsync add <name> to add a cognitive.");
 }
-function displayCognitive(cognitive) {
-  const typeIcon = getCognitiveIcon2(cognitive.type);
-  const typeLabel = pc8.dim(`[${cognitive.type}]`);
-  logger.log(`  ${typeIcon} ${pc8.bold(pc8.white(cognitive.name))} ${typeLabel}`);
-  logger.log(`    ${pc8.dim(truncate(cognitive.description, 60))}`);
-  const meta = [];
-  meta.push(pc8.dim(`v${cognitive.version}`));
-  meta.push(pc8.dim(cognitive.category));
-  if (cognitive.downloads > 0) {
-    meta.push(pc8.dim(`${cognitive.downloads} downloads`));
-  }
-  logger.log(`    ${meta.join(" \xB7 ")}`);
-  if (cognitive.tags.length > 0) {
-    const tags = cognitive.tags.slice(0, 5).map((t) => pc8.cyan(t)).join(" ");
-    logger.log(`    ${tags}`);
-  }
-  logger.line();
+function getProviderLabel(provider) {
+  const labels = {
+    claude: "Claude (Anthropic)",
+    openai: "OpenAI (GPT)",
+    gemini: "Gemini (Google)",
+    cursor: "Cursor IDE",
+    windsurf: "Windsurf IDE",
+    copilot: "GitHub Copilot"
+  };
+  return labels[provider];
 }
-function getCognitiveIcon2(type) {
-  const icons = {
-    skill: pc8.blue("\u25C6"),
-    agent: pc8.magenta("\u25C6"),
-    prompt: pc8.yellow("\u25C6"),
-    workflow: pc8.cyan("\u25C6"),
-    tool: pc8.green("\u25C6")
+function getProviderHint(provider) {
+  const hints = {
+    claude: "Claude Code, Claude Desktop",
+    openai: "ChatGPT, API",
+    gemini: "Google AI Studio",
+    cursor: "AI-first code editor",
+    windsurf: "AI-powered IDE",
+    copilot: "VS Code integration"
   };
-  return icons[type];
+  return hints[provider];
 }
-function truncate(text2, maxLength) {
-  if (text2.length <= maxLength) return text2;
-  return text2.slice(0, maxLength - 3) + "...";
+function showSuccessMessage(setup, configPath, storagePath) {
+  logger.line();
+  p.note(
+    [
+      `${pc4.dim("Config:")}   ${pc4.cyan(configPath)}`,
+      `${pc4.dim("Storage:")}  ${pc4.cyan(storagePath)}`,
+      "",
+      `${pc4.dim("Providers:")} ${setup.providers.map((p2) => pc4.green(p2)).join(", ") || pc4.dim("none")}`
+    ].join("\n"),
+    `Project "${setup.name}" initialized!`
+  );
+  logger.line();
+  logger.bold("  Next Steps:");
+  logger.line();
+  logger.log(`  ${pc4.cyan("1.")} Browse available cognitives:`);
+  logger.log(`     ${pc4.dim("$")} synapsync list --remote`);
+  logger.line();
+  logger.log(`  ${pc4.cyan("2.")} Add cognitives:`);
+  logger.log(`     ${pc4.dim("$")} synapsync add code-reviewer`);
+  logger.log(`     ${pc4.dim("$")} synapsync add github:user/my-skill`);
+  logger.line();
+  p.outro(pc4.green("Happy syncing!"));
 }
-function registerSearchCommand(program) {
-  program.command("search [query]").description("Search for cognitives in the registry").option("-t, --type <type>", "Filter by type (skill, agent, prompt, workflow, tool)").option("-c, --category <category>", "Filter by category").option("--tag <tag>", "Filter by tag").option("-l, --limit <number>", "Limit results", "20").option("--json", "Output as JSON").action(async (query, options) => {
-    await executeSearchCommand(query, options);
+function registerInitCommand(program) {
+  program.command("init").description("Initialize a new SynapSync project").option("-n, --name <name>", "Project name").option("-d, --description <desc>", "Project description").option("-p, --provider <providers...>", "Enable providers (claude, openai, etc.)").option("-y, --yes", "Skip prompts and use defaults").action(async (options) => {
+    await executeInitCommand({
+      ...options.name !== void 0 && { name: options.name },
+      ...options.description !== void 0 && { description: options.description },
+      ...options.provider !== void 0 && { providers: options.provider },
+      ...options.yes !== void 0 && { yes: options.yes }
+    });
   });
 }
 
-// src/commands/add.ts
-init_esm_shims();
-import * as fs8 from "fs";
-import * as path10 from "path";
-import pc9 from "picocolors";
-
-// src/services/sync/engine.ts
-init_esm_shims();
-import * as path9 from "path";
-
-// src/services/scanner/scanner.ts
-init_esm_shims();
-import * as fs5 from "fs";
-import * as path6 from "path";
-import * as crypto from "crypto";
-
-// src/services/scanner/parser.ts
+// src/commands/config.ts
 init_esm_shims();
-function parseFrontmatter(content) {
-  const match = content.match(/^---\n([\s\S]*?)\n---/);
-  if (match?.[1] === void 0) {
-    return {};
+import pc5 from "picocolors";
+function executeConfigCommand(args) {
+  const options = parseConfigArgs(args);
+  const configManager = ConfigManager.findConfig();
+  if (configManager === null) {
+    logger.line();
+    logger.error("No SynapSync project found.");
+    logger.hint("Run /init to initialize a project.");
+    return;
   }
-  try {
-    return parseYaml(match[1]);
-  } catch {
-    return {};
+  switch (options.action) {
+    case "list":
+      showConfigList(configManager);
+      break;
+    case "get":
+      showConfigValue(configManager, options.key ?? "");
+      break;
+    case "set":
+      setConfigValue(configManager, options.key ?? "", options.value ?? "");
+      break;
   }
 }
-function parseYaml(yaml2) {
-  const result = {};
-  const lines = yaml2.split("\n");
-  let currentKey = null;
-  let currentArray = null;
-  for (const line of lines) {
-    if (line.trim() === "" || line.trim().startsWith("#")) {
-      continue;
-    }
-    if (line.match(/^\s+-\s+/)) {
-      const value = line.replace(/^\s+-\s+/, "").trim();
-      if (currentArray !== null) {
-        currentArray.push(cleanValue(value));
-      }
-      continue;
-    }
-    const colonIndex = line.indexOf(":");
-    if (colonIndex > 0) {
-      const key = line.slice(0, colonIndex).trim();
-      const rawValue = line.slice(colonIndex + 1).trim();
-      if (currentKey !== null && currentArray !== null) {
-        setNestedValue2(result, currentKey, currentArray);
-        currentArray = null;
-      }
-      currentKey = key;
-      if (rawValue === "" || rawValue === "|" || rawValue === ">") {
-        currentArray = [];
-      } else if (rawValue.startsWith("[") && rawValue.endsWith("]")) {
-        const arrayContent = rawValue.slice(1, -1);
-        const items = arrayContent.split(",").map((item) => cleanValue(item.trim()));
-        setNestedValue2(result, key, items);
-        currentKey = null;
-      } else {
-        setNestedValue2(result, key, cleanValue(rawValue));
-        currentKey = null;
-      }
-    }
+function showConfigList(configManager) {
+  const flatConfig = configManager.flatten();
+  logger.line();
+  logger.bold("  Configuration");
+  logger.line();
+  const groups = {};
+  for (const [key, value] of Object.entries(flatConfig)) {
+    const parts = key.split(".");
+    const group2 = parts[0] ?? "other";
+    groups[group2] ??= {};
+    groups[group2][key] = value;
   }
-  if (currentKey !== null && currentArray !== null) {
-    setNestedValue2(result, currentKey, currentArray);
+  for (const [group2, values] of Object.entries(groups)) {
+    logger.log(`  ${pc5.cyan(group2)}:`);
+    for (const [key, value] of Object.entries(values)) {
+      const displayKey = key.replace(`${group2}.`, "");
+      const displayValue = formatValue(value);
+      logger.log(`    ${pc5.dim(displayKey.padEnd(30))} ${displayValue}`);
+    }
+    logger.line();
   }
-  return result;
+  logger.hint(`Config file: ${configManager.getProjectRoot()}/synapsync.config.yaml`);
 }
-function cleanValue(value) {
-  if (value.startsWith('"') && value.endsWith('"') || value.startsWith("'") && value.endsWith("'")) {
-    return value.slice(1, -1);
+function showConfigValue(configManager, key) {
+  if (key === "") {
+    logger.line();
+    logger.error("Key is required.");
+    logger.hint("Usage: /config get <key>");
+    logger.hint("Example: /config get cli.theme");
+    return;
+  }
+  const value = configManager.get(key);
+  logger.line();
+  if (value === void 0) {
+    logger.warning(`Key not found: ${pc5.cyan(key)}`);
+    logger.line();
+    logger.hint("Use /config list to see all available keys.");
+  } else {
+    logger.log(`  ${pc5.cyan(key)} = ${formatValue(value)}`);
   }
-  return value;
-}
-function setNestedValue2(obj, key, value) {
-  obj[key] = value;
 }
-function extractVersion(metadata, content) {
-  if (metadata.version !== void 0) {
-    return metadata.version;
+function setConfigValue(configManager, key, value) {
+  if (key === "") {
+    logger.line();
+    logger.error("Key is required.");
+    logger.hint("Usage: /config set <key> <value>");
+    logger.hint("Example: /config set cli.theme dark");
+    return;
   }
-  const versionMatch = content.match(/version:\s*['"]?([0-9]+\.[0-9]+\.[0-9]+)['"]?/i);
-  if (versionMatch?.[1] !== void 0) {
-    return versionMatch[1];
+  if (value === "") {
+    logger.line();
+    logger.error("Value is required.");
+    logger.hint("Usage: /config set <key> <value>");
+    return;
   }
-  return "1.0.0";
+  const existingValue = configManager.get(key);
+  const isNewKey = existingValue === void 0;
+  const parsedValue = parseValue(value);
+  configManager.set(key, parsedValue);
+  configManager.save();
+  logger.line();
+  if (isNewKey) {
+    logger.warning(`Created new key: ${pc5.cyan(key)}`);
+  }
+  logger.success(`${pc5.cyan(key)} = ${formatValue(parsedValue)}`);
 }
-function extractName(metadata, dirName, content) {
-  if (metadata.name !== void 0) {
-    return metadata.name;
+function parseConfigArgs(args) {
+  const parts = args.trim().split(/\s+/);
+  const action = (parts[0] ?? "list").toLowerCase();
+  if (action === "" || action === "list") {
+    return { action: "list" };
   }
-  const titleMatch = content.match(/^#\s+(.+)$/m);
-  if (titleMatch?.[1] !== void 0) {
-    return titleMatch[1].toLowerCase().replace(/[^a-z0-9]+/g, "-").replace(/^-|-$/g, "");
+  if (action === "get") {
+    return {
+      action: "get",
+      key: parts[1] ?? ""
+    };
   }
-  return dirName;
-}
+  if (action === "set") {
+    return {
+      action: "set",
+      key: parts[1] ?? "",
+      value: parts.slice(2).join(" ")
+    };
+  }
+  return {
+    action: "get",
+    key: action
+  };
+}
+function formatValue(value) {
+  if (value === null || value === void 0) {
+    return pc5.dim("(not set)");
+  }
+  if (typeof value === "boolean") {
+    return value ? pc5.green("true") : pc5.red("false");
+  }
+  if (typeof value === "number") {
+    return pc5.yellow(String(value));
+  }
+  if (typeof value === "string") {
+    return pc5.white(`"${value}"`);
+  }
+  if (Array.isArray(value)) {
+    return pc5.dim(`[${value.join(", ")}]`);
+  }
+  return pc5.dim(JSON.stringify(value));
+}
+function parseValue(value) {
+  if (value.toLowerCase() === "true") return true;
+  if (value.toLowerCase() === "false") return false;
+  const num = Number(value);
+  if (!isNaN(num) && value.trim() !== "") return num;
+  return value;
+}
+function registerConfigCommand(program) {
+  const configCmd = program.command("config").description("Manage project configuration");
+  configCmd.command("list").description("Show all configuration values").action(() => {
+    executeConfigCommand("list");
+  });
+  configCmd.command("get <key>").description("Get a configuration value").action((key) => {
+    executeConfigCommand(`get ${key}`);
+  });
+  configCmd.command("set <key> <value>").description("Set a configuration value").action((key, value) => {
+    executeConfigCommand(`set ${key} ${value}`);
+  });
+  configCmd.action(() => {
+    executeConfigCommand("list");
+  });
+}
 
-// src/services/scanner/scanner.ts
-var CognitiveScanner = class {
-  synapSyncDir;
-  constructor(synapSyncDir) {
-    this.synapSyncDir = synapSyncDir;
+// src/commands/status.ts
+init_esm_shims();
+import * as fs6 from "fs";
+import * as path7 from "path";
+import pc6 from "picocolors";
+function executeStatusCommand(_args = "") {
+  const status = getProjectStatus();
+  logger.line();
+  if (!status.initialized) {
+    showNotInitialized();
+    return;
   }
-  /**
-   * Scan the filesystem for cognitives
-   */
-  scan(options = {}) {
-    const cognitives = [];
-    const errors = [];
-    const typesToScan = options.types ?? COGNITIVE_TYPES;
-    for (const type of typesToScan) {
-      const typeDir = path6.join(this.synapSyncDir, `${type}s`);
-      if (!fs5.existsSync(typeDir)) {
-        continue;
+  showProjectStatus(status);
+}
+function getProjectStatus() {
+  const configManager = ConfigManager.findConfig();
+  if (configManager === null) {
+    return {
+      initialized: false,
+      cognitives: createEmptyCognitiveCount(),
+      providers: []
+    };
+  }
+  const config = configManager.getConfig();
+  const projectRoot = configManager.getProjectRoot();
+  const storagePath = configManager.getSynapSyncDir();
+  const cognitives = countCognitives(storagePath);
+  const providers = getProviderStatuses(config, projectRoot);
+  const lastSync = getLastSyncTime(storagePath);
+  const status = {
+    initialized: true,
+    projectName: config.name,
+    projectRoot,
+    configPath: path7.join(projectRoot, "synapsync.config.yaml"),
+    storagePath,
+    cognitives,
+    providers
+  };
+  if (lastSync !== void 0) {
+    status.lastSync = lastSync;
+  }
+  return status;
+}
+function createEmptyCognitiveCount() {
+  const counts = {};
+  for (const type of COGNITIVE_TYPES) {
+    counts[type] = 0;
+  }
+  return counts;
+}
+function countCognitives(storagePath) {
+  const counts = createEmptyCognitiveCount();
+  for (const type of COGNITIVE_TYPES) {
+    const typePath = path7.join(storagePath, `${type}s`);
+    if (fs6.existsSync(typePath)) {
+      try {
+        const entries = fs6.readdirSync(typePath, { withFileTypes: true });
+        counts[type] = entries.filter(
+          (e) => e.isDirectory() || e.isSymbolicLink() && !e.name.startsWith(".")
+        ).length;
+      } catch {
+        counts[type] = 0;
       }
-      const categories = this.listDirectories(typeDir);
-      for (const category of categories) {
-        if (options.categories !== void 0 && !options.categories.includes(category)) {
-          continue;
-        }
-        const categoryDir = path6.join(typeDir, category);
-        const cognitiveDirs = this.listDirectories(categoryDir);
-        for (const cognitiveDir of cognitiveDirs) {
-          try {
-            const cognitive = this.scanCognitive(
-              path6.join(categoryDir, cognitiveDir),
-              type,
-              category
-            );
-            if (cognitive !== null) {
-              cognitives.push(cognitive);
-            }
-          } catch (error) {
-            errors.push({
-              path: path6.join(categoryDir, cognitiveDir),
-              error: error instanceof Error ? error.message : "Unknown error"
-            });
+    }
+  }
+  return counts;
+}
+function getProviderStatuses(config, projectRoot) {
+  const statuses = [];
+  for (const provider of SUPPORTED_PROVIDERS) {
+    const providerConfig = config.sync?.providers?.[provider];
+    const enabled = providerConfig?.enabled ?? false;
+    const providerPath = path7.join(projectRoot, `.${provider}`);
+    let cognitivesCount = 0;
+    if (fs6.existsSync(providerPath)) {
+      try {
+        const subdirs = ["skills", "agents", "prompts", "workflows", "tools"];
+        for (const subdir of subdirs) {
+          const subdirPath = path7.join(providerPath, subdir);
+          if (fs6.existsSync(subdirPath)) {
+            const entries = fs6.readdirSync(subdirPath);
+            cognitivesCount += entries.filter((e) => !e.startsWith(".")).length;
           }
         }
+      } catch {
       }
     }
-    return cognitives;
+    statuses.push({
+      name: provider,
+      enabled,
+      connected: false,
+      // TODO: Check actual connection status
+      cognitivesCount
+    });
   }
-  /**
-   * Scan a single cognitive directory
-   */
-  scanCognitive(cognitiveDir, type, category) {
-    const filePath = this.findCognitiveFile(cognitiveDir, type);
-    if (filePath === null) {
-      return null;
-    }
-    const content = fs5.readFileSync(filePath, "utf-8");
-    const metadata = parseFrontmatter(content);
-    const dirName = path6.basename(cognitiveDir);
-    const fileName = path6.basename(filePath);
-    const name = extractName(metadata, dirName, content);
-    const version2 = extractVersion(metadata, content);
-    const hash = this.computeHash(content);
-    return {
-      name,
-      type,
-      category: metadata.category ?? category,
-      path: cognitiveDir,
-      filePath,
-      fileName,
-      // Add original filename
-      hash,
-      metadata: {
-        ...metadata,
-        name,
-        version: version2
-      }
-    };
+  return statuses;
+}
+function getLastSyncTime(storagePath) {
+  const manifestPath = path7.join(storagePath, "manifest.json");
+  if (!fs6.existsSync(manifestPath)) {
+    return void 0;
   }
-  /**
-   * Find the cognitive file in a directory
-   * Checks for legacy fixed filename first, then any file with matching extension
-   */
-  findCognitiveFile(cognitiveDir, type) {
-    const legacyFileName = COGNITIVE_FILE_NAMES[type];
-    const legacyPath = path6.join(cognitiveDir, legacyFileName);
-    if (fs5.existsSync(legacyPath)) {
-      return legacyPath;
-    }
-    const extension = COGNITIVE_FILE_EXTENSIONS[type];
-    if (!fs5.existsSync(cognitiveDir)) {
-      return null;
-    }
-    const files = fs5.readdirSync(cognitiveDir);
-    for (const file of files) {
-      if (file.endsWith(extension) && !file.startsWith(".")) {
-        const fullPath = path6.join(cognitiveDir, file);
-        const stat = fs5.statSync(fullPath);
-        if (stat.isFile()) {
-          return fullPath;
-        }
+  try {
+    const content = fs6.readFileSync(manifestPath, "utf-8");
+    const manifest = JSON.parse(content);
+    return manifest.lastUpdated;
+  } catch {
+    return void 0;
+  }
+}
+function showNotInitialized() {
+  logger.bold("  Project Status");
+  logger.line();
+  logger.log(`  ${pc6.red("\u25CF")} ${pc6.dim("Not initialized")}`);
+  logger.line();
+  logger.hint("Run /init to initialize a SynapSync project.");
+}
+function showProjectStatus(status) {
+  logger.bold(`  ${status.projectName ?? "SynapSync Project"}`);
+  logger.line();
+  logger.log(`  ${pc6.green("\u25CF")} ${pc6.dim("Initialized")}`);
+  logger.log(`  ${pc6.dim("Root:")} ${status.projectRoot}`);
+  logger.line();
+  logger.bold("  Cognitives");
+  const totalCognitives = Object.values(status.cognitives).reduce((a, b) => a + b, 0);
+  if (totalCognitives === 0) {
+    logger.log(`  ${pc6.dim("No cognitives installed")}`);
+  } else {
+    for (const type of COGNITIVE_TYPES) {
+      const count = status.cognitives[type];
+      if (count > 0) {
+        const icon = getCognitiveIcon(type);
+        logger.log(`  ${icon} ${pc6.white(count.toString().padStart(3))} ${type}s`);
       }
     }
-    return null;
+    logger.log(`  ${pc6.dim("\u2500\u2500\u2500")}`);
+    logger.log(`  ${pc6.bold(totalCognitives.toString().padStart(5))} total`);
   }
-  /**
-   * Compare scanned cognitives with manifest and return differences
-   */
-  compare(scanned, manifestCognitives) {
-    const result = {
-      found: scanned,
-      new: [],
-      removed: [],
-      modified: [],
-      unchanged: 0,
-      errors: []
-    };
-    const manifestMap = /* @__PURE__ */ new Map();
-    for (const cognitive of manifestCognitives) {
-      manifestMap.set(cognitive.name, cognitive);
-    }
-    const scannedMap = /* @__PURE__ */ new Map();
-    for (const cognitive of scanned) {
-      scannedMap.set(cognitive.name, cognitive);
+  logger.line();
+  logger.bold("  Providers");
+  const enabledProviders = status.providers.filter((p2) => p2.enabled);
+  if (enabledProviders.length === 0) {
+    logger.log(`  ${pc6.dim("No providers enabled")}`);
+  } else {
+    for (const provider of enabledProviders) {
+      const icon = provider.cognitivesCount > 0 ? pc6.green("\u25CF") : pc6.yellow("\u25CB");
+      const syncStatus = provider.cognitivesCount > 0 ? pc6.dim(`(${provider.cognitivesCount} synced)`) : pc6.dim("(not synced)");
+      logger.log(`  ${icon} ${pc6.white(provider.name)} ${syncStatus}`);
     }
-    for (const scannedCognitive of scanned) {
-      const manifestCognitive = manifestMap.get(scannedCognitive.name);
-      if (manifestCognitive === void 0) {
-        result.new.push(scannedCognitive);
-      } else if (manifestCognitive.hash !== void 0 && manifestCognitive.hash !== scannedCognitive.hash) {
-        result.modified.push(scannedCognitive);
+  }
+  logger.line();
+  if (status.lastSync !== void 0) {
+    const syncDate = new Date(status.lastSync);
+    const relativeTime = getRelativeTime(syncDate);
+    logger.log(`  ${pc6.dim("Last updated:")} ${relativeTime}`);
+    logger.line();
+  }
+  logger.hint("Run /help for available commands.");
+}
+function getCognitiveIcon(type) {
+  const icons = {
+    skill: pc6.blue("\u25C6"),
+    agent: pc6.magenta("\u25C6"),
+    prompt: pc6.yellow("\u25C6"),
+    workflow: pc6.cyan("\u25C6"),
+    tool: pc6.green("\u25C6")
+  };
+  return icons[type];
+}
+function getRelativeTime(date) {
+  const now = /* @__PURE__ */ new Date();
+  const diffMs = now.getTime() - date.getTime();
+  const diffMins = Math.floor(diffMs / 6e4);
+  const diffHours = Math.floor(diffMins / 60);
+  const diffDays = Math.floor(diffHours / 24);
+  if (diffMins < 1) return "just now";
+  if (diffMins < 60) return `${diffMins} minute${diffMins === 1 ? "" : "s"} ago`;
+  if (diffHours < 24) return `${diffHours} hour${diffHours === 1 ? "" : "s"} ago`;
+  if (diffDays < 7) return `${diffDays} day${diffDays === 1 ? "" : "s"} ago`;
+  return date.toLocaleDateString();
+}
+function registerStatusCommand(program) {
+  program.command("status").description("Show project status").action(() => {
+    executeStatusCommand();
+  });
+}
+
+// src/commands/providers.ts
+init_esm_shims();
+import * as fs7 from "fs";
+import * as path8 from "path";
+import pc7 from "picocolors";
+function executeProvidersCommand(args) {
+  const parts = args.trim().split(/\s+/);
+  const subcommand = parts[0]?.toLowerCase() ?? "";
+  const configManager = ConfigManager.findConfig();
+  if (configManager === null) {
+    logger.line();
+    logger.error("No SynapSync project found.");
+    logger.hint("Run /init to initialize a project.");
+    return;
+  }
+  switch (subcommand) {
+    case "":
+    case "list":
+      listProviders(configManager);
+      break;
+    case "enable":
+      enableProvider(configManager, parts[1]);
+      break;
+    case "disable":
+      disableProvider(configManager, parts[1]);
+      break;
+    case "path":
+      setProviderPath(configManager, parts[1], parts[2]);
+      break;
+    default:
+      if (SUPPORTED_PROVIDERS.includes(subcommand)) {
+        showProviderInfo(configManager, subcommand);
       } else {
-        result.unchanged++;
-      }
-    }
-    for (const manifestCognitive of manifestCognitives) {
-      if (!scannedMap.has(manifestCognitive.name)) {
-        result.removed.push(manifestCognitive.name);
+        logger.line();
+        logger.error(`Unknown subcommand: ${subcommand}`);
+        logger.hint("Usage: /providers [list|enable|disable|path]");
       }
-    }
-    return result;
   }
-  /**
-   * Convert a scanned cognitive to a manifest cognitive
-   */
-  toManifestCognitive(scanned) {
-    return {
-      name: scanned.name,
-      type: scanned.type,
-      category: scanned.category,
-      version: scanned.metadata.version ?? "1.0.0",
-      installedAt: (/* @__PURE__ */ new Date()).toISOString(),
-      source: "local",
-      hash: scanned.hash
-    };
+}
+function listProviders(configManager) {
+  const providers = getProvidersInfo(configManager);
+  logger.line();
+  logger.bold("  Providers");
+  logger.line();
+  logger.log(
+    `  ${pc7.dim("Provider".padEnd(12))} ${pc7.dim("Status".padEnd(10))} ${pc7.dim("Path".padEnd(20))} ${pc7.dim("Directory")}`
+  );
+  logger.log(`  ${pc7.dim("\u2500".repeat(60))}`);
+  for (const provider of providers) {
+    const statusIcon = provider.enabled ? pc7.green("\u25CF") : pc7.dim("\u25CB");
+    const statusText = provider.enabled ? pc7.green("enabled") : pc7.dim("disabled");
+    const pathText = pc7.cyan(provider.path);
+    const existsText = provider.exists ? pc7.green("\u2713 exists") : pc7.dim("\u2717 missing");
+    logger.log(
+      `  ${statusIcon} ${pc7.white(provider.name.padEnd(10))} ${statusText.padEnd(19)} ${pathText.padEnd(29)} ${existsText}`
+    );
   }
-  /**
-   * Compute content hash for change detection
-   */
-  computeHash(content) {
-    return crypto.createHash("sha256").update(content).digest("hex").slice(0, 16);
+  logger.line();
+  const enabledCount = providers.filter((p2) => p2.enabled).length;
+  logger.log(`  ${pc7.dim("Enabled:")} ${enabledCount} of ${providers.length} providers`);
+  logger.line();
+  logger.hint("Use /providers enable <name> or /providers disable <name>");
+}
+function enableProvider(configManager, providerName) {
+  if (providerName === void 0 || providerName === "") {
+    logger.line();
+    logger.error("Provider name is required.");
+    logger.hint("Usage: /providers enable <provider>");
+    logger.hint(`Available: ${SUPPORTED_PROVIDERS.join(", ")}`);
+    return;
+  }
+  const provider = providerName.toLowerCase();
+  if (!SUPPORTED_PROVIDERS.includes(provider)) {
+    logger.line();
+    logger.error(`Unknown provider: ${provider}`);
+    logger.hint(`Available: ${SUPPORTED_PROVIDERS.join(", ")}`);
+    return;
+  }
+  const currentValue = configManager.get(`sync.providers.${provider}.enabled`);
+  if (currentValue === true) {
+    logger.line();
+    logger.info(`Provider '${provider}' is already enabled.`);
+    return;
+  }
+  configManager.set(`sync.providers.${provider}.enabled`, true);
+  const defaultPaths = PROVIDER_PATHS[provider];
+  const currentPaths = configManager.get(`sync.providers.${provider}.paths`);
+  if (currentPaths === void 0) {
+    configManager.set(`sync.providers.${provider}.paths`, defaultPaths);
+  }
+  configManager.save();
+  logger.line();
+  logger.success(`Provider '${pc7.cyan(provider)}' enabled`);
+  logger.log(`  ${pc7.dim("Path:")} ${defaultPaths.skill.split("/")[0]}/`);
+  logger.line();
+  logger.hint("Run /sync to synchronize cognitives to this provider.");
+}
+function disableProvider(configManager, providerName) {
+  if (providerName === void 0 || providerName === "") {
+    logger.line();
+    logger.error("Provider name is required.");
+    logger.hint("Usage: /providers disable <provider>");
+    return;
+  }
+  const provider = providerName.toLowerCase();
+  if (!SUPPORTED_PROVIDERS.includes(provider)) {
+    logger.line();
+    logger.error(`Unknown provider: ${provider}`);
+    logger.hint(`Available: ${SUPPORTED_PROVIDERS.join(", ")}`);
+    return;
+  }
+  const currentValue = configManager.get(`sync.providers.${provider}.enabled`);
+  if (currentValue !== true) {
+    logger.line();
+    logger.info(`Provider '${provider}' is already disabled.`);
+    return;
+  }
+  configManager.set(`sync.providers.${provider}.enabled`, false);
+  configManager.save();
+  logger.line();
+  logger.success(`Provider '${pc7.cyan(provider)}' disabled`);
+}
+function setProviderPath(configManager, providerName, newPath) {
+  if (providerName === void 0 || providerName === "") {
+    logger.line();
+    logger.error("Provider name is required.");
+    logger.hint("Usage: /providers path <provider> <path>");
+    return;
+  }
+  if (newPath === void 0 || newPath === "") {
+    logger.line();
+    logger.error("Path is required.");
+    logger.hint("Usage: /providers path <provider> <path>");
+    logger.hint("Example: /providers path claude .claude-code/");
+    return;
+  }
+  const provider = providerName.toLowerCase();
+  if (!SUPPORTED_PROVIDERS.includes(provider)) {
+    logger.line();
+    logger.error(`Unknown provider: ${provider}`);
+    logger.hint(`Available: ${SUPPORTED_PROVIDERS.join(", ")}`);
+    return;
+  }
+  const normalizedPath = newPath.endsWith("/") ? newPath : `${newPath}/`;
+  const cognitiveTypes = ["skill", "agent", "prompt", "workflow", "tool"];
+  for (const type of cognitiveTypes) {
+    configManager.set(`sync.providers.${provider}.paths.${type}`, `${normalizedPath}${type}s`);
+  }
+  configManager.save();
+  logger.line();
+  logger.success(`Updated paths for '${pc7.cyan(provider)}'`);
+  logger.log(`  ${pc7.dim("Base path:")} ${pc7.cyan(normalizedPath)}`);
+  logger.line();
+}
+function showProviderInfo(configManager, provider) {
+  const config = configManager.getConfig();
+  const projectRoot = configManager.getProjectRoot();
+  const providerConfig = config.sync?.providers?.[provider];
+  const enabled = providerConfig?.enabled ?? false;
+  const paths = providerConfig?.paths ?? PROVIDER_PATHS[provider];
+  logger.line();
+  logger.bold(`  ${getProviderDisplayName(provider)}`);
+  logger.line();
+  const statusIcon = enabled ? pc7.green("\u25CF") : pc7.dim("\u25CB");
+  const statusText = enabled ? pc7.green("Enabled") : pc7.dim("Disabled");
+  logger.log(`  ${pc7.dim("Status:")}  ${statusIcon} ${statusText}`);
+  logger.line();
+  logger.log(`  ${pc7.dim("Paths:")}`);
+  const cognitiveTypes = ["skill", "agent", "prompt", "workflow", "tool"];
+  for (const type of cognitiveTypes) {
+    const typePath = paths[type] ?? "";
+    const fullPath = path8.join(projectRoot, typePath);
+    const exists = fs7.existsSync(fullPath);
+    const existsIcon = exists ? pc7.green("\u2713") : pc7.dim("\u2717");
+    logger.log(`    ${pc7.dim(type.padEnd(10))} ${pc7.cyan(typePath)} ${existsIcon}`);
+  }
+  logger.line();
+}
+function getProvidersInfo(configManager) {
+  const config = configManager.getConfig();
+  const projectRoot = configManager.getProjectRoot();
+  const providers = [];
+  for (const provider of SUPPORTED_PROVIDERS) {
+    const providerConfig = config.sync?.providers?.[provider];
+    const enabled = providerConfig?.enabled ?? false;
+    const basePath = providerConfig?.paths?.skill?.split("/")[0] ?? `.${provider}`;
+    const fullPath = path8.join(projectRoot, basePath);
+    const exists = fs7.existsSync(fullPath);
+    providers.push({
+      name: provider,
+      enabled,
+      path: `${basePath}/`,
+      exists
+    });
+  }
+  return providers;
+}
+function getProviderDisplayName(provider) {
+  const names = {
+    claude: "Claude (Anthropic)",
+    openai: "OpenAI (GPT)",
+    gemini: "Gemini (Google)",
+    cursor: "Cursor IDE",
+    windsurf: "Windsurf IDE",
+    copilot: "GitHub Copilot"
+  };
+  return names[provider];
+}
+function registerProvidersCommand(program) {
+  const providersCmd = program.command("providers").description("Manage provider configuration");
+  providersCmd.command("list", { isDefault: true }).description("List all providers and their status").action(() => {
+    executeProvidersCommand("list");
+  });
+  providersCmd.command("enable <provider>").description("Enable a provider").action((provider) => {
+    executeProvidersCommand(`enable ${provider}`);
+  });
+  providersCmd.command("disable <provider>").description("Disable a provider").action((provider) => {
+    executeProvidersCommand(`disable ${provider}`);
+  });
+  providersCmd.command("path <provider> <path>").description("Set custom sync path for a provider").action((provider, newPath) => {
+    executeProvidersCommand(`path ${provider} ${newPath}`);
+  });
+  providersCmd.action(() => {
+    executeProvidersCommand("list");
+  });
+}
+
+// src/commands/search.ts
+init_esm_shims();
+import pc8 from "picocolors";
+
+// src/services/registry/client.ts
+init_esm_shims();
+var RegistryClient = class {
+  baseUrl;
+  indexCache = null;
+  indexCacheTime = 0;
+  cacheTtl;
+  constructor(options = {}) {
+    this.baseUrl = options.baseUrl ?? REGISTRY_BASE_URL;
+    this.cacheTtl = options.cacheTtl ?? 5 * 60 * 1e3;
   }
+  // ============================================
+  // Index Operations
+  // ============================================
   /**
-   * List directories in a path
+   * Fetch the registry index
    */
-  listDirectories(dirPath) {
-    if (!fs5.existsSync(dirPath)) {
-      return [];
+  async getIndex(forceRefresh = false) {
+    const now = Date.now();
+    if (!forceRefresh && this.indexCache !== null && now - this.indexCacheTime < this.cacheTtl) {
+      return this.indexCache;
     }
-    return fs5.readdirSync(dirPath, { withFileTypes: true }).filter((dirent) => dirent.isDirectory()).filter((dirent) => !dirent.name.startsWith(".")).map((dirent) => dirent.name);
-  }
-  /**
-   * Detect cognitive type from directory contents
-   */
-  detectType(cognitiveDir) {
-    for (const type of COGNITIVE_TYPES) {
-      const fileName = COGNITIVE_FILE_NAMES[type];
-      const filePath = path6.join(cognitiveDir, fileName);
-      if (fs5.existsSync(filePath)) {
-        return type;
-      }
+    const url = `${this.baseUrl}/${REGISTRY_INDEX_FILE}`;
+    const response = await this.fetch(url);
+    if (!response.ok) {
+      throw new RegistryError(`Failed to fetch registry index: ${response.status} ${response.statusText}`, url);
     }
-    return null;
+    const index = await response.json();
+    this.indexCache = index;
+    this.indexCacheTime = now;
+    return index;
   }
   /**
-   * Get cognitive count by type
+   * Get total count of cognitives in registry
    */
-  countByType(cognitives) {
-    const counts = {
-      skill: 0,
-      agent: 0,
-      prompt: 0,
-      workflow: 0,
-      tool: 0
-    };
-    for (const cognitive of cognitives) {
-      counts[cognitive.type]++;
-    }
-    return counts;
-  }
-};
-
-// src/services/manifest/manager.ts
-init_esm_shims();
-import * as fs6 from "fs";
-import * as path7 from "path";
-
-// src/services/manifest/types.ts
-init_esm_shims();
-var DEFAULT_MANIFEST = {
-  version: "1.0.0",
-  lastUpdated: (/* @__PURE__ */ new Date()).toISOString(),
-  cognitives: {},
-  syncs: {}
-};
-
-// src/services/manifest/manager.ts
-var ManifestManager = class {
-  manifestPath;
-  manifest;
-  constructor(synapSyncDir) {
-    this.manifestPath = path7.join(synapSyncDir, "manifest.json");
-    this.manifest = this.load();
+  async getCount() {
+    const index = await this.getIndex();
+    return index.totalCognitives;
   }
+  // ============================================
+  // Search Operations
+  // ============================================
   /**
-   * Load manifest from disk
+   * Search for cognitives in the registry
    */
-  load() {
-    if (!fs6.existsSync(this.manifestPath)) {
-      return { ...DEFAULT_MANIFEST };
+  async search(query, options = {}) {
+    const index = await this.getIndex();
+    let results = [...index.cognitives];
+    if (query !== void 0 && query.trim() !== "") {
+      const q = query.toLowerCase();
+      results = results.filter(
+        (c) => c.name.toLowerCase().includes(q) || c.description.toLowerCase().includes(q) || c.tags.some((t) => t.toLowerCase().includes(q))
+      );
     }
-    try {
-      const content = fs6.readFileSync(this.manifestPath, "utf-8");
-      const parsed = JSON.parse(content);
-      return {
-        version: parsed.version ?? DEFAULT_MANIFEST.version,
-        lastUpdated: parsed.lastUpdated ?? DEFAULT_MANIFEST.lastUpdated,
-        cognitives: parsed.cognitives ?? {},
-        syncs: parsed.syncs ?? {}
-      };
-    } catch {
-      return { ...DEFAULT_MANIFEST };
+    if (options.type !== void 0) {
+      results = results.filter((c) => c.type === options.type);
+    }
+    if (options.category !== void 0) {
+      results = results.filter((c) => c.category === options.category);
+    }
+    if (options.tag !== void 0) {
+      const tag = options.tag.toLowerCase();
+      results = results.filter((c) => c.tags.some((t) => t.toLowerCase() === tag));
     }
+    const total = results.length;
+    if (options.limit !== void 0 && options.limit > 0) {
+      results = results.slice(0, options.limit);
+    }
+    const filters = {};
+    if (options.type !== void 0) filters.type = options.type;
+    if (options.category !== void 0) filters.category = options.category;
+    if (options.tag !== void 0) filters.tag = options.tag;
+    return {
+      cognitives: results,
+      total,
+      ...query !== void 0 ? { query } : {},
+      filters
+    };
   }
   /**
-   * Save manifest to disk
+   * Find a cognitive by name
    */
-  save() {
-    this.manifest.lastUpdated = (/* @__PURE__ */ new Date()).toISOString();
-    const content = JSON.stringify(this.manifest, null, 2);
-    fs6.writeFileSync(this.manifestPath, content, "utf-8");
+  async findByName(name) {
+    const index = await this.getIndex();
+    return index.cognitives.find((c) => c.name === name) ?? null;
   }
   /**
-   * Get the current manifest
+   * List all cognitives
    */
-  getManifest() {
-    return this.manifest;
+  async list(options = {}) {
+    const result = await this.search(void 0, options);
+    return result.cognitives;
   }
+  // ============================================
+  // Download Operations
+  // ============================================
   /**
-   * Get all cognitives from manifest
+   * Get the manifest for a cognitive
    */
-  getCognitives() {
-    return Object.values(this.manifest.cognitives);
+  async getManifest(cognitiveEntry) {
+    const url = `${this.baseUrl}/${cognitiveEntry.path}/${REGISTRY_MANIFEST_FILE}`;
+    const response = await this.fetch(url);
+    if (!response.ok) {
+      throw new RegistryError(
+        `Failed to fetch manifest for ${cognitiveEntry.name}: ${response.status} ${response.statusText}`,
+        url
+      );
+    }
+    return await response.json();
   }
   /**
-   * Get a specific cognitive by name
+   * Get the content file for a cognitive
    */
-  getCognitive(name) {
-    return this.manifest.cognitives[name];
+  async getContent(cognitiveEntry, manifest) {
+    const url = `${this.baseUrl}/${cognitiveEntry.path}/${manifest.file}`;
+    const response = await this.fetch(url);
+    if (!response.ok) {
+      throw new RegistryError(
+        `Failed to fetch content for ${cognitiveEntry.name}: ${response.status} ${response.statusText}`,
+        url
+      );
+    }
+    return response.text();
   }
   /**
-   * Check if a cognitive exists in manifest
+   * Download a cognitive (manifest + content)
    */
-  hasCognitive(name) {
-    return this.manifest.cognitives[name] !== void 0;
+  async download(name) {
+    const entry = await this.findByName(name);
+    if (entry === null) {
+      throw new CognitiveNotFoundError(name);
+    }
+    const manifest = await this.getManifest(entry);
+    const content = await this.getContent(entry, manifest);
+    return {
+      manifest,
+      content,
+      path: entry.path
+    };
   }
   /**
-   * Add a cognitive to manifest
+   * Download additional assets for a cognitive
    */
-  addCognitive(cognitive) {
-    this.manifest.cognitives[cognitive.name] = cognitive;
+  async downloadAsset(cognitiveEntry, assetPath) {
+    const url = `${this.baseUrl}/${cognitiveEntry.path}/${assetPath}`;
+    const response = await this.fetch(url);
+    if (!response.ok) {
+      throw new RegistryError(
+        `Failed to fetch asset ${assetPath} for ${cognitiveEntry.name}: ${response.status} ${response.statusText}`,
+        url
+      );
+    }
+    return response.text();
   }
+  // ============================================
+  // Utility Methods
+  // ============================================
   /**
-   * Update a cognitive in manifest
+   * Check if registry is reachable
    */
-  updateCognitive(name, updates) {
-    const existing = this.manifest.cognitives[name];
-    if (existing !== void 0) {
-      this.manifest.cognitives[name] = { ...existing, ...updates };
+  async ping() {
+    try {
+      const url = `${this.baseUrl}/${REGISTRY_INDEX_FILE}`;
+      const response = await this.fetch(url, { method: "HEAD" });
+      return response.ok;
+    } catch {
+      return false;
     }
   }
   /**
-   * Remove a cognitive from manifest
+   * Clear the cache
    */
-  removeCognitive(name) {
-    if (this.manifest.cognitives[name] !== void 0) {
-      delete this.manifest.cognitives[name];
-      return true;
+  clearCache() {
+    this.indexCache = null;
+    this.indexCacheTime = 0;
+  }
+  /**
+   * Get the base URL
+   */
+  getBaseUrl() {
+    return this.baseUrl;
+  }
+  // ============================================
+  // Private Methods
+  // ============================================
+  async fetch(url, options) {
+    try {
+      return await fetch(url, {
+        ...options,
+        headers: {
+          "User-Agent": "SynapSync-CLI",
+          ...options?.headers
+        }
+      });
+    } catch (error) {
+      if (error instanceof Error) {
+        throw new RegistryError(`Network error: ${error.message}`, url);
+      }
+      throw new RegistryError("Network error", url);
     }
-    return false;
   }
-  /**
-   * Reconcile manifest with scanned cognitives
-   * Returns what was added, removed, and updated
-   */
-  reconcile(scannedCognitives) {
-    const result = {
-      added: [],
-      removed: [],
-      updated: [],
-      unchanged: 0
-    };
-    const scannedMap = /* @__PURE__ */ new Map();
-    for (const cognitive of scannedCognitives) {
-      scannedMap.set(cognitive.name, cognitive);
+};
+var RegistryError = class extends Error {
+  constructor(message, url) {
+    super(message);
+    this.url = url;
+    this.name = "RegistryError";
+  }
+};
+var CognitiveNotFoundError = class extends Error {
+  constructor(cognitiveName) {
+    super(`Cognitive '${cognitiveName}' not found in registry`);
+    this.cognitiveName = cognitiveName;
+    this.name = "CognitiveNotFoundError";
+  }
+};
+
+// src/commands/search.ts
+async function executeSearchCommand(query, options) {
+  logger.line();
+  const validatedOptions = validateOptions(options);
+  if (validatedOptions === null) {
+    return;
+  }
+  const searchingText = query !== void 0 && query.trim() !== "" ? `Searching for "${query}"...` : "Fetching cognitives from registry...";
+  logger.log(`  ${pc8.dim(searchingText)}`);
+  try {
+    const client = new RegistryClient();
+    const isReachable = await client.ping();
+    if (!isReachable) {
+      logger.line();
+      logger.error("Unable to reach the registry. Check your internet connection.");
+      return;
     }
-    for (const name of Object.keys(this.manifest.cognitives)) {
-      if (!scannedMap.has(name)) {
-        result.removed.push(name);
-      }
+    const searchOpts = {};
+    if (validatedOptions.type !== void 0) searchOpts.type = validatedOptions.type;
+    if (validatedOptions.category !== void 0) searchOpts.category = validatedOptions.category;
+    if (validatedOptions.tag !== void 0) searchOpts.tag = validatedOptions.tag;
+    if (validatedOptions.limit !== void 0) searchOpts.limit = validatedOptions.limit;
+    const result = await client.search(query, searchOpts);
+    process.stdout.write("\x1B[1A\x1B[2K");
+    if (options.json === true) {
+      console.log(JSON.stringify(result, null, 2));
+      return;
     }
-    for (const scanned of scannedCognitives) {
-      const existing = this.manifest.cognitives[scanned.name];
-      if (existing === void 0) {
-        result.added.push(scanned);
-      } else if (scanned.hash !== void 0 && existing.hash !== scanned.hash) {
-        result.updated.push(scanned);
-      } else {
-        result.unchanged++;
-      }
+    displaySearchResults(result.cognitives, query, result.total);
+  } catch (error) {
+    logger.line();
+    if (error instanceof RegistryError) {
+      logger.error(`Registry error: ${error.message}`);
+    } else if (error instanceof Error) {
+      logger.error(`Search failed: ${error.message}`);
+    } else {
+      logger.error("Search failed with unknown error");
     }
-    return result;
   }
-  /**
-   * Apply reconciliation result to manifest
-   */
-  applyReconciliation(result) {
-    for (const name of result.removed) {
-      delete this.manifest.cognitives[name];
+}
+function validateOptions(options) {
+  const validated = {};
+  if (options.type !== void 0) {
+    if (!COGNITIVE_TYPES.includes(options.type)) {
+      logger.error(`Invalid type: ${options.type}`);
+      logger.hint(`Valid types: ${COGNITIVE_TYPES.join(", ")}`);
+      return null;
     }
-    for (const cognitive of result.added) {
-      this.manifest.cognitives[cognitive.name] = cognitive;
+    validated.type = options.type;
+  }
+  if (options.category !== void 0) {
+    if (!CATEGORIES.includes(options.category)) {
+      logger.error(`Invalid category: ${options.category}`);
+      logger.hint(`Valid categories: ${CATEGORIES.join(", ")}`);
+      return null;
     }
-    for (const cognitive of result.updated) {
-      const existing = this.manifest.cognitives[cognitive.name];
-      if (existing !== void 0) {
-        const updated = {
-          ...existing,
-          ...cognitive,
-          // Keep original installation info
-          installedAt: existing.installedAt,
-          source: existing.source
-        };
-        if (existing.sourceUrl !== void 0) {
-          updated.sourceUrl = existing.sourceUrl;
-        }
-        this.manifest.cognitives[cognitive.name] = updated;
-      }
+    validated.category = options.category;
+  }
+  if (options.tag !== void 0) {
+    validated.tag = options.tag;
+  }
+  if (options.limit !== void 0) {
+    const limit = parseInt(options.limit, 10);
+    if (isNaN(limit) || limit < 1) {
+      logger.error("Limit must be a positive number");
+      return null;
     }
+    validated.limit = limit;
   }
-  /**
-   * Get provider sync state
-   */
-  getProviderSync(provider) {
-    return this.manifest.syncs[provider];
+  return validated;
+}
+function displaySearchResults(cognitives, query, total) {
+  if (query !== void 0 && query.trim() !== "") {
+    logger.bold(`  Search Results for "${query}"`);
+  } else {
+    logger.bold("  Registry Cognitives");
   }
-  /**
-   * Update provider sync state
-   */
-  setProviderSync(provider, state) {
-    this.manifest.syncs[provider] = state;
+  logger.line();
+  if (cognitives.length === 0) {
+    logger.log(`  ${pc8.dim("No cognitives found")}`);
+    logger.line();
+    logger.hint("Try a different search query or remove filters.");
+    return;
   }
-  /**
-   * Get all synced cognitives for a provider
-   */
-  getSyncedCognitives(provider) {
-    return this.manifest.syncs[provider]?.cognitives ?? [];
+  if (cognitives.length < total) {
+    logger.log(`  ${pc8.dim(`Showing ${cognitives.length} of ${total} results`)}`);
+  } else {
+    logger.log(`  ${pc8.dim(`Found ${total} cognitive${total === 1 ? "" : "s"}`)}`);
   }
-  /**
-   * Get cognitive count
-   */
-  getCognitiveCount() {
-    return Object.keys(this.manifest.cognitives).length;
+  logger.line();
+  for (const cognitive of cognitives) {
+    displayCognitive(cognitive);
   }
-  /**
-   * Get cognitives by type
-   */
-  getCognitivesByType(type) {
-    return Object.values(this.manifest.cognitives).filter((c) => c.type === type);
+  logger.line();
+  logger.hint("Run synapsync add <name> to add a cognitive.");
+}
+function displayCognitive(cognitive) {
+  const typeIcon = getCognitiveIcon2(cognitive.type);
+  const typeLabel = pc8.dim(`[${cognitive.type}]`);
+  logger.log(`  ${typeIcon} ${pc8.bold(pc8.white(cognitive.name))} ${typeLabel}`);
+  logger.log(`    ${pc8.dim(truncate(cognitive.description, 60))}`);
+  const meta = [];
+  meta.push(pc8.dim(`v${cognitive.version}`));
+  meta.push(pc8.dim(cognitive.category));
+  if (cognitive.downloads > 0) {
+    meta.push(pc8.dim(`${cognitive.downloads} downloads`));
   }
-  /**
-   * Get cognitives by source
-   */
-  getCognitivesBySource(source) {
-    return Object.values(this.manifest.cognitives).filter((c) => c.source === source);
+  logger.log(`    ${meta.join(" \xB7 ")}`);
+  if (cognitive.tags.length > 0) {
+    const tags = cognitive.tags.slice(0, 5).map((t) => pc8.cyan(t)).join(" ");
+    logger.log(`    ${tags}`);
   }
-};
+  logger.line();
+}
+function getCognitiveIcon2(type) {
+  const icons = {
+    skill: pc8.blue("\u25C6"),
+    agent: pc8.magenta("\u25C6"),
+    prompt: pc8.yellow("\u25C6"),
+    workflow: pc8.cyan("\u25C6"),
+    tool: pc8.green("\u25C6")
+  };
+  return icons[type];
+}
+function truncate(text2, maxLength) {
+  if (text2.length <= maxLength) return text2;
+  return text2.slice(0, maxLength - 3) + "...";
+}
+function registerSearchCommand(program) {
+  program.command("search [query]").description("Search for cognitives in the registry").option("-t, --type <type>", "Filter by type (skill, agent, prompt, workflow, tool)").option("-c, --category <category>", "Filter by category").option("--tag <tag>", "Filter by tag").option("-l, --limit <number>", "Limit results", "20").option("--json", "Output as JSON").action(async (query, options) => {
+    await executeSearchCommand(query, options);
+  });
+}
+
+// src/commands/add.ts
+init_esm_shims();
+import * as fs9 from "fs";
+import * as path11 from "path";
+import pc9 from "picocolors";
+
+// src/services/sync/engine.ts
+init_esm_shims();
+import * as path10 from "path";
 
 // src/services/symlink/manager.ts
 init_esm_shims();
-import * as fs7 from "fs";
-import * as path8 from "path";
+import * as fs8 from "fs";
+import * as path9 from "path";
 var SymlinkManager = class {
   projectRoot;
   synapSyncDir;
@@ -2659,12 +2891,12 @@ var SymlinkManager = class {
     }
     if (process.platform === "win32") {
       try {
-        const testSource = path8.join(this.synapSyncDir, ".symlink-test");
-        const testTarget = path8.join(this.synapSyncDir, ".symlink-test-target");
-        fs7.writeFileSync(testTarget, "test", "utf-8");
-        fs7.symlinkSync(testTarget, testSource);
-        fs7.unlinkSync(testSource);
-        fs7.unlinkSync(testTarget);
+        const testSource = path9.join(this.synapSyncDir, ".symlink-test");
+        const testTarget = path9.join(this.synapSyncDir, ".symlink-test-target");
+        fs8.writeFileSync(testTarget, "test", "utf-8");
+        fs8.symlinkSync(testTarget, testSource);
+        fs8.unlinkSync(testSource);
+        fs8.unlinkSync(testTarget);
         this.supportsSymlinks = true;
       } catch {
         this.supportsSymlinks = false;
@@ -2767,7 +2999,7 @@ var SymlinkManager = class {
           cognitiveType: cognitive.type,
           sourcePath: cognitive.path,
           // Directory path
-          targetPath: path8.join(this.projectRoot, typeDir, cognitive.name),
+          targetPath: path9.join(this.projectRoot, typeDir, cognitive.name),
           isFile: false
         });
       } else {
@@ -2777,7 +3009,7 @@ var SymlinkManager = class {
           cognitiveType: cognitive.type,
           sourcePath: cognitive.filePath,
           // File path
-          targetPath: path8.join(this.projectRoot, typeDir, fileName),
+          targetPath: path9.join(this.projectRoot, typeDir, fileName),
           isFile: true
         });
       }
@@ -2794,12 +3026,12 @@ var SymlinkManager = class {
     for (const cognitiveType of COGNITIVE_TYPES) {
       const typeDir = providerPaths[cognitiveType];
       if (typeDir === void 0) continue;
-      const fullPath = path8.join(this.projectRoot, typeDir);
-      if (!fs7.existsSync(fullPath)) continue;
-      const entries = fs7.readdirSync(fullPath, { withFileTypes: true });
+      const fullPath = path9.join(this.projectRoot, typeDir);
+      if (!fs8.existsSync(fullPath)) continue;
+      const entries = fs8.readdirSync(fullPath, { withFileTypes: true });
       for (const entry of entries) {
         if (entry.name.startsWith(".")) continue;
-        const entryPath = path8.join(fullPath, entry.name);
+        const entryPath = path9.join(fullPath, entry.name);
         if (entry.isFile() || entry.isDirectory() || entry.isSymbolicLink()) {
           const info = this.getLinkInfo(entryPath, cognitiveType);
           if (info !== null) {
@@ -2815,13 +3047,13 @@ var SymlinkManager = class {
    */
   getLinkInfo(linkPath, cognitiveType) {
     try {
-      const stats = fs7.lstatSync(linkPath);
+      const stats = fs8.lstatSync(linkPath);
       const isSymlink = stats.isSymbolicLink();
-      const baseName = path8.basename(linkPath);
+      const baseName = path9.basename(linkPath);
       let isDirectory = stats.isDirectory();
       if (isSymlink) {
         try {
-          const realStats = fs7.statSync(linkPath);
+          const realStats = fs8.statSync(linkPath);
           isDirectory = realStats.isDirectory();
         } catch {
           isDirectory = !baseName.match(/\.(md|yaml)$/i);
@@ -2831,9 +3063,9 @@ var SymlinkManager = class {
       let target = "";
       let isValid = false;
       if (isSymlink) {
-        target = fs7.readlinkSync(linkPath);
-        const resolvedTarget = path8.resolve(path8.dirname(linkPath), target);
-        isValid = fs7.existsSync(resolvedTarget);
+        target = fs8.readlinkSync(linkPath);
+        const resolvedTarget = path9.resolve(path9.dirname(linkPath), target);
+        isValid = fs8.existsSync(resolvedTarget);
       } else if (stats.isDirectory()) {
         target = linkPath;
         isValid = true;
@@ -2861,11 +3093,11 @@ var SymlinkManager = class {
     const method = this.getMethod(options);
     const isFile = mapping.isFile ?? false;
     try {
-      const targetDir = path8.dirname(mapping.targetPath);
-      if (!fs7.existsSync(targetDir)) {
-        fs7.mkdirSync(targetDir, { recursive: true });
+      const targetDir = path9.dirname(mapping.targetPath);
+      if (!fs8.existsSync(targetDir)) {
+        fs8.mkdirSync(targetDir, { recursive: true });
       }
-      if (fs7.existsSync(mapping.targetPath)) {
+      if (fs8.existsSync(mapping.targetPath)) {
         if (options.force === true) {
           this.removeLink(mapping.targetPath);
         } else {
@@ -2879,11 +3111,11 @@ var SymlinkManager = class {
         }
       }
       if (method === "symlink") {
-        const relativePath = path8.relative(targetDir, mapping.sourcePath);
-        fs7.symlinkSync(relativePath, mapping.targetPath, isFile ? "file" : "dir");
+        const relativePath = path9.relative(targetDir, mapping.sourcePath);
+        fs8.symlinkSync(relativePath, mapping.targetPath, isFile ? "file" : "dir");
       } else {
         if (isFile) {
-          fs7.copyFileSync(mapping.sourcePath, mapping.targetPath);
+          fs8.copyFileSync(mapping.sourcePath, mapping.targetPath);
         } else {
           this.copyDirectory(mapping.sourcePath, mapping.targetPath);
         }
@@ -2898,7 +3130,7 @@ var SymlinkManager = class {
       if (method === "symlink" && options.copy !== true) {
         try {
           if (isFile) {
-            fs7.copyFileSync(mapping.sourcePath, mapping.targetPath);
+            fs8.copyFileSync(mapping.sourcePath, mapping.targetPath);
           } else {
             this.copyDirectory(mapping.sourcePath, mapping.targetPath);
           }
@@ -2931,26 +3163,26 @@ var SymlinkManager = class {
    * Remove a symlink, file, or directory
    */
   removeLink(linkPath) {
-    const stats = fs7.lstatSync(linkPath);
+    const stats = fs8.lstatSync(linkPath);
     if (stats.isSymbolicLink() || stats.isFile()) {
-      fs7.unlinkSync(linkPath);
+      fs8.unlinkSync(linkPath);
     } else if (stats.isDirectory()) {
-      fs7.rmSync(linkPath, { recursive: true });
+      fs8.rmSync(linkPath, { recursive: true });
     }
   }
   /**
    * Copy a directory recursively
    */
   copyDirectory(source, target) {
-    fs7.mkdirSync(target, { recursive: true });
-    const entries = fs7.readdirSync(source, { withFileTypes: true });
+    fs8.mkdirSync(target, { recursive: true });
+    const entries = fs8.readdirSync(source, { withFileTypes: true });
     for (const entry of entries) {
-      const sourcePath = path8.join(source, entry.name);
-      const targetPath = path8.join(target, entry.name);
+      const sourcePath = path9.join(source, entry.name);
+      const targetPath = path9.join(target, entry.name);
       if (entry.isDirectory()) {
         this.copyDirectory(sourcePath, targetPath);
       } else {
-        fs7.copyFileSync(sourcePath, targetPath);
+        fs8.copyFileSync(sourcePath, targetPath);
       }
     }
   }
@@ -2979,8 +3211,8 @@ var SymlinkManager = class {
         broken.push(link);
       } else {
         if (link.isSymlink) {
-          const resolvedTarget = path8.resolve(path8.dirname(link.path), link.target);
-          if (!resolvedTarget.includes(path8.basename(this.synapSyncDir))) {
+          const resolvedTarget = path9.resolve(path9.dirname(link.path), link.target);
+          if (!resolvedTarget.includes(path9.basename(this.synapSyncDir))) {
             orphaned.push(link);
           } else {
             valid.push(link);
@@ -3021,7 +3253,7 @@ var SyncEngine = class {
   projectRoot;
   config;
   constructor(synapSyncDir, projectRoot, config) {
-    this.projectRoot = projectRoot ?? path9.dirname(synapSyncDir);
+    this.projectRoot = projectRoot ?? path10.dirname(synapSyncDir);
     this.config = config ?? null;
     this.scanner = new CognitiveScanner(synapSyncDir);
     this.manifest = new ManifestManager(synapSyncDir);
@@ -3361,6 +3593,7 @@ async function executeAddCommand(source, options) {
           }
         }
       }
+      regenerateAgentsMd(projectRoot, synapSyncDir);
       logger.line();
     }
   } catch (error) {
@@ -3381,7 +3614,7 @@ function parseSource(source) {
   if (source.startsWith("./") || source.startsWith("/") || source.startsWith("../")) {
     return {
       type: "local",
-      name: path10.basename(source),
+      name: path11.basename(source),
       path: source
     };
   }
@@ -3418,7 +3651,7 @@ async function installFromRegistry(name, options, configManager) {
   const manifest = downloaded.manifest;
   const category = options.category ?? manifest.category;
   const targetDir = getTargetDir(configManager, manifest.type, category, manifest.name);
-  if (fs8.existsSync(targetDir) && options.force !== true) {
+  if (fs9.existsSync(targetDir) && options.force !== true) {
     logger.line();
     logger.error(`Cognitive '${manifest.name}' is already installed.`);
     logger.hint("Use --force to overwrite.");
@@ -3431,7 +3664,7 @@ async function installFromRegistry(name, options, configManager) {
   logger.log(`  ${pc9.green("\u2713")} Installed ${pc9.bold(manifest.name)} ${pc9.dim(`v${manifest.version}`)}`);
   logger.log(`    ${pc9.dim("Type:")} ${manifest.type}`);
   logger.log(`    ${pc9.dim("Category:")} ${category}`);
-  logger.log(`    ${pc9.dim("Location:")} ${path10.relative(process.cwd(), targetDir)}`);
+  logger.log(`    ${pc9.dim("Location:")} ${path11.relative(process.cwd(), targetDir)}`);
   return true;
 }
 async function downloadAssets(client, name, _manifest) {
@@ -3452,8 +3685,8 @@ async function downloadAssets(client, name, _manifest) {
   return assets;
 }
 function installFromLocal(sourcePath, options, configManager) {
-  const absolutePath = path10.resolve(process.cwd(), sourcePath);
-  if (!fs8.existsSync(absolutePath)) {
+  const absolutePath = path11.resolve(process.cwd(), sourcePath);
+  if (!fs9.existsSync(absolutePath)) {
     throw new Error(`Path not found: ${absolutePath}`);
   }
   const detected = detectCognitiveType(absolutePath);
@@ -3464,13 +3697,13 @@ function installFromLocal(sourcePath, options, configManager) {
   }
   const cognitiveType = options.type ?? detected?.type ?? "skill";
   const fileName = detected?.fileName ?? COGNITIVE_FILE_NAMES[cognitiveType];
-  const filePath = path10.join(absolutePath, fileName);
-  if (!fs8.existsSync(filePath)) {
+  const filePath = path11.join(absolutePath, fileName);
+  if (!fs9.existsSync(filePath)) {
     throw new Error(`Cognitive file not found: ${filePath}`);
   }
-  const content = fs8.readFileSync(filePath, "utf-8");
+  const content = fs9.readFileSync(filePath, "utf-8");
   const metadata = parseMetadata(content);
-  const name = metadata["name"] ?? path10.basename(absolutePath);
+  const name = metadata["name"] ?? path11.basename(absolutePath);
   const category = options.category ?? metadata["category"] ?? "general";
   const manifest = {
     name,
@@ -3488,18 +3721,18 @@ function installFromLocal(sourcePath, options, configManager) {
     updatedAt: (/* @__PURE__ */ new Date()).toISOString()
   };
   const targetDir = getTargetDir(configManager, cognitiveType, category, name);
-  if (fs8.existsSync(targetDir) && options.force !== true) {
+  if (fs9.existsSync(targetDir) && options.force !== true) {
     logger.line();
     logger.error(`Cognitive '${name}' is already installed.`);
     logger.hint("Use --force to overwrite.");
     return false;
   }
   const assets = /* @__PURE__ */ new Map();
-  const assetsDir = path10.join(absolutePath, "assets");
-  if (fs8.existsSync(assetsDir)) {
-    const assetFiles = fs8.readdirSync(assetsDir);
+  const assetsDir = path11.join(absolutePath, "assets");
+  if (fs9.existsSync(assetsDir)) {
+    const assetFiles = fs9.readdirSync(assetsDir);
     for (const file of assetFiles) {
-      const assetContent = fs8.readFileSync(path10.join(assetsDir, file), "utf-8");
+      const assetContent = fs9.readFileSync(path11.join(assetsDir, file), "utf-8");
       assets.set(`assets/${file}`, assetContent);
     }
   }
@@ -3510,18 +3743,18 @@ function installFromLocal(sourcePath, options, configManager) {
   logger.log(`    ${pc9.dim("Type:")} ${cognitiveType}`);
   logger.log(`    ${pc9.dim("Category:")} ${category}`);
   logger.log(`    ${pc9.dim("Source:")} local`);
-  logger.log(`    ${pc9.dim("Location:")} ${path10.relative(process.cwd(), targetDir)}`);
+  logger.log(`    ${pc9.dim("Location:")} ${path11.relative(process.cwd(), targetDir)}`);
   return true;
 }
 function detectCognitiveType(dirPath) {
   for (const type of COGNITIVE_TYPES) {
     const fileName = COGNITIVE_FILE_NAMES[type];
-    if (fs8.existsSync(path10.join(dirPath, fileName))) {
+    if (fs9.existsSync(path11.join(dirPath, fileName))) {
       return { type, fileName };
     }
   }
-  if (!fs8.existsSync(dirPath)) return null;
-  const files = fs8.readdirSync(dirPath);
+  if (!fs9.existsSync(dirPath)) return null;
+  const files = fs9.readdirSync(dirPath);
   for (const file of files) {
     if (file.endsWith(".yaml") && !file.startsWith(".")) {
       return { type: "workflow", fileName: file };
@@ -3529,7 +3762,7 @@ function detectCognitiveType(dirPath) {
   }
   for (const file of files) {
     if (file.endsWith(".md") && !file.startsWith(".")) {
-      const content = fs8.readFileSync(path10.join(dirPath, file), "utf-8");
+      const content = fs9.readFileSync(path11.join(dirPath, file), "utf-8");
       const metadata = parseMetadata(content);
       const detectedType = metadata["type"] ?? "skill";
       if (COGNITIVE_TYPES.includes(detectedType)) {
@@ -3573,25 +3806,25 @@ function installFromGitHub(_source, _options, _configManager) {
 }
 function getTargetDir(configManager, type, category, name) {
   const synapSyncDir = configManager.getSynapSyncDir();
-  return path10.join(synapSyncDir, `${type}s`, category, name);
+  return path11.join(synapSyncDir, `${type}s`, category, name);
 }
 function saveCognitive(targetDir, manifest, content, assets) {
-  fs8.mkdirSync(targetDir, { recursive: true });
-  const mainFilePath = path10.join(targetDir, manifest.file);
-  fs8.writeFileSync(mainFilePath, content, "utf-8");
+  fs9.mkdirSync(targetDir, { recursive: true });
+  const mainFilePath = path11.join(targetDir, manifest.file);
+  fs9.writeFileSync(mainFilePath, content, "utf-8");
   for (const [assetPath, assetContent] of assets) {
-    const fullPath = path10.join(targetDir, assetPath);
-    const assetDir = path10.dirname(fullPath);
-    fs8.mkdirSync(assetDir, { recursive: true });
-    fs8.writeFileSync(fullPath, assetContent, "utf-8");
+    const fullPath = path11.join(targetDir, assetPath);
+    const assetDir = path11.dirname(fullPath);
+    fs9.mkdirSync(assetDir, { recursive: true });
+    fs9.writeFileSync(fullPath, assetContent, "utf-8");
   }
 }
 function updateProjectManifest(configManager, manifest, source) {
   const synapSyncDir = configManager.getSynapSyncDir();
-  const manifestPath = path10.join(synapSyncDir, "manifest.json");
+  const manifestPath = path11.join(synapSyncDir, "manifest.json");
   let projectManifest;
-  if (fs8.existsSync(manifestPath)) {
-    const content = fs8.readFileSync(manifestPath, "utf-8");
+  if (fs9.existsSync(manifestPath)) {
+    const content = fs9.readFileSync(manifestPath, "utf-8");
     projectManifest = JSON.parse(content);
   } else {
     projectManifest = {
@@ -3615,7 +3848,7 @@ function updateProjectManifest(configManager, manifest, source) {
   }
   projectManifest.cognitives[manifest.name] = entry;
   projectManifest.lastUpdated = (/* @__PURE__ */ new Date()).toISOString();
-  fs8.writeFileSync(manifestPath, JSON.stringify(projectManifest, null, 2), "utf-8");
+  fs9.writeFileSync(manifestPath, JSON.stringify(projectManifest, null, 2), "utf-8");
 }
 function registerAddCommand(program) {
   program.command("add <source>").description("Add a cognitive from registry, local path, or GitHub").option("-t, --type <type>", "Cognitive type (skill, agent, prompt, workflow, tool)").option("-c, --category <category>", "Category (overrides default)").option("-f, --force", "Overwrite if already installed").action(async (source, options) => {
@@ -3625,8 +3858,8 @@ function registerAddCommand(program) {
 
 // src/commands/list.ts
 init_esm_shims();
-import * as fs9 from "fs";
-import * as path11 from "path";
+import * as fs10 from "fs";
+import * as path12 from "path";
 import pc10 from "picocolors";
 async function executeListCommand(options) {
   logger.line();
@@ -3746,8 +3979,8 @@ function validateOptions2(options) {
 }
 function readManifest(configManager) {
   const synapSyncDir = configManager.getSynapSyncDir();
-  const manifestPath = path11.join(synapSyncDir, "manifest.json");
-  if (!fs9.existsSync(manifestPath)) {
+  const manifestPath = path12.join(synapSyncDir, "manifest.json");
+  if (!fs10.existsSync(manifestPath)) {
     return {
       version: "1.0.0",
       lastUpdated: (/* @__PURE__ */ new Date()).toISOString(),
@@ -3756,7 +3989,7 @@ function readManifest(configManager) {
     };
   }
   try {
-    const content = fs9.readFileSync(manifestPath, "utf-8");
+    const content = fs10.readFileSync(manifestPath, "utf-8");
     return JSON.parse(content);
   } catch {
     return {
@@ -3865,8 +4098,8 @@ function registerListCommand(program) {
 
 // src/commands/uninstall.ts
 init_esm_shims();
-import * as fs10 from "fs";
-import * as path12 from "path";
+import * as fs11 from "fs";
+import * as path13 from "path";
 import pc11 from "picocolors";
 function executeUninstallCommand(name, options) {
   logger.line();
@@ -3896,14 +4129,15 @@ function executeUninstallCommand(name, options) {
   try {
     if (options.keepFiles !== true) {
       const cognitiveDir = getCognitiveDir(configManager, cognitive);
-      if (fs10.existsSync(cognitiveDir)) {
-        fs10.rmSync(cognitiveDir, { recursive: true, force: true });
-        logger.log(`  ${pc11.dim("Removed files from")} ${path12.relative(process.cwd(), cognitiveDir)}`);
+      if (fs11.existsSync(cognitiveDir)) {
+        fs11.rmSync(cognitiveDir, { recursive: true, force: true });
+        logger.log(`  ${pc11.dim("Removed files from")} ${path13.relative(process.cwd(), cognitiveDir)}`);
       }
     }
     delete manifest.cognitives[name];
     manifest.lastUpdated = (/* @__PURE__ */ new Date()).toISOString();
     saveManifest(configManager, manifest);
+    regenerateAgentsMd(configManager.getProjectRoot(), configManager.getSynapSyncDir());
     logger.line();
     logger.log(`  ${pc11.green("\u2713")} Uninstalled ${pc11.bold(name)}`);
     logger.line();
@@ -3919,8 +4153,8 @@ function executeUninstallCommand(name, options) {
 }
 function readManifest2(configManager) {
   const synapSyncDir = configManager.getSynapSyncDir();
-  const manifestPath = path12.join(synapSyncDir, "manifest.json");
-  if (!fs10.existsSync(manifestPath)) {
+  const manifestPath = path13.join(synapSyncDir, "manifest.json");
+  if (!fs11.existsSync(manifestPath)) {
     return {
       version: "1.0.0",
       lastUpdated: (/* @__PURE__ */ new Date()).toISOString(),
@@ -3929,7 +4163,7 @@ function readManifest2(configManager) {
     };
   }
   try {
-    const content = fs10.readFileSync(manifestPath, "utf-8");
+    const content = fs11.readFileSync(manifestPath, "utf-8");
     return JSON.parse(content);
   } catch {
     return {
@@ -3942,12 +4176,12 @@ function readManifest2(configManager) {
 }
 function saveManifest(configManager, manifest) {
   const synapSyncDir = configManager.getSynapSyncDir();
-  const manifestPath = path12.join(synapSyncDir, "manifest.json");
-  fs10.writeFileSync(manifestPath, JSON.stringify(manifest, null, 2), "utf-8");
+  const manifestPath = path13.join(synapSyncDir, "manifest.json");
+  fs11.writeFileSync(manifestPath, JSON.stringify(manifest, null, 2), "utf-8");
 }
 function getCognitiveDir(configManager, cognitive) {
   const synapSyncDir = configManager.getSynapSyncDir();
-  return path12.join(synapSyncDir, `${cognitive.type}s`, cognitive.category, cognitive.name);
+  return path13.join(synapSyncDir, `${cognitive.type}s`, cognitive.category, cognitive.name);
 }
 function registerUninstallCommand(program) {
   program.command("uninstall <name>").alias("rm").description("Uninstall a cognitive").option("-f, --force", "Skip confirmation").option("--keep-files", "Remove from manifest but keep files").action((name, options) => {
@@ -3998,6 +4232,11 @@ function executeSyncCommand(options) {
       }
     } : void 0
   );
+  if (options.dryRun !== true) {
+    const synapSyncDir2 = configManager.getSynapSyncDir();
+    const projectRoot2 = configManager.getProjectRoot();
+    regenerateAgentsMd(projectRoot2, synapSyncDir2);
+  }
   if (options.json === true) {
     console.log(JSON.stringify(result, null, 2));
     return;
@@ -4231,8 +4470,8 @@ function registerSyncCommand(program) {
 
 // src/commands/update.ts
 init_esm_shims();
-import * as fs11 from "fs";
-import * as path13 from "path";
+import * as fs12 from "fs";
+import * as path14 from "path";
 import pc13 from "picocolors";
 
 // src/services/maintenance/update-checker.ts
@@ -4411,18 +4650,18 @@ async function executeUpdateCommand(cognitiveName, options = {}) {
       const downloaded = await registry.download(update.name);
       const manifestEntry = installed.find((c) => c.name === update.name);
       if (manifestEntry === void 0) continue;
-      const targetDir = path13.join(
+      const targetDir = path14.join(
         synapSyncDir,
         `${update.type}s`,
         update.category,
         update.name
       );
       const fileName = COGNITIVE_FILE_NAMES[update.type];
-      const filePath = path13.join(targetDir, fileName);
-      if (!fs11.existsSync(targetDir)) {
-        fs11.mkdirSync(targetDir, { recursive: true });
+      const filePath = path14.join(targetDir, fileName);
+      if (!fs12.existsSync(targetDir)) {
+        fs12.mkdirSync(targetDir, { recursive: true });
       }
-      fs11.writeFileSync(filePath, downloaded.content, "utf-8");
+      fs12.writeFileSync(filePath, downloaded.content, "utf-8");
       manifest.updateCognitive(update.name, {
         version: update.latestVersion
       });
@@ -4442,6 +4681,7 @@ async function executeUpdateCommand(cognitiveName, options = {}) {
   const config = configManager.getConfig();
   const syncEngine = new SyncEngine(synapSyncDir, projectRoot, config);
   syncEngine.sync();
+  regenerateAgentsMd(projectRoot, synapSyncDir);
   logger.line();
   if (updated.length > 0) {
     logger.log(`  ${pc13.green("\u2713")} Updated ${updated.length} cognitive(s)`);
@@ -4485,8 +4725,8 @@ import pc14 from "picocolors";
 
 // src/services/maintenance/doctor.ts
 init_esm_shims();
-import * as fs12 from "fs";
-import * as path14 from "path";
+import * as fs13 from "fs";
+import * as path15 from "path";
 var DoctorService = class {
   projectRoot;
   synapSyncDir;
@@ -4581,7 +4821,7 @@ var DoctorService = class {
     };
   }
   checkSynapSyncDir() {
-    if (fs12.existsSync(this.synapSyncDir)) {
+    if (fs13.existsSync(this.synapSyncDir)) {
       return {
         id: "synapsync-dir",
         name: ".synapsync Directory",
@@ -4601,8 +4841,8 @@ var DoctorService = class {
     };
   }
   checkConfig() {
-    const configPath = path14.join(this.projectRoot, "synapsync.config.yaml");
-    if (fs12.existsSync(configPath)) {
+    const configPath = path15.join(this.projectRoot, "synapsync.config.yaml");
+    if (fs13.existsSync(configPath)) {
       if (this.config !== null) {
         return {
           id: "config-valid",
@@ -4632,8 +4872,8 @@ var DoctorService = class {
     };
   }
   checkManifest() {
-    const manifestPath = path14.join(this.synapSyncDir, "manifest.json");
-    if (!fs12.existsSync(manifestPath)) {
+    const manifestPath = path15.join(this.synapSyncDir, "manifest.json");
+    if (!fs13.existsSync(manifestPath)) {
       return {
         id: "manifest-exists",
         name: "Manifest File",
@@ -4644,7 +4884,7 @@ var DoctorService = class {
       };
     }
     try {
-      const content = fs12.readFileSync(manifestPath, "utf-8");
+      const content = fs13.readFileSync(manifestPath, "utf-8");
       JSON.parse(content);
       return {
         id: "manifest-exists",
@@ -4666,7 +4906,7 @@ var DoctorService = class {
     }
   }
   checkManifestConsistency() {
-    if (!fs12.existsSync(this.synapSyncDir)) {
+    if (!fs13.existsSync(this.synapSyncDir)) {
       return {
         id: "manifest-consistency",
         name: "Manifest Consistency",
@@ -4863,13 +5103,13 @@ var DoctorService = class {
     }
   }
   fixSynapSyncDir() {
-    if (!fs12.existsSync(this.synapSyncDir)) {
-      fs12.mkdirSync(this.synapSyncDir, { recursive: true });
+    if (!fs13.existsSync(this.synapSyncDir)) {
+      fs13.mkdirSync(this.synapSyncDir, { recursive: true });
     }
     for (const type of COGNITIVE_TYPES) {
-      const typeDir = path14.join(this.synapSyncDir, `${type}s`);
-      if (!fs12.existsSync(typeDir)) {
-        fs12.mkdirSync(typeDir, { recursive: true });
+      const typeDir = path15.join(this.synapSyncDir, `${type}s`);
+      if (!fs13.existsSync(typeDir)) {
+        fs13.mkdirSync(typeDir, { recursive: true });
       }
     }
   }
@@ -5045,8 +5285,8 @@ import pc15 from "picocolors";
 
 // src/services/maintenance/cleaner.ts
 init_esm_shims();
-import * as fs13 from "fs";
-import * as path15 from "path";
+import * as fs14 from "fs";
+import * as path16 from "path";
 var CleanerService = class {
   projectRoot;
   synapSyncDir;
@@ -5106,8 +5346,8 @@ var CleanerService = class {
     const cleaned = [];
     const errors = [];
     let bytes = 0;
-    const cacheDir = path15.join(this.synapSyncDir, "cache");
-    if (!fs13.existsSync(cacheDir)) {
+    const cacheDir = path16.join(this.synapSyncDir, "cache");
+    if (!fs14.existsSync(cacheDir)) {
       return { cleaned, bytes, errors };
     }
     try {
@@ -5178,14 +5418,14 @@ var CleanerService = class {
     const errors = [];
     let bytes = 0;
     const tempPatterns = [
-      path15.join(this.synapSyncDir, ".tmp"),
-      path15.join(this.synapSyncDir, "temp"),
-      path15.join(this.synapSyncDir, "*.tmp"),
-      path15.join(this.synapSyncDir, "*.temp")
+      path16.join(this.synapSyncDir, ".tmp"),
+      path16.join(this.synapSyncDir, "temp"),
+      path16.join(this.synapSyncDir, "*.tmp"),
+      path16.join(this.synapSyncDir, "*.temp")
     ];
     for (const pattern of tempPatterns) {
       if (!pattern.includes("*")) {
-        if (fs13.existsSync(pattern)) {
+        if (fs14.existsSync(pattern)) {
           const size = this.getSize(pattern);
           cleaned.push({
             type: "temp",
@@ -5205,14 +5445,14 @@ var CleanerService = class {
           }
         }
       } else {
-        const dir = path15.dirname(pattern);
-        const ext = path15.extname(pattern);
-        if (fs13.existsSync(dir)) {
+        const dir = path16.dirname(pattern);
+        const ext = path16.extname(pattern);
+        if (fs14.existsSync(dir)) {
           try {
-            const entries = fs13.readdirSync(dir);
+            const entries = fs14.readdirSync(dir);
             for (const entry of entries) {
               if (entry.endsWith(ext.slice(1))) {
-                const fullPath = path15.join(dir, entry);
+                const fullPath = path16.join(dir, entry);
                 const size = this.getSize(fullPath);
                 cleaned.push({
                   type: "temp",
@@ -5248,9 +5488,9 @@ var CleanerService = class {
    */
   listDirectory(dir) {
     const items = [];
-    const entries = fs13.readdirSync(dir, { withFileTypes: true });
+    const entries = fs14.readdirSync(dir, { withFileTypes: true });
     for (const entry of entries) {
-      const fullPath = path15.join(dir, entry.name);
+      const fullPath = path16.join(dir, entry.name);
       items.push(fullPath);
       if (entry.isDirectory()) {
         items.push(...this.listDirectory(fullPath));
@@ -5263,15 +5503,15 @@ var CleanerService = class {
    */
   getSize(itemPath) {
     try {
-      const stats = fs13.statSync(itemPath);
+      const stats = fs14.statSync(itemPath);
       if (stats.isFile()) {
         return stats.size;
       }
       if (stats.isDirectory()) {
         let size = 0;
-        const entries = fs13.readdirSync(itemPath, { withFileTypes: true });
+        const entries = fs14.readdirSync(itemPath, { withFileTypes: true });
         for (const entry of entries) {
-          size += this.getSize(path15.join(itemPath, entry.name));
+          size += this.getSize(path16.join(itemPath, entry.name));
         }
         return size;
       }
@@ -5284,11 +5524,11 @@ var CleanerService = class {
    * Remove a file or directory
    */
   removeItem(itemPath) {
-    const stats = fs13.lstatSync(itemPath);
+    const stats = fs14.lstatSync(itemPath);
     if (stats.isSymbolicLink() || stats.isFile()) {
-      fs13.unlinkSync(itemPath);
+      fs14.unlinkSync(itemPath);
     } else if (stats.isDirectory()) {
-      fs13.rmSync(itemPath, { recursive: true });
+      fs14.rmSync(itemPath, { recursive: true });
     }
   }
   /**
@@ -5421,8 +5661,8 @@ function registerCleanCommand(program) {
 
 // src/commands/purge.ts
 init_esm_shims();
-import * as fs14 from "fs";
-import * as path16 from "path";
+import * as fs15 from "fs";
+import * as path17 from "path";
 import pc16 from "picocolors";
 function executePurgeCommand(options) {
   logger.line();
@@ -5448,17 +5688,23 @@ function executePurgeCommand(options) {
   let removedCount = 0;
   try {
     removedCount += removeProviderSymlinks(projectRoot, synapSyncDir);
-    if (fs14.existsSync(synapSyncDir)) {
-      fs14.rmSync(synapSyncDir, { recursive: true, force: true });
-      logger.log(`  ${pc16.red("\u2717")} Removed ${path16.relative(projectRoot, synapSyncDir)}/`);
+    if (fs15.existsSync(synapSyncDir)) {
+      fs15.rmSync(synapSyncDir, { recursive: true, force: true });
+      logger.log(`  ${pc16.red("\u2717")} Removed ${path17.relative(projectRoot, synapSyncDir)}/`);
       removedCount++;
     }
-    const configPath = path16.join(projectRoot, "synapsync.config.yaml");
-    if (fs14.existsSync(configPath)) {
-      fs14.unlinkSync(configPath);
+    const configPath = path17.join(projectRoot, "synapsync.config.yaml");
+    if (fs15.existsSync(configPath)) {
+      fs15.unlinkSync(configPath);
       logger.log(`  ${pc16.red("\u2717")} Removed synapsync.config.yaml`);
       removedCount++;
     }
+    const agentsMdPath = path17.join(projectRoot, AGENTS_MD_FILE_NAME);
+    if (fs15.existsSync(agentsMdPath)) {
+      fs15.unlinkSync(agentsMdPath);
+      logger.log(`  ${pc16.red("\u2717")} Removed ${AGENTS_MD_FILE_NAME}`);
+      removedCount++;
+    }
     if (cleanGitignore(projectRoot)) {
       logger.log(`  ${pc16.red("\u2717")} Cleaned SynapSync entries from .gitignore`);
       removedCount++;
@@ -5483,18 +5729,22 @@ function collectItemsToRemove(projectRoot, synapSyncDir) {
   const items = [];
   const symlinks = findSynapSyncSymlinks(projectRoot, synapSyncDir);
   for (const link of symlinks) {
-    items.push(`${path16.relative(projectRoot, link)} (symlink)`);
+    items.push(`${path17.relative(projectRoot, link)} (symlink)`);
   }
-  if (fs14.existsSync(synapSyncDir)) {
-    items.push(path16.relative(projectRoot, synapSyncDir) + "/");
+  if (fs15.existsSync(synapSyncDir)) {
+    items.push(path17.relative(projectRoot, synapSyncDir) + "/");
   }
-  const configPath = path16.join(projectRoot, "synapsync.config.yaml");
-  if (fs14.existsSync(configPath)) {
+  const configPath = path17.join(projectRoot, "synapsync.config.yaml");
+  if (fs15.existsSync(configPath)) {
     items.push("synapsync.config.yaml");
   }
-  const gitignorePath = path16.join(projectRoot, ".gitignore");
-  if (fs14.existsSync(gitignorePath)) {
-    const content = fs14.readFileSync(gitignorePath, "utf-8");
+  const agentsMdPath = path17.join(projectRoot, AGENTS_MD_FILE_NAME);
+  if (fs15.existsSync(agentsMdPath)) {
+    items.push(AGENTS_MD_FILE_NAME);
+  }
+  const gitignorePath = path17.join(projectRoot, ".gitignore");
+  if (fs15.existsSync(gitignorePath)) {
+    const content = fs15.readFileSync(gitignorePath, "utf-8");
     if (content.includes("# SynapSync")) {
       items.push(".gitignore (SynapSync entries)");
     }
@@ -5503,18 +5753,18 @@ function collectItemsToRemove(projectRoot, synapSyncDir) {
 }
 function findSynapSyncSymlinks(projectRoot, synapSyncDir) {
   const symlinks = [];
-  const resolvedSynapSync = path16.resolve(synapSyncDir);
+  const resolvedSynapSync = path17.resolve(synapSyncDir);
   for (const provider of SUPPORTED_PROVIDERS) {
     const providerPaths = PROVIDER_PATHS[provider];
     for (const type of COGNITIVE_TYPES) {
-      const typePath = path16.join(projectRoot, providerPaths[type]);
-      if (!fs14.existsSync(typePath)) continue;
+      const typePath = path17.join(projectRoot, providerPaths[type]);
+      if (!fs15.existsSync(typePath)) continue;
       try {
-        const entries = fs14.readdirSync(typePath, { withFileTypes: true });
+        const entries = fs15.readdirSync(typePath, { withFileTypes: true });
         for (const entry of entries) {
-          const fullPath = path16.join(typePath, entry.name);
+          const fullPath = path17.join(typePath, entry.name);
           if (entry.isSymbolicLink()) {
-            const target = path16.resolve(typePath, fs14.readlinkSync(fullPath));
+            const target = path17.resolve(typePath, fs15.readlinkSync(fullPath));
             if (target.startsWith(resolvedSynapSync)) {
               symlinks.push(fullPath);
             }
@@ -5529,21 +5779,21 @@ function findSynapSyncSymlinks(projectRoot, synapSyncDir) {
 function removeProviderSymlinks(projectRoot, synapSyncDir) {
   const symlinks = findSynapSyncSymlinks(projectRoot, synapSyncDir);
   for (const link of symlinks) {
-    fs14.unlinkSync(link);
-    logger.log(`  ${pc16.red("\u2717")} Removed symlink ${path16.relative(projectRoot, link)}`);
+    fs15.unlinkSync(link);
+    logger.log(`  ${pc16.red("\u2717")} Removed symlink ${path17.relative(projectRoot, link)}`);
   }
   return symlinks.length;
 }
 function cleanGitignore(projectRoot) {
-  const gitignorePath = path16.join(projectRoot, ".gitignore");
-  if (!fs14.existsSync(gitignorePath)) return false;
-  const content = fs14.readFileSync(gitignorePath, "utf-8");
+  const gitignorePath = path17.join(projectRoot, ".gitignore");
+  if (!fs15.existsSync(gitignorePath)) return false;
+  const content = fs15.readFileSync(gitignorePath, "utf-8");
   if (!content.includes("# SynapSync")) return false;
   const cleaned = content.replace(/\n?# SynapSync\n\.synapsync\/manifest\.json\n\*\.local\.yaml\n?/g, "").replace(/^\s*\n$/gm, "\n");
   if (cleaned.trim() === "") {
-    fs14.unlinkSync(gitignorePath);
+    fs15.unlinkSync(gitignorePath);
   } else {
-    fs14.writeFileSync(gitignorePath, cleaned, "utf-8");
+    fs15.writeFileSync(gitignorePath, cleaned, "utf-8");
   }
   return true;
 }