diff --git a/bin/cli.js b/bin/cli.js
index 3b9fc3e..e9afde1 100755
--- a/bin/cli.js
+++ b/bin/cli.js
@@ -18,15 +18,24 @@ const API_HEADERS = {
 
 function parseArgs(argv) {
   const out = {
+    command: "install",
     installDir: "~/.claude",
     force: false,
     dryRun: false,
     list: false,
     update: false,
     tag: null,
+    module: null,
+    yes: false,
   };
 
-  for (let i = 0; i < argv.length; i++) {
+  let i = 0;
+  if (argv[i] && !argv[i].startsWith("-")) {
+    out.command = argv[i];
+    i++;
+  }
+
+  for (; i < argv.length; i++) {
     const a = argv[i];
     if (a === "--install-dir") out.installDir = argv[++i];
     else if (a === "--force") out.force = true;
@@ -34,6 +43,8 @@ function parseArgs(argv) {
     else if (a === "--list") out.list = true;
     else if (a === "--update") out.update = true;
     else if (a === "--tag") out.tag = argv[++i];
+    else if (a === "--module") out.module = argv[++i];
+    else if (a === "-y" || a === "--yes") out.yes = true;
     else if (a === "-h" || a === "--help") out.help = true;
     else throw new Error(`Unknown arg: ${a}`);
   }
@@ -51,6 +62,8 @@ function printHelp() {
       "  npx github:cexll/myclaude --list",
       "  npx github:cexll/myclaude --update",
       "  npx github:cexll/myclaude --install-dir ~/.claude --force",
+      "  npx github:cexll/myclaude uninstall",
+      "  npx github:cexll/myclaude uninstall --module bmad,do -y",
       "",
       "Options:",
       "  --install-dir <path>   Default: ~/.claude",
@@ -59,6 +72,8 @@ function printHelp() {
       "  --list                 List installable items and exit",
       "  --update               Update already installed modules",
       "  --tag <tag>            Install a specific GitHub tag",
+      "  --module <names>       For uninstall: comma-separated module names",
+      "  -y, --yes              For uninstall: skip confirmation prompt",
     ].join("\n") + "\n"
   );
 }
@@ -202,6 +217,187 @@ function readInstalledModuleNamesFromStatus(installDir) {
   }
 }
 
+function loadInstalledStatus(installDir) {
+  const p = path.join(installDir, "installed_modules.json");
+  if (!fs.existsSync(p)) return { modules: {} };
+  try {
+    const json = JSON.parse(fs.readFileSync(p, "utf8"));
+    const modules = json && json.modules;
+    if (!modules || typeof modules !== "object" || Array.isArray(modules)) return { modules: {} };
+    return { ...json, modules };
+  } catch {
+    return { modules: {} };
+  }
+}
+
+function saveInstalledStatus(installDir, status) {
+  const p = path.join(installDir, "installed_modules.json");
+  fs.mkdirSync(installDir, { recursive: true });
+  fs.writeFileSync(p, JSON.stringify(status, null, 2) + "\n", "utf8");
+}
+
+function upsertModuleStatus(installDir, moduleResult) {
+  const status = loadInstalledStatus(installDir);
+  status.modules = status.modules || {};
+  status.modules[moduleResult.module] = moduleResult;
+  status.updated_at = new Date().toISOString();
+  saveInstalledStatus(installDir, status);
+}
+
+function deleteModuleStatus(installDir, moduleName) {
+  const status = loadInstalledStatus(installDir);
+  if (status.modules && Object.prototype.hasOwnProperty.call(status.modules, moduleName)) {
+    delete status.modules[moduleName];
+    status.updated_at = new Date().toISOString();
+    saveInstalledStatus(installDir, status);
+  }
+}
+
+function loadSettings(installDir) {
+  const p = path.join(installDir, "settings.json");
+  if (!fs.existsSync(p)) return {};
+  try {
+    return JSON.parse(fs.readFileSync(p, "utf8"));
+  } catch {
+    return {};
+  }
+}
+
+function saveSettings(installDir, settings) {
+  const p = path.join(installDir, "settings.json");
+  fs.mkdirSync(installDir, { recursive: true });
+  fs.writeFileSync(p, JSON.stringify(settings, null, 2) + "\n", "utf8");
+}
+
+function isPlainObject(x) {
+  return !!x && typeof x === "object" && !Array.isArray(x);
+}
+
+function deepEqual(a, b) {
+  if (a === b) return true;
+  if (Array.isArray(a) && Array.isArray(b)) {
+    if (a.length !== b.length) return false;
+    for (let i = 0; i < a.length; i++) if (!deepEqual(a[i], b[i])) return false;
+    return true;
+  }
+  if (isPlainObject(a) && isPlainObject(b)) {
+    const aKeys = Object.keys(a);
+    const bKeys = Object.keys(b);
+    if (aKeys.length !== bKeys.length) return false;
+    for (const k of aKeys) {
+      if (!Object.prototype.hasOwnProperty.call(b, k)) return false;
+      if (!deepEqual(a[k], b[k])) return false;
+    }
+    return true;
+  }
+  return false;
+}
+
+function hooksEqual(h1, h2) {
+  if (!isPlainObject(h1) || !isPlainObject(h2)) return false;
+  const a = { ...h1 };
+  const b = { ...h2 };
+  delete a.__module__;
+  delete b.__module__;
+  return deepEqual(a, b);
+}
+
+function replaceHookVariables(obj, pluginRoot) {
+  if (typeof obj === "string") return obj.replace(/\$\{CLAUDE_PLUGIN_ROOT\}/g, pluginRoot);
+  if (Array.isArray(obj)) return obj.map((v) => replaceHookVariables(v, pluginRoot));
+  if (isPlainObject(obj)) {
+    const out = {};
+    for (const [k, v] of Object.entries(obj)) out[k] = replaceHookVariables(v, pluginRoot);
+    return out;
+  }
+  return obj;
+}
+
+function mergeHooksToSettings(moduleName, hooksConfig, installDir, pluginRoot) {
+  if (!hooksConfig || !isPlainObject(hooksConfig)) return false;
+  const rawHooks = hooksConfig.hooks;
+  if (!rawHooks || !isPlainObject(rawHooks)) return false;
+
+  const settings = loadSettings(installDir);
+  if (!settings.hooks || !isPlainObject(settings.hooks)) settings.hooks = {};
+
+  const moduleHooks = pluginRoot ? replaceHookVariables(rawHooks, pluginRoot) : rawHooks;
+  let modified = false;
+
+  for (const [hookType, hookEntries] of Object.entries(moduleHooks)) {
+    if (!Array.isArray(hookEntries)) continue;
+    if (!Array.isArray(settings.hooks[hookType])) settings.hooks[hookType] = [];
+
+    for (const entry of hookEntries) {
+      if (!isPlainObject(entry)) continue;
+      const entryCopy = { ...entry, __module__: moduleName };
+
+      let exists = false;
+      for (const existing of settings.hooks[hookType]) {
+        if (existing && existing.__module__ === moduleName && hooksEqual(existing, entryCopy)) {
+          exists = true;
+          break;
+        }
+      }
+      if (!exists) {
+        settings.hooks[hookType].push(entryCopy);
+        modified = true;
+      }
+    }
+  }
+
+  if (modified) saveSettings(installDir, settings);
+  return modified;
+}
+
+function unmergeHooksFromSettings(moduleName, installDir) {
+  const settings = loadSettings(installDir);
+  if (!settings.hooks || !isPlainObject(settings.hooks)) return false;
+
+  let modified = false;
+  for (const hookType of Object.keys(settings.hooks)) {
+    const entries = settings.hooks[hookType];
+    if (!Array.isArray(entries)) continue;
+    const kept = entries.filter((e) => !(e && e.__module__ === moduleName));
+    if (kept.length !== entries.length) {
+      settings.hooks[hookType] = kept;
+      modified = true;
+    }
+    if (!settings.hooks[hookType].length) {
+      delete settings.hooks[hookType];
+      modified = true;
+    }
+  }
+
+  if (modified) saveSettings(installDir, settings);
+  return modified;
+}
+
+function mergeModuleHooks(moduleName, mod, installDir) {
+  const ops = Array.isArray(mod && mod.operations) ? mod.operations : [];
+  let merged = false;
+
+  for (const op of ops) {
+    if (!op || op.type !== "copy_dir") continue;
+    const target = typeof op.target === "string" ? op.target : "";
+    if (!target) continue;
+
+    const targetDir = path.join(installDir, target);
+    const hooksFile = path.join(targetDir, "hooks", "hooks.json");
+    if (!fs.existsSync(hooksFile)) continue;
+
+    let hooksConfig;
+    try {
+      hooksConfig = JSON.parse(fs.readFileSync(hooksFile, "utf8"));
+    } catch {
+      continue;
+    }
+    if (mergeHooksToSettings(moduleName, hooksConfig, installDir, targetDir)) merged = true;
+  }
+
+  return merged;
+}
+
 async function dirExists(p) {
   try {
     return (await fs.promises.stat(p)).isDirectory();
@@ -305,7 +501,8 @@ async function updateInstalledModules(installDir, tag, config, dryRun) {
     await fs.promises.mkdir(installDir, { recursive: true });
     for (const name of toUpdate) {
       process.stdout.write(`Updating module: ${name}\n`);
-      await applyModule(name, config, repoRoot, installDir, true);
+      const r = await applyModule(name, config, repoRoot, installDir, true);
+      upsertModuleStatus(installDir, r);
     }
   } finally {
     if (tmp) await rmTree(tmp);
@@ -513,11 +710,12 @@ async function extractTarGz(archivePath, destDir) {
 }
 
 async function copyFile(src, dst, force) {
-  if (!force && fs.existsSync(dst)) return;
+  if (!force && fs.existsSync(dst)) return false;
   await fs.promises.mkdir(path.dirname(dst), { recursive: true });
   await fs.promises.copyFile(src, dst);
   const st = await fs.promises.stat(src);
   await fs.promises.chmod(dst, st.mode);
+  return true;
 }
 
 async function copyDirRecursive(src, dst, force) {
@@ -534,6 +732,7 @@ async function copyDirRecursive(src, dst, force) {
 }
 
 async function mergeDir(src, installDir, force) {
+  const installed = [];
   const subdirs = await fs.promises.readdir(src, { withFileTypes: true });
   for (const d of subdirs) {
     if (!d.isDirectory()) continue;
@@ -543,9 +742,11 @@ async function mergeDir(src, installDir, force) {
     const entries = await fs.promises.readdir(srcSub, { withFileTypes: true });
     for (const e of entries) {
       if (!e.isFile()) continue;
-      await copyFile(path.join(srcSub, e.name), path.join(dstSub, e.name), force);
+      const didCopy = await copyFile(path.join(srcSub, e.name), path.join(dstSub, e.name), force);
+      if (didCopy) installed.push(`${d.name}/${e.name}`);
     }
   }
+  return installed;
 }
 
 function runInstallSh(repoRoot, installDir) {
@@ -577,33 +778,154 @@ async function applyModule(moduleName, config, repoRoot, installDir, force) {
   const mod = config && config.modules && config.modules[moduleName];
   if (!mod) throw new Error(`Unknown module: ${moduleName}`);
   const ops = Array.isArray(mod.operations) ? mod.operations : [];
+  const result = {
+    module: moduleName,
+    status: "success",
+    operations: [],
+    installed_at: new Date().toISOString(),
+  };
+  const mergeDirFiles = [];
 
   for (const op of ops) {
     const type = op && op.type;
-    if (type === "copy_file") {
-      await copyFile(
-        path.join(repoRoot, op.source),
-        path.join(installDir, op.target),
-        force
-      );
-    } else if (type === "copy_dir") {
-      await copyDirRecursive(
-        path.join(repoRoot, op.source),
-        path.join(installDir, op.target),
-        force
-      );
-    } else if (type === "merge_dir") {
-      await mergeDir(path.join(repoRoot, op.source), installDir, force);
-    } else if (type === "run_command") {
-      const cmd = typeof op.command === "string" ? op.command.trim() : "";
-      if (cmd !== "bash install.sh") {
-        throw new Error(`Refusing run_command: ${cmd || "(empty)"}`);
+    try {
+      if (type === "copy_file") {
+        await copyFile(path.join(repoRoot, op.source), path.join(installDir, op.target), force);
+      } else if (type === "copy_dir") {
+        await copyDirRecursive(path.join(repoRoot, op.source), path.join(installDir, op.target), force);
+      } else if (type === "merge_dir") {
+        mergeDirFiles.push(...(await mergeDir(path.join(repoRoot, op.source), installDir, force)));
+      } else if (type === "run_command") {
+        const cmd = typeof op.command === "string" ? op.command.trim() : "";
+        if (cmd !== "bash install.sh") {
+          throw new Error(`Refusing run_command: ${cmd || "(empty)"}`);
+        }
+        await runInstallSh(repoRoot, installDir);
+      } else {
+        throw new Error(`Unsupported operation type: ${type}`);
       }
-      await runInstallSh(repoRoot, installDir);
-    } else {
-      throw new Error(`Unsupported operation type: ${type}`);
+      result.operations.push({ type, status: "success" });
+    } catch (err) {
+      result.status = "failed";
+      result.operations.push({
+        type,
+        status: "failed",
+        error: err && err.message ? err.message : String(err),
+      });
+      throw err;
     }
   }
+
+  if (mergeDirFiles.length) result.merge_dir_files = mergeDirFiles;
+
+  try {
+    if (mergeModuleHooks(moduleName, mod, installDir)) {
+      result.has_hooks = true;
+      result.operations.push({ type: "merge_hooks", status: "success" });
+    }
+  } catch (err) {
+    result.operations.push({
+      type: "merge_hooks",
+      status: "failed",
+      error: err && err.message ? err.message : String(err),
+    });
+  }
+
+  return result;
+}
+
+async function tryRemoveEmptyDir(p) {
+  try {
+    const entries = await fs.promises.readdir(p);
+    if (!entries.length) await fs.promises.rmdir(p);
+  } catch {
+    // ignore
+  }
+}
+
+async function removePathIfExists(p) {
+  if (!fs.existsSync(p)) return;
+  const st = await fs.promises.lstat(p);
+  if (st.isDirectory()) {
+    await rmTree(p);
+    return;
+  }
+  try {
+    await fs.promises.unlink(p);
+  } catch (err) {
+    if (!err || err.code !== "ENOENT") throw err;
+  }
+}
+
+async function uninstallModule(moduleName, config, repoRoot, installDir, dryRun) {
+  const mod = config && config.modules && config.modules[moduleName];
+  if (!mod) throw new Error(`Unknown module: ${moduleName}`);
+  const ops = Array.isArray(mod.operations) ? mod.operations : [];
+  const status = loadInstalledStatus(installDir);
+  const moduleStatus = (status.modules && status.modules[moduleName]) || {};
+  const recordedMerge = Array.isArray(moduleStatus.merge_dir_files) ? moduleStatus.merge_dir_files : null;
+
+  for (const op of ops) {
+    const type = op && op.type;
+    if (type === "copy_file" || type === "copy_dir") {
+      const target = typeof op.target === "string" ? op.target : "";
+      if (!target) continue;
+      const p = path.join(installDir, target);
+      if (dryRun) process.stdout.write(`- remove ${p}\n`);
+      else await removePathIfExists(p);
+      continue;
+    }
+
+    if (type !== "merge_dir") continue;
+    const source = typeof op.source === "string" ? op.source : "";
+    if (!source) continue;
+
+    if (recordedMerge && recordedMerge.length) {
+      for (const rel of recordedMerge) {
+        const parts = String(rel).split("/").filter(Boolean);
+        if (parts.includes("..")) continue;
+        const p = path.join(installDir, ...parts);
+        if (dryRun) process.stdout.write(`- remove ${p}\n`);
+        else {
+          await removePathIfExists(p);
+          await tryRemoveEmptyDir(path.dirname(p));
+        }
+      }
+      continue;
+    }
+
+    const srcDir = path.join(repoRoot, source);
+    if (!(await dirExists(srcDir))) continue;
+    const subdirs = await fs.promises.readdir(srcDir, { withFileTypes: true });
+    for (const d of subdirs) {
+      if (!d.isDirectory()) continue;
+      const srcSub = path.join(srcDir, d.name);
+      const entries = await fs.promises.readdir(srcSub, { withFileTypes: true });
+      for (const e of entries) {
+        if (!e.isFile()) continue;
+        const dst = path.join(installDir, d.name, e.name);
+        if (!fs.existsSync(dst)) continue;
+        try {
+          const [srcBuf, dstBuf] = await Promise.all([
+            fs.promises.readFile(path.join(srcSub, e.name)),
+            fs.promises.readFile(dst),
+          ]);
+          if (Buffer.compare(srcBuf, dstBuf) !== 0) continue;
+        } catch {
+          continue;
+        }
+        if (dryRun) process.stdout.write(`- remove ${dst}\n`);
+        else {
+          await removePathIfExists(dst);
+          await tryRemoveEmptyDir(path.dirname(dst));
+        }
+      }
+    }
+  }
+
+  if (dryRun) return;
+  unmergeHooksFromSettings(moduleName, installDir);
+  deleteModuleStatus(installDir, moduleName);
 }
 
 async function installSelected(picks, tag, config, installDir, force, dryRun) {
@@ -647,7 +969,8 @@ async function installSelected(picks, tag, config, installDir, force, dryRun) {
       }
       if (p.kind === "module") {
         process.stdout.write(`Installing module: ${p.moduleName}\n`);
-        await applyModule(p.moduleName, config, repoRoot, installDir, force);
+        const r = await applyModule(p.moduleName, config, repoRoot, installDir, force);
+        upsertModuleStatus(installDir, r);
         continue;
       }
       if (p.kind === "skill") {
@@ -672,8 +995,77 @@ async function main() {
   }
 
   const installDir = expandHome(args.installDir);
+  if (args.command !== "install" && args.command !== "uninstall") {
+    throw new Error(`Unknown command: ${args.command}`);
+  }
   if (args.list && args.update) throw new Error("Cannot combine --list and --update");
 
+  if (args.command === "uninstall") {
+    const config = readLocalConfig();
+    const repoRoot = repoRootFromHere();
+    const fromStatus = readInstalledModuleNamesFromStatus(installDir);
+    const installed = fromStatus || (await detectInstalledModuleNames(config, repoRoot, installDir));
+    const installedSet = new Set(installed);
+
+    let toRemove = [];
+    if (args.module) {
+      const v = String(args.module).trim();
+      if (v.toLowerCase() === "all") {
+        toRemove = installed;
+      } else {
+        toRemove = v
+          .split(",")
+          .map((s) => s.trim())
+          .filter(Boolean);
+      }
+    } else {
+      const modules = (config && config.modules) || {};
+      const items = [];
+      for (const [name, mod] of Object.entries(modules)) {
+        if (!installedSet.has(name)) continue;
+        const desc = mod && typeof mod.description === "string" ? mod.description : "";
+        items.push({
+          id: `module:${name}`,
+          label: `module:${name}${desc ? ` - ${desc}` : ""}`,
+          kind: "module",
+          moduleName: name,
+        });
+      }
+      if (!items.length) {
+        process.stdout.write(`No installed modules found in ${installDir}.\n`);
+        return;
+      }
+      const picks = await promptMultiSelect(items, "myclaude uninstall");
+      toRemove = picks.map((p) => p.moduleName);
+    }
+
+    toRemove = toRemove.filter((m) => installedSet.has(m));
+    if (!toRemove.length) {
+      process.stdout.write("Nothing selected.\n");
+      return;
+    }
+
+    if (!args.yes && !args.dryRun) {
+      if (!process.stdin.isTTY) {
+        throw new Error("No TTY. Use -y/--yes to skip confirmation.");
+      }
+      const rl = readline.createInterface({ input: process.stdin, output: process.stdout });
+      const answer = await new Promise((resolve) => rl.question("Confirm uninstall? (y/N): ", resolve));
+      rl.close();
+      if (String(answer).trim().toLowerCase() !== "y") {
+        process.stdout.write("Cancelled.\n");
+        return;
+      }
+    }
+
+    for (const name of toRemove) {
+      process.stdout.write(`Uninstalling module: ${name}\n`);
+      await uninstallModule(name, config, repoRoot, installDir, args.dryRun);
+    }
+    process.stdout.write("Done.\n");
+    return;
+  }
+
   let tag = args.tag;
   if (!tag) {
     try {
diff --git a/install.py b/install.py
index 00e6747..4fe6fc7 100644
--- a/install.py
+++ b/install.py
@@ -518,6 +518,11 @@ def uninstall_module(name: str, cfg: Dict[str, Any], ctx: Dict[str, Any]) -> Dic
 
     install_dir = ctx["install_dir"]
     removed_paths = []
+    status = load_installed_status(ctx)
+    module_status = status.get("modules", {}).get(name, {})
+    merge_dir_files = module_status.get("merge_dir_files", [])
+    if not isinstance(merge_dir_files, list):
+        merge_dir_files = []
 
     for op in cfg.get("operations", []):
         op_type = op.get("type")
@@ -531,7 +536,55 @@ def uninstall_module(name: str, cfg: Dict[str, Any], ctx: Dict[str, Any]) -> Dic
                         target.unlink()
                     removed_paths.append(str(target))
                     write_log({"level": "INFO", "message": f"Removed: {target}"}, ctx)
-            # merge_dir and merge_json are harder to uninstall cleanly, skip
+            elif op_type == "merge_dir":
+                if not merge_dir_files:
+                    write_log(
+                        {
+                            "level": "WARNING",
+                            "message": f"No merge_dir_files recorded for {name}; skip merge_dir uninstall",
+                        },
+                        ctx,
+                    )
+                    continue
+
+                for rel in dict.fromkeys(merge_dir_files):
+                    rel_path = Path(str(rel))
+                    if rel_path.is_absolute() or ".." in rel_path.parts:
+                        write_log(
+                            {
+                                "level": "WARNING",
+                                "message": f"Skip unsafe merge_dir path for {name}: {rel}",
+                            },
+                            ctx,
+                        )
+                        continue
+
+                    target = (install_dir / rel_path).resolve()
+                    if target == install_dir or install_dir not in target.parents:
+                        write_log(
+                            {
+                                "level": "WARNING",
+                                "message": f"Skip out-of-tree merge_dir path for {name}: {rel}",
+                            },
+                            ctx,
+                        )
+                        continue
+
+                    if target.exists():
+                        if target.is_dir():
+                            shutil.rmtree(target)
+                        else:
+                            target.unlink()
+                        removed_paths.append(str(target))
+                        write_log({"level": "INFO", "message": f"Removed: {target}"}, ctx)
+
+                    parent = target.parent
+                    while parent != install_dir and parent.exists():
+                        try:
+                            parent.rmdir()
+                        except OSError:
+                            break
+                        parent = parent.parent
         except Exception as exc:
             write_log({"level": "WARNING", "message": f"Failed to remove {op.get('target', 'unknown')}: {exc}"}, ctx)
 
@@ -720,7 +773,9 @@ def execute_module(name: str, cfg: Dict[str, Any], ctx: Dict[str, Any]) -> Dict[
             elif op_type == "copy_file":
                 op_copy_file(op, ctx)
             elif op_type == "merge_dir":
-                op_merge_dir(op, ctx)
+                merged = op_merge_dir(op, ctx)
+                if merged:
+                    result.setdefault("merge_dir_files", []).extend(merged)
             elif op_type == "merge_json":
                 op_merge_json(op, ctx)
             elif op_type == "run_command":
@@ -792,7 +847,7 @@ def op_copy_dir(op: Dict[str, Any], ctx: Dict[str, Any]) -> None:
     write_log({"level": "INFO", "message": f"Copied dir {src} -> {dst}"}, ctx)
 
 
-def op_merge_dir(op: Dict[str, Any], ctx: Dict[str, Any]) -> None:
+def op_merge_dir(op: Dict[str, Any], ctx: Dict[str, Any]) -> List[str]:
     """Merge source dir's subdirs (commands/, agents/, etc.) into install_dir."""
     src = _source_path(op, ctx)
     install_dir = ctx["install_dir"]
@@ -813,6 +868,7 @@ def op_merge_dir(op: Dict[str, Any], ctx: Dict[str, Any]) -> None:
                 merged.append(f"{subdir.name}/{f.name}")
 
     write_log({"level": "INFO", "message": f"Merged {src.name}: {', '.join(merged) or 'no files'}"}, ctx)
+    return merged
 
 
 def op_copy_file(op: Dict[str, Any], ctx: Dict[str, Any]) -> None: