refactor: scaffold module registries and default-module layout

Additive change — existing code paths still run via inline fallbacks.
Prepares core for per-module extractions in PR #3 onward.

Four registries added with empty defaults:
  - delivery action handlers (delivery.ts)
  - router inbound gate (router.ts)
  - response dispatcher (index.ts)
  - MCP tool self-registration (container/agent-runner/src/mcp-tools/server.ts)

Default modules moved to src/modules/ for signaling:
  - src/modules/typing/       (extracted from delivery.ts)
  - src/modules/mount-security/ (moved from src/mount-security.ts)

Both are imported directly by core — no hook, no registry. Removal
requires editing core imports.

Migrator now keys applied rows by name (uniqueness) so module
migrations can pick arbitrary version numbers. Stored version column
is auto-assigned as an applied-order sequence.

sqlite_master guards added around core calls into module-owned tables
(user_roles, agent_destinations, pending_questions). No-ops today;
load-bearing after the owning modules are extracted.

MODULE-HOOK markers placed at scheduling's two skill-edit sites
(host-sweep.ts recurrence call, poll-loop.ts pre-task gate). PR #4
replaces the marked blocks when scheduling moves to its module.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

src/modules/index.ts

@@ -0,0 +1,16 @@
+/**
+ * Modules barrel.
+ *
+ * Each module self-registers at import time. This barrel is imported by
+ * src/index.ts for side effects (registry registrations, typing impl setup,
+ * etc.). Core runs with an empty barrel — the registries have inline
+ * fallbacks and `sqlite_master` guards.
+ *
+ * Default modules (ship with main, direct core import):
+ *   - src/modules/typing/        → imported directly by router/delivery/container-runner
+ *   - src/modules/mount-security/ → imported directly by container-runner
+ *
+ * Registry-based modules (installed via /add-<name> skills, pulled from the
+ * `modules` branch): append imports below.
+ */
+export {};

src/modules/mount-security/index.ts

@@ -0,0 +1,389 @@
+/**
+ * Mount Security Module for NanoClaw
+ *
+ * Validates additional mounts against an allowlist stored OUTSIDE the project root.
+ * This prevents container agents from modifying security configuration.
+ *
+ * Allowlist location: ~/.config/nanoclaw/mount-allowlist.json
+ */
+import fs from 'fs';
+import os from 'os';
+import path from 'path';
+import { MOUNT_ALLOWLIST_PATH } from '../../config.js';
+import { log } from '../../log.js';
+
+export interface AdditionalMount {
+  hostPath: string;
+  containerPath?: string;
+  readonly?: boolean;
+}
+
+export interface MountAllowlist {
+  allowedRoots: AllowedRoot[];
+  blockedPatterns: string[];
+}
+
+export interface AllowedRoot {
+  path: string;
+  allowReadWrite: boolean;
+  description?: string;
+}
+
+// Cache the allowlist in memory - only reloads on process restart
+let cachedAllowlist: MountAllowlist | null = null;
+let allowlistLoadError: string | null = null;
+
+/**
+ * Default blocked patterns - paths that should never be mounted
+ */
+const DEFAULT_BLOCKED_PATTERNS = [
+  '.ssh',
+  '.gnupg',
+  '.gpg',
+  '.aws',
+  '.azure',
+  '.gcloud',
+  '.kube',
+  '.docker',
+  'credentials',
+  '.env',
+  '.netrc',
+  '.npmrc',
+  '.pypirc',
+  'id_rsa',
+  'id_ed25519',
+  'private_key',
+  '.secret',
+];
+
+/**
+ * Load the mount allowlist from the external config location.
+ * Returns null if the file doesn't exist or is invalid.
+ * Result is cached in memory for the lifetime of the process.
+ */
+export function loadMountAllowlist(): MountAllowlist | null {
+  if (cachedAllowlist !== null) {
+    return cachedAllowlist;
+  }
+
+  if (allowlistLoadError !== null) {
+    // Already tried and failed, don't spam logs
+    return null;
+  }
+
+  try {
+    if (!fs.existsSync(MOUNT_ALLOWLIST_PATH)) {
+      // Do NOT cache this as an error — file may be created later without restart.
+      // Only parse/structural errors are permanently cached.
+      log.warn(
+        'Mount allowlist not found - additional mounts will be BLOCKED. Create the file to enable additional mounts.',
+        { path: MOUNT_ALLOWLIST_PATH },
+      );
+      return null;
+    }
+
+    const content = fs.readFileSync(MOUNT_ALLOWLIST_PATH, 'utf-8');
+    const allowlist = JSON.parse(content) as MountAllowlist;
+
+    // Validate structure
+    if (!Array.isArray(allowlist.allowedRoots)) {
+      throw new Error('allowedRoots must be an array');
+    }
+
+    if (!Array.isArray(allowlist.blockedPatterns)) {
+      throw new Error('blockedPatterns must be an array');
+    }
+
+    // Merge with default blocked patterns
+    const mergedBlockedPatterns = [...new Set([...DEFAULT_BLOCKED_PATTERNS, ...allowlist.blockedPatterns])];
+    allowlist.blockedPatterns = mergedBlockedPatterns;
+
+    cachedAllowlist = allowlist;
+    log.info('Mount allowlist loaded successfully', {
+      path: MOUNT_ALLOWLIST_PATH,
+      allowedRoots: allowlist.allowedRoots.length,
+      blockedPatterns: allowlist.blockedPatterns.length,
+    });
+
+    return cachedAllowlist;
+  } catch (err) {
+    allowlistLoadError = err instanceof Error ? err.message : String(err);
+    log.error('Failed to load mount allowlist - additional mounts will be BLOCKED', {
+      path: MOUNT_ALLOWLIST_PATH,
+      error: allowlistLoadError,
+    });
+    return null;
+  }
+}
+
+/**
+ * Expand ~ to home directory and resolve to absolute path
+ */
+function expandPath(p: string): string {
+  const homeDir = process.env.HOME || os.homedir();
+  if (p.startsWith('~/')) {
+    return path.join(homeDir, p.slice(2));
+  }
+  if (p === '~') {
+    return homeDir;
+  }
+  return path.resolve(p);
+}
+
+/**
+ * Get the real path, resolving symlinks.
+ * Returns null if the path doesn't exist.
+ */
+function getRealPath(p: string): string | null {
+  try {
+    return fs.realpathSync(p);
+  } catch {
+    return null;
+  }
+}
+
+/**
+ * Check if a path matches any blocked pattern
+ */
+function matchesBlockedPattern(realPath: string, blockedPatterns: string[]): string | null {
+  const pathParts = realPath.split(path.sep);
+
+  for (const pattern of blockedPatterns) {
+    // Check if any path component matches the pattern
+    for (const part of pathParts) {
+      if (part === pattern || part.includes(pattern)) {
+        return pattern;
+      }
+    }
+
+    // Also check if the full path contains the pattern
+    if (realPath.includes(pattern)) {
+      return pattern;
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Check if a real path is under an allowed root
+ */
+function findAllowedRoot(realPath: string, allowedRoots: AllowedRoot[]): AllowedRoot | null {
+  for (const root of allowedRoots) {
+    const expandedRoot = expandPath(root.path);
+    const realRoot = getRealPath(expandedRoot);
+
+    if (realRoot === null) {
+      // Allowed root doesn't exist, skip it
+      continue;
+    }
+
+    // Check if realPath is under realRoot
+    const relative = path.relative(realRoot, realPath);
+    if (!relative.startsWith('..') && !path.isAbsolute(relative)) {
+      return root;
+    }
+  }
+
+  return null;
+}
+
+/**
+ * Validate the container path to prevent escaping /workspace/extra/
+ */
+function isValidContainerPath(containerPath: string): boolean {
+  // Must not contain .. to prevent path traversal
+  if (containerPath.includes('..')) {
+    return false;
+  }
+
+  // Must not be absolute (it will be prefixed with /workspace/extra/)
+  if (containerPath.startsWith('/')) {
+    return false;
+  }
+
+  // Must not be empty
+  if (!containerPath || containerPath.trim() === '') {
+    return false;
+  }
+
+  // Must not contain colons — prevents Docker -v option injection (e.g., "repo:rw")
+  if (containerPath.includes(':')) {
+    return false;
+  }
+
+  return true;
+}
+
+export interface MountValidationResult {
+  allowed: boolean;
+  reason: string;
+  realHostPath?: string;
+  resolvedContainerPath?: string;
+  effectiveReadonly?: boolean;
+}
+
+/**
+ * Validate a single additional mount against the allowlist.
+ * Returns validation result with reason.
+ */
+export function validateMount(mount: AdditionalMount): MountValidationResult {
+  const allowlist = loadMountAllowlist();
+
+  // If no allowlist, block all additional mounts
+  if (allowlist === null) {
+    return {
+      allowed: false,
+      reason: `No mount allowlist configured at ${MOUNT_ALLOWLIST_PATH}`,
+    };
+  }
+
+  // Derive containerPath from hostPath basename if not specified
+  const containerPath = mount.containerPath || path.basename(mount.hostPath);
+
+  // Validate container path (cheap check)
+  if (!isValidContainerPath(containerPath)) {
+    return {
+      allowed: false,
+      reason: `Invalid container path: "${containerPath}" - must be relative, non-empty, and not contain ".."`,
+    };
+  }
+
+  // Expand and resolve the host path
+  const expandedPath = expandPath(mount.hostPath);
+  const realPath = getRealPath(expandedPath);
+
+  if (realPath === null) {
+    return {
+      allowed: false,
+      reason: `Host path does not exist: "${mount.hostPath}" (expanded: "${expandedPath}")`,
+    };
+  }
+
+  // Check against blocked patterns
+  const blockedMatch = matchesBlockedPattern(realPath, allowlist.blockedPatterns);
+  if (blockedMatch !== null) {
+    return {
+      allowed: false,
+      reason: `Path matches blocked pattern "${blockedMatch}": "${realPath}"`,
+    };
+  }
+
+  // Check if under an allowed root
+  const allowedRoot = findAllowedRoot(realPath, allowlist.allowedRoots);
+  if (allowedRoot === null) {
+    return {
+      allowed: false,
+      reason: `Path "${realPath}" is not under any allowed root. Allowed roots: ${allowlist.allowedRoots
+        .map((r) => expandPath(r.path))
+        .join(', ')}`,
+    };
+  }
+
+  // Determine effective readonly status.
+  // RW is only granted if the mount explicitly requests it AND the allowed
+  // root permits it. Otherwise it's forced read-only.
+  const requestedReadWrite = mount.readonly === false;
+  let effectiveReadonly = true;
+
+  if (requestedReadWrite) {
+    if (!allowedRoot.allowReadWrite) {
+      log.info('Mount forced to read-only - root does not allow read-write', {
+        mount: mount.hostPath,
+        root: allowedRoot.path,
+      });
+    } else {
+      effectiveReadonly = false;
+    }
+  }
+
+  return {
+    allowed: true,
+    reason: `Allowed under root "${allowedRoot.path}"${allowedRoot.description ? ` (${allowedRoot.description})` : ''}`,
+    realHostPath: realPath,
+    resolvedContainerPath: containerPath,
+    effectiveReadonly,
+  };
+}
+
+/**
+ * Validate all additional mounts for a group.
+ * Returns array of validated mounts (only those that passed validation).
+ * Logs warnings for rejected mounts.
+ */
+export function validateAdditionalMounts(
+  mounts: AdditionalMount[],
+  groupName: string,
+): Array<{
+  hostPath: string;
+  containerPath: string;
+  readonly: boolean;
+}> {
+  const validatedMounts: Array<{
+    hostPath: string;
+    containerPath: string;
+    readonly: boolean;
+  }> = [];
+
+  for (const mount of mounts) {
+    const result = validateMount(mount);
+
+    if (result.allowed) {
+      validatedMounts.push({
+        hostPath: result.realHostPath!,
+        containerPath: `/workspace/extra/${result.resolvedContainerPath}`,
+        readonly: result.effectiveReadonly!,
+      });
+
+      log.debug('Mount validated successfully', {
+        group: groupName,
+        hostPath: result.realHostPath,
+        containerPath: result.resolvedContainerPath,
+        readonly: result.effectiveReadonly,
+        reason: result.reason,
+      });
+    } else {
+      log.warn('Additional mount REJECTED', {
+        group: groupName,
+        requestedPath: mount.hostPath,
+        containerPath: mount.containerPath,
+        reason: result.reason,
+      });
+    }
+  }
+
+  return validatedMounts;
+}
+
+/**
+ * Generate a template allowlist file for users to customize
+ */
+export function generateAllowlistTemplate(): string {
+  const template: MountAllowlist = {
+    allowedRoots: [
+      {
+        path: '~/projects',
+        allowReadWrite: true,
+        description: 'Development projects',
+      },
+      {
+        path: '~/repos',
+        allowReadWrite: true,
+        description: 'Git repositories',
+      },
+      {
+        path: '~/Documents/work',
+        allowReadWrite: false,
+        description: 'Work documents (read-only)',
+      },
+    ],
+    blockedPatterns: [
+      // Additional patterns beyond defaults
+      'password',
+      'secret',
+      'token',
+    ],
+  };
+
+  return JSON.stringify(template, null, 2);
+}

src/modules/typing/index.ts

@@ -0,0 +1,165 @@
+/**
+ * Typing indicator refresh — default module.
+ *
+ * Most platforms expire a typing indicator after 5–10s, so a one-shot
+ * call on message arrival goes stale long before the agent finishes
+ * thinking. This module keeps it alive by re-firing `setTyping` on a
+ * short interval — but only while the agent is actually WORKING, gated
+ * on the heartbeat file's mtime after an initial grace period.
+ *
+ * After delivering a user-facing message, the refresh is paused for
+ * POST_DELIVERY_PAUSE_MS so the client-side indicator can visually
+ * clear.
+ *
+ * Default module status:
+ *   - Lives in src/modules/ for signaling (not really core), but ships
+ *     on main and is imported directly by core. No registry, no hook.
+ *   - Removing requires editing src/router.ts, src/delivery.ts, and
+ *     src/container-runner.ts to drop the calls.
+ */
+import fs from 'fs';
+
+import { heartbeatPath } from '../../session-manager.js';
+
+const TYPING_REFRESH_MS = 4000;
+/**
+ * Grace window from startTypingRefresh: fire typing unconditionally
+ * for this long regardless of heartbeat state. Covers container
+ * spawn/wake latency (5–12s on cold start before first heartbeat).
+ */
+const TYPING_GRACE_MS = 15000;
+/**
+ * After the grace window, a heartbeat must be mtimed within this
+ * many ms of now to count as "agent is working." Heartbeats land
+ * every few hundred ms during active work, so 6s is well above
+ * the working floor and small enough to stop typing quickly when
+ * the agent goes idle.
+ */
+const HEARTBEAT_FRESH_MS = 6000;
+/**
+ * After we deliver a user-facing message, pause typing for this
+ * long so the client-side indicator has time to visually clear.
+ * Tuned for the longest common expiry (Discord ~10s). The interval
+ * stays running; ticks inside the pause just skip the setTyping call.
+ */
+const POST_DELIVERY_PAUSE_MS = 10000;
+
+interface TypingAdapter {
+  setTyping?(channelType: string, platformId: string, threadId: string | null): Promise<void>;
+}
+
+interface TypingTarget {
+  agentGroupId: string;
+  channelType: string;
+  platformId: string;
+  threadId: string | null;
+  interval: NodeJS.Timeout;
+  startedAt: number;
+  pausedUntil: number; // epoch ms; 0 = not paused
+}
+
+let adapter: TypingAdapter | null = null;
+const typingRefreshers = new Map<string, TypingTarget>();
+
+/**
+ * Bind the typing module to the channel delivery adapter so it can
+ * call `setTyping`. Called once by `src/delivery.ts` inside
+ * `setDeliveryAdapter`. Passing a fresh adapter replaces the prior
+ * binding and leaves active refreshers in place (they'll use the
+ * new adapter on their next tick).
+ */
+export function setTypingAdapter(a: TypingAdapter): void {
+  adapter = a;
+}
+
+async function triggerTyping(channelType: string, platformId: string, threadId: string | null): Promise<void> {
+  try {
+    await adapter?.setTyping?.(channelType, platformId, threadId);
+  } catch {
+    // Typing is best-effort — don't let it fail delivery or routing.
+  }
+}
+
+function isHeartbeatFresh(agentGroupId: string, sessionId: string): boolean {
+  const hbPath = heartbeatPath(agentGroupId, sessionId);
+  try {
+    const stat = fs.statSync(hbPath);
+    return Date.now() - stat.mtimeMs < HEARTBEAT_FRESH_MS;
+  } catch {
+    return false;
+  }
+}
+
+export function startTypingRefresh(
+  sessionId: string,
+  agentGroupId: string,
+  channelType: string,
+  platformId: string,
+  threadId: string | null,
+): void {
+  const existing = typingRefreshers.get(sessionId);
+  if (existing) {
+    // Already refreshing. Fire an immediate tick for the new inbound
+    // event and reset the grace window — the new message restarts
+    // the container-wake latency budget. Also clear any lingering
+    // post-delivery pause: a new inbound means the user expects
+    // typing to show immediately.
+    triggerTyping(channelType, platformId, threadId).catch(() => {});
+    existing.startedAt = Date.now();
+    existing.pausedUntil = 0;
+    return;
+  }
+
+  // Immediate tick + periodic refresh.
+  triggerTyping(channelType, platformId, threadId).catch(() => {});
+  const startedAt = Date.now();
+  const interval = setInterval(() => {
+    const entry = typingRefreshers.get(sessionId);
+    if (!entry) return; // stopped externally since this tick was scheduled
+
+    // Inside a post-delivery pause: skip setTyping but keep the
+    // interval running so we resume automatically once the pause
+    // expires.
+    if (entry.pausedUntil > Date.now()) return;
+
+    const withinGrace = Date.now() - entry.startedAt < TYPING_GRACE_MS;
+    if (withinGrace || isHeartbeatFresh(entry.agentGroupId, sessionId)) {
+      triggerTyping(entry.channelType, entry.platformId, entry.threadId).catch(() => {});
+      return;
+    }
+
+    // Out of grace AND heartbeat stale — agent is idle, stop refreshing.
+    clearInterval(entry.interval);
+    typingRefreshers.delete(sessionId);
+  }, TYPING_REFRESH_MS);
+  // unref so a stale refresher can't hold the event loop alive.
+  interval.unref();
+  typingRefreshers.set(sessionId, {
+    agentGroupId,
+    channelType,
+    platformId,
+    threadId,
+    interval,
+    startedAt,
+    pausedUntil: 0,
+  });
+}
+
+/**
+ * Pause the typing refresh for POST_DELIVERY_PAUSE_MS. Called after
+ * a user-facing message is delivered so the client-side indicator
+ * has a chance to visually clear before the agent's next SDK event
+ * pushes it back on. No-op if no refresh is active for this session.
+ */
+export function pauseTypingRefreshAfterDelivery(sessionId: string): void {
+  const entry = typingRefreshers.get(sessionId);
+  if (!entry) return;
+  entry.pausedUntil = Date.now() + POST_DELIVERY_PAUSE_MS;
+}
+
+export function stopTypingRefresh(sessionId: string): void {
+  const entry = typingRefreshers.get(sessionId);
+  if (!entry) return;
+  clearInterval(entry.interval);
+  typingRefreshers.delete(sessionId);
+}