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/db/connection.ts

@@ -31,3 +31,18 @@ export function closeDb(): void {
   _db?.close();
   _db = null;
 }
+
+/**
+ * Check whether a table exists. Used by core code that touches
+ * module-owned tables so that an uninstalled module degrades silently
+ * instead of raising SQLite errors. Cheap: a single indexed lookup on
+ * sqlite_master. Results are not cached — a module install adds the
+ * table at runtime (next service start), and callers may run before
+ * or after that boundary.
+ */
+export function hasTable(db: Database.Database, name: string): boolean {
+  const row = db.prepare(`SELECT 1 FROM sqlite_master WHERE type='table' AND name = ? LIMIT 1`).get(name) as
+    | { '1': number }
+    | undefined;
+  return row !== undefined;
+}

src/db/migrations/index.ts

@@ -32,29 +32,34 @@ export function runMigrations(db: Database.Database): void {
       name    TEXT NOT NULL,
       applied TEXT NOT NULL
     );
+    CREATE UNIQUE INDEX IF NOT EXISTS idx_schema_version_name ON schema_version(name);
   `);
 
-  const currentVersion =
-    (db.prepare('SELECT MAX(version) as v FROM schema_version').get() as { v: number | null })?.v ?? 0;
-
-  const pending = migrations.filter((m) => m.version > currentVersion);
+  // Uniqueness is keyed on `name`, not `version`. This lets module
+  // migrations (added later by install skills) pick arbitrary version
+  // numbers without coordinating across modules. `version` stays on
+  // the Migration object as an ordering hint within the barrel array;
+  // the stored `version` column is auto-assigned at insert time as an
+  // applied-order number.
+  const applied = new Set<string>(
+    (db.prepare('SELECT name FROM schema_version').all() as { name: string }[]).map((r) => r.name),
+  );
+  const pending = migrations.filter((m) => !applied.has(m.name));
   if (pending.length === 0) return;
 
-  log.info('Running migrations', {
-    from: currentVersion,
-    to: pending[pending.length - 1].version,
-    count: pending.length,
-  });
+  log.info('Running migrations', { count: pending.length });
 
   for (const m of pending) {
     db.transaction(() => {
       m.up(db);
+      const next =
+        (db.prepare('SELECT COALESCE(MAX(version), 0) + 1 AS v FROM schema_version').get() as { v: number }).v;
       db.prepare('INSERT INTO schema_version (version, name, applied) VALUES (?, ?, ?)').run(
-        m.version,
+        next,
         m.name,
         new Date().toISOString(),
       );
     })();
-    log.info('Migration applied', { version: m.version, name: m.name });
+    log.info('Migration applied', { name: m.name });
   }
 }