Dev watcher misses routes created inside a previously absent nested directory

[ScriptedAlchemy]

Reproduction

While running agent-bundle dev --install-host claude --install-host codex for examples/audiobook-curator on main b435f7b917:

1. The project had no src/events/ directory; the adopted manifest had no hook executables.
2. Create src/events/session/start.ts with a valid standalone sessionStart event route.
3. Wait >15 seconds. The adopted epoch and manifest do not change; no hook document/executable is emitted.
4. Stop and restart the same dev command. The first build immediately emits both Claude and Codex sessionStart hook executables and hooks.json.

The watcher sees edits to known inputs but does not discover a new route under a previously absent nested directory.

Acceptance

• Start the foreground dev server with no src/events/ directory.
• Create src/events/session/start.ts (including the missing parent directories).
• The watcher publishes a new epoch containing the event route and its host bindings without restarting.
• Deleting that route publishes another epoch with the generated hook output removed, without touching unrelated routes.
• Cover at least one other route root that can be absent initially (for example src/mcp/<server>/tools) through the same discovery mechanism; do not add route-kind-specific watchers.

Related: #652 shared-content add/delete acceptance, #683 native host proof.