fix(instance): run bootstrap from instance store

[kitlangton]

Summary

• Move instance bootstrap into InstanceStore.boot so every load/reload path runs plugins and core initialization before exposing the instance.
• Split the bootstrap service tag from its implementation to avoid importing the app bootstrap graph from low-level store code.
• Add regression coverage for the boundary invariant and plugin-registered agents.

Fixes #25450

Tests

• bun typecheck
• bun run test test/project/instance-bootstrap-regression.test.ts test/agent/plugin-agent-regression.test.ts test/project/instance.test.ts
• bun run test test/server/httpapi-instance-context.test.ts
• bun run test test/plugin/trigger.test.ts
• push hook: bun turbo typecheck