runtime-bootstrap-and-test-isolation

Activate this skill when adding a new manager, adding a new tool category, writing or debugging tool unit tests, diagnosing tool-visibility failures, investigating startup performance, or extending/maintaining/debugging the two-tier tool discovery system (tool_index) — even if the user doesn't explicitly ask about the runtime architecture or "tool discovery." Covers: (1) the four-stage bootstrap sequence and which layer owns which changes, (2) adding a new manager via @lru_cache singleton factories in runtime.py, (3) the three-stage decorator replacement system that enables test isolation without a live controller, (4) lazy loading mechanics and tools_manifest.json regeneration that controls which tool categories are visible, (5) the permission model's two safety axes, and (6) the two-tier tool_index discovery layer: the FastMCP named-param wrapper vs. the silent args: dict trap, compact-vs-full schema tiers (include_schemas), Worker cloud parity, and SKILL.md runtime manifest sync.