#1150 fix: Improve Unity reload recovery and skill setup reliability

Summary

• Unity reload and restart recovery now avoids waiting synchronously for dynamic-code runtime shutdown.
• Skill setup defaults to the flat folder layout, and runtime/test assemblies stay out of player builds.

User Impact

• Unity is less likely to freeze when a domain reload starts while the editor-side server or dynamic-code runtime is still active.
• Agents get the expected flat skill layout by default, reducing setup confusion across CLI targets.
• Player builds avoid pulling in runtime test and demo assemblies.

Changes

• Moves domain reload shutdown into the v3 server lifecycle and readiness flow, with non-blocking runtime shutdown signaling.
• Keeps the bridge server stop path from disposing the whole server instance during reload recovery.
• Updates skill target installation defaults and regenerates native CLI binaries.
• Excludes demo and runtime test assemblies from player builds and covers the assembly boundaries with focused tests.

Verification

• Packages/src/Cli~/dist/darwin-arm64/uloop compile --project-path /Users/a12115/ghq/hatayama/unity-cli-loop
• Unity EditMode focused tests: 127 passed, 0 failed
• Unity OnionAssemblyDependencyTests: 80 passed, 0 failed
• scripts/check-go-cli.sh
• codex-review v3-beta: no accepted/actionable findings