Issue for this PR

N/A

Type of change

• Bug fix
• New feature
• Refactor / code improvement
• Documentation

What does this PR do?

Moves ten more core tests from manual defaultLayer composition to the node graph system.

• Uses LayerNode.compile(...) for direct global service test environments.
• Uses AppNodeBuilder.build(...) for app/location-scoped graphs.
• Keeps directly-yielded transitive services as explicit graph roots.
• Binds synthetic Location.node implementations in location-focused tests instead of composing ad hoc default layers.
• Uses LayerNode.replace(...) for test-specific layer overrides.

How did you verify your code works?

• bun test "test/ripgrep.test.ts" "test/filesystem/search.test.ts" "test/git.test.ts" "test/effect/cross-spawn-spawner.test.ts" "test/integration.test.ts" "test/location-filesystem.test.ts" "test/location-mutation.test.ts" "test/skill.test.ts" "test/plugin/skill.test.ts" "test/system-context/builtins.test.ts" in packages/core
• bun typecheck in packages/core
• Pre-push bun turbo typecheck

Screenshots / recordings

N/A - no UI changes.

Checklist

• I have tested my changes locally
• I have not included unrelated changes in this PR

If you do not follow this template your PR will be automatically rejected.