fix: scope source analysis to mapped output roots

[shblue21]

Summary

• Keep Java source and source-folder analysis scoped to mapped output roots.
• Align TypeScript target resolution and the Java runner around sourcepath-aware loose class mapping.
• Preserve archive/direct bytecode handling while reducing duplicate resolver tests.

Test Plan

• npm run compile && npm run test:l1:unit
• npm run test:unit
• npm run lint
• git diff --check