Issue for this PR

N/A

Type of change

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

What does this PR do?

Moves several core tests from hand-written defaultLayer composition to the new app node graph builder.

• Converts project, project directory, question, session projector, and session todo tests to use AppNodeBuilder.build(...) where appropriate.
• Keeps direct test dependencies explicit by adding dependency nodes as graph roots when tests yield those services directly.
• Replaces the manual SessionV2.layer setup in the session projector test with a node graph that binds SessionExecution.node to a noop execution node.
• Renames app node builder usage to AppNodeBuilder.build(...) for clarity.
• Leaves specialized local layer overrides in place where tests intentionally exercise a narrow layer boundary.

How did you verify your code works?

• bun typecheck in packages/core
• bun test test/project.test.ts test/project-directories.test.ts test/question.test.ts test/session-projector.test.ts test/session-todo.test.ts in packages/core

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.