test: stage only declared fixture paths in repo fixture commits #328

Summary

The new repo fixture builder currently commits fixture changes with git add --all inside the temporary fixture repository.

That is acceptable for the first slice because the fixture root is isolated and path escapes are rejected, but it is still a broad staging primitive. Future fixture tests would be more precise if commits staged only the paths declared by prior fixture operations.

Why

A canonical fixture builder should make repository stories explicit. Broad staging can accidentally hide undeclared generated files or helper artifacts inside a fixture, especially once fuzz/stress overlays arrive.

Scope

• Track changed fixture-relative paths produced by withFile, deleteFile, and chmod operations.
• Stage only those paths during commit().
• Preserve support for intentional whole-repo commits only via an explicit option if needed.
• Keep path escape checks and temp repo isolation intact.
• Add regression coverage proving an undeclared untracked file inside the fixture root is not silently committed.

Acceptance Criteria

• Fixture commits no longer use broad git add --all by default.
• Tests prove undeclared files remain untracked unless explicitly added by builder operations.
• Existing fixture-builder self-tests stay green.

Related

• test: build canonical repo fixture builder with base repos and overlays #311
• test: migrate repo-shaped suites onto the canonical repo fixture builder #316
• PR Add canonical repo fixture builder #327