fix: thread real project_root into VerificationEngine from pipeline/autofix

[omsherikar]

Problem

RefactronPipeline carries a correct project_root, but AutoFixEngine.fix_file() always constructs VerificationEngine(project_root=file_path.parent) (refactron/autofix/engine.py). That breaks monorepos and any layout where tests or config live above the edited file.

Impact

• TestSuiteGate._find_relevant_tests searches from the wrong root when callers do not pass an explicit root.
• Behavior diverges from refactron verify --project-root, which already accepts a root.

Suggested direction

• Add an optional project_root: Optional[Path] to fix_file() (default: derive from file, or walk to VCS root).
• Have RefactronPipeline.apply() pass self.project_root into fix_file.
• Add/adjust tests so verification uses the pipeline root, not only file_path.parent.

References

• refactron/autofix/engine.py (verification block)
• refactron/core/pipeline.py (apply → fix_file)