[chore: benchmark-sync] update scanning logic and prevent filename collision

[beginwebdev2002]

Updated vibe-check-runner.js to run both git log and git ls-files to gather modified/untracked files. Appended the filepath to the temporary source file name to prevent conflicts during AST generation when iterating over multiple files.

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PR created automatically by Jules for task 16185492505760596598 started by @beginwebdev2002

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