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[include-cleaner] Fix a race issue when editing multiple files. (#76960)
We have a previous fix be861b6, which snapshots all processing files. It works most of times, the snapshot (InMemoryFileSystem) is based on the file path. The file-path-based lookup can fail in a subtle way for some tricky cases (we encounter it internally), which will result in reading a corrupted file. This is a different fix, we don't modify files on the fly, instead, we write files when the tool finishes for all files.
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