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Is it possible that the "Open With ..." function opens the commit file and not the working directory file.
The steps performed by the SourceGit software would be:
creation of the file (like the Save As of the same menu) but in a temporary folder of the system
opening of the temporary file with default software (like the current Open With)
The name of the temporary file could be name~sha1.ext
example to open the file README.md from commit 67cf232
name of the temporary file: README~67cf23267.md