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I have a git repository that is normalised to LF line endings and I have the following:
# Attempt auto-detection of text files, as a fail-safe measure.
# Normal text files with conversion for CRLF to LF.
*.cs text merge=csharp
*.csproj text merge=union
*.sln text eol=crlf merge=union
*.xml text merge=union
# Binary files that should not be converted
however MonoDevelop does not convert the checked out files to CRLF line endings on Windows - instead keeping the line endings LF.
MonoDevelop also fails to convert text file's CRLF line endings back to LF on commit (resulting on a diff with the entire document deleted and added back with different line endings - instead of just showing the change).
I have verified that msysgit does behave as expected (and that core.autocrlf is NOT set).
This is a known issue. It will be fixed when we switch to libgit2sharp as our git provider.
*** This bug has been marked as a duplicate of bug 3675 ***