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VisualStudio writes the UTF-8 BOM at the start of the csproj files. MonoDevelop does not. If MonoDevelop is saving a file that when it opened had a BOM, it should persist that BOM back to the file. This is a constant problem with diffs across VS and MD in our team.
Effectively the same problem as bug 2612.
The attached is a daily problem for us in reviews and git fighting, showing both the boolean serialization issue and the BOM issue.
Created attachment 1201 [details]
Diff in Review Board showing constant VS/MD fighting with BOM and boolean serialization differences.
fixed in git master