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External diff tool cmd shows \r\n and does not launch

For some strange reason, the external diff in Sourcetree stopped working after recent upgrade (I want to use Beyond Compare). Here is the process viewer log:

"Command": "git\r\n-c diff.mnemonicprefix=false -c core.quotepath=false --no-optional-locks -c credential.helper= -c credential.helper=\"C:/Users/<username>/AppData/Local/ATLASS~1/SOURCE~1/GIT_EX~1/GIT-CR~1.EXE\" difftool -y --tool=sourcetree --\r\nfilename.xml",
"Directory": "C:\\Users\\<Username>\\Project",
"Status": "Finished",
"Duration": "00:00:01.1855150",
"CallerContext": "GetExternalDiffProcess",
"Output": "Unknown merge tool sourcetree\nfatal: external diff died, stopping at <ProjectDir>/filename.xml\n"

As you can see, the git command contains "\r\n" in the command line. The git command with this "\r\n" does not work even in the terminal. If I remove "\r\n" from the command line and paste the command in terminal, it works fine. I am suspecting this "\r\n" to be a source of the problem, but I have no idea where it's coming from.

At the end, the log shows an error message about merge tool. I don't understand what that means. Here is my .gitconfig file.

autocrlf = true
name = My name
email =
tool = bc3
[difftool "bc3"]
path = "c:\\Program Files (x86)\\Beyond Compare 3\\Bcompare.exe"
trustExitCode = true

I am using Windows 10, 1809.

Can someone help?

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