Git mergetool generates unwanted .orig files

A possible solution from git config:

git config --global mergetool.keepBackup false

After performing a merge, the original file with conflict markers can be saved as a file with a .orig extension.
If this variable is set to false then this file is not preserved.
Defaults to true (i.e. keep the backup files).

The alternative being not adding or ignoring those files, as suggested in this gitguru article,

git mergetool saves the merge-conflict version of the file with a “.orig” suffix.
Make sure to delete it before adding and committing the merge or add *.orig to your .gitignore.

Berik suggests in the comments to use:

find . -name \*.orig 
find . -name \*.orig -delete

Charles Bailey advises in his answer to be aware of internal diff tool settings which could also generate those backup files, no matter what git settings are.

• kdiff3 has its own settings (see "Directory merge" in its manual).
• other tools like WinMerge can have their own backup file extension (WinMerge: .bak, as mentioned in its manual).

So you need to reset those settings as well.

You have to be a little careful with using kdiff3 as while git mergetool can be configured to save a .orig file during merging, the default behaviour for kdiff3 is to also save a .orig backup file independently of git mergetool.

You have to make sure that mergetool backup is off:

git config --global mergetool.keepBackup false

and also that kdiff3's settings are set to not create a backup:

Configure/Options => Directory Merge => Backup Files (*.orig)

Or just add

*.orig

to your global gitignore

If you're working on a Windows machine - you can turn off backups with this command

git config --global mergetool.keepBackup false

If you don't want to do that, you can easily delete all the .orig files using this powershell command

ls -Recurse C:\path\to\repository\*.orig | rm