To avoid data loss, Syncthing creates a temporary file during transfer
with the name ~syncthing~.{filename}.tmp

If the transfer completes successfully, then it moves that file in place
of the previous version. It's a new inode, not an update of the previous
inode, so the hard link will be lost.

Instead of using hard links, you could share your git repo folder
directly using Syncthing, but use an .stignore file to exclude the files
that you want to keep private (such as the .git directory).

https://docs.syncthing.net/users/ignoring.html

-Tim


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