My ~/.mrconfig is simply a long list of sections like

[code/somename]
checkout = git clone someurl somename

In my $HOME I have a softlink code that links to a data partition ('/storage/code. In this setup mr up complains mr update: no repositories found to work on. If I remove the softlink and run mr up, it works as expected (as in, it creates a directory ~/code and starts cloning the now missing repos).

mr version 1.20180726 on FreeBSD 14.1-p2