When runing M-x esup, a new emacs instance opens a frame and prompts me “Symbolic link to Git-controlled source file; follow link? (yes or no) ”.
This is because ~/.emacs.d is a symbolic link to ~/configfiles/config/emacs/, which lives inside a Git repository.
Interestingly enough, this also happens when evaluating (esup "/home/michael/configfiles/config/emacs/init.el") in the *scratch* buffer, at which point I would have expected the prompt to no longer show as the ~/.emacs.d symlink should no longer be involved.
I found a workaround, but it’s quite a big hammer: placing (setq vc-follow-symlinks t) in /etc/emacs/site-start.el