Halting upgrade because of some files/directories being present

I would appreciate if NC abandoned the idea of stopping the upgrade just because some file or directory is in the root directory, or the tree, that isn’t expected to be there by NC.

We use ISPconfig and with that comes the “stats” and “error” directory and every time I try to upgrade NC it halts because of that those directories are there.

We also have our own directory structure that we place in core/skeleton so that every use gets access to the directories and files we have there. The way the NC installer works now is that it halts when it doesn’t recognize files or directories and files in the directory tree. This is quite annoying.

Now upgrading to 20.0.1 it stopped again, first at the stats and error directories created by ISPconfig, and then after I deleted those, at “Delete old files”.

Why does it have to be this way?

If it absolutely has to be this way, then why not during the installation let the installation script ask for an exclusion list for files and directories that are ok to be in the tree of files and directories, or just ask per file if it should remain or be deleted.

Is there perhaps an existing workaround for this, except downloading all of it and run the update from the command line?