Today in a bright moment I felt I’d better use the functions.php file and add it to the aggregated-theme.

My new convention

A mu-plugin should be a plugin for adding functionality which needs to be available for all, or at least a lot of blogs.

The functions.php file includes functions which are related to a specific blog.

So adding extra functionality to the aggregated-theme should be done by functions.php instead of mu-plugins.

Apparently one of my plugins was outputting an extra couple lines of non-php at the end of the file.

I found this solution:

• With plugins, extra lines after the php-end seems to be the source of the problem

I tweaked my plugins and now the issue seems to be solved. Great!

Might not be an issue for WordPress, maybe only WordPress MU.

Note: this fix is also needed for all files included in the theme of course!