file locations are embedded in the program's source code, thus the programmer's choice. Complain to them. Better yet, submit patches to the projects.
Originally Posted by t.s.
With open source apps, the distributions should be able to change it, but that's a lot of work if you're bundling hundreds of apps (both for the initial changes and for maintaining the changes on newer versions). Thus nobody does it for only little benefit. The solution is to get patches upstream.
Where 'little benefit' means:
and I still live and am in no way constricted by their presence in my daily tasks.
~> ls -A1 ~ | grep '^\.' | wc -l