[horde] Modifying files -- best practice?

[Tim Streit]

Greetings,

I'm just going through and doing some themeing, and I'm wondering what is best practice to customize some files.   

-Themes -- no prob.  Create a new theme.
-Templates -- ??   For example, most files are using PNG files, I'd rather use SVG - personal preference.  I can modify some files to use this, but I assume next update will undo my work.
-/imp/lib/Flag/Imap# vim Deleted.php  -  this is an example of something small-- I want to change the color of an email marked as deleted.  

I know on config files, we insert '.local' into the name and put the changes there, and it works.  Is this the same for ALL php files?    Looking for some insight.

Thanks,