Simple items

Can I just put a .pk3 into my data directory for this? I don't want to have to replace anything in the data.pk3 folder.

I'll quote my own post from earlier in this thread. It is NOT needed to remove or change anything in the original data pk3s. You can build a "plug-and-play" package for simple items by having empty files with the same path as the original dds files you want the engine to ignore. An empty file in a pk3 loaded after any other file will discard that file from the engine's filesystem.

Oh, if dds priority is the issue, here's how you can fix it, nifrek: Just have an empty .dds file at the right path (next to the .tga). By empty I mean completely empty, not even a linebreak. That way, the engine will discard the file from the original data pk3 when loading this new pk3 and use the tga instead.

EDIT: Put the attached file in your personal data directory (~/.xonotic/data in *NIX, My Saved Games\Xonotic\data or something like that in Windows)
EDIT2: K__, take note, this is much easier to maintain, there's no risk of forgetting an uncompressed file somewhere since it's all bundled together. No mess and easy to undo.
EDIT3: Please tell me if that doesn't work, I assumed only dds/*.dds files got in the way, there seems to be some duplication (or rather symlinking) going on in the PK3 but I'm working off git and have no means to test dds.