(This is technically not a bug, but more a generic issue)
The new stiched texture feature places the resulting files directly in the home directory on Linux (or at least Ubuntu).
Steps to reproduce:
1) Start Minecraft 13w02a/b
2) Open a world (I'm not 100% sure if this is necessary)
3) Close Minecraft
4) Open a Terminal and run ls on your home directory.
The texture files would be tucked away in the .minecraft folder, and/or deleted after Minecraft exited.
What actually happened:
stitched_terrain.png and stitched_items.png were in my home folder.
I know that this isn't actually a bug, and more of an improvement, but this is a bit annoying.
Run the launcher from a terminal, in (for example) the .minecraft directory.
"path_to_minecraft_jar" (for me, this was ./minecraft.jar because that's where I put the launcher)