Transform Permanently
This page should give a simple explanation of the Transform Permananetly command... work in progress, feel free to add.
shunted from the beginner faq:
When you're trying to rotate a brush and it doesn't want to, it just changes shape as you try to rotate it, this is what to do.
Brush Context Menu → Transform → Transform Permanently
Also use Transform Permanently on brushes which you've scaled, etc.
Alignment
Align the textures *after* you used transform permanently, since it will reset your brush completely, including the alignments of the textures. Try to use it while you're finishing your map, and only if you're positive you won't change the brush anymore.
