The easiest way to create a patch is described here:
http://wordpress.org/download/svn/
Can I create patches from older
version or must I use trunk?
You should create the patch against the same version you want it applied against.
In other words, don’t expect a patch created against WP 3.0.1 to apply cleanly on WP 3.1-alpha.
If I’m working on a project using the released version (3.0.1) can I modify it and create a patch for core or do I have to download and set up a pristine and new copy of trunk and newly make my modifications there?
You don’t have to set up a new installation for each new patch. You can just use svn revert to get back to a pristine copy.
Also, the database doesn’t have to be clean each time. Actually, it’s better if you have some modifications, to simulate a live environment.
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