Cache folders are being generated in the output folder. This wasn't happening with earlier releases, and I believe it is a bug.
OSX 10.8 Mountain Lion; phpDoc 2.0.0b4

Have you specified a different folder in the configuration file? If not, this is to be expected.
@boenrobot thanks - I tried finding information on this, but wasn't able to. Which configuration setting should I be looking for?
It's the "/phpdoc/parser/target" element. See this page for an example configuration file.
The docs are somewhat out of date currently, as they still reference "structure.xml" - since b1, "structure.xml" is replaced with the "phpdoc-cache-*" stuff, and structure.xml is instead only generated later (by the Transformer) when a template says it needs it.
Ah, okay - I just upgraded from a12 and hadn't seen this before and the other bugs surrounding packages and namespaces made me think this was another bug.
Thanks for your help.
phpdocumentor
-parser
--target CACHE-DIR
My full command
phpdoc -d PROJECT_DIR -t DOCS_DIR --ignore "/dir1/,/dir2/" --cache-folder CACHE_DIR
use option "--cache-folder CACHE_DIR"
Most helpful comment
My full command
use option "--cache-folder CACHE_DIR"