re: missing files in the .../docs - I forgot to check those in sorry!.
re: incompletely transformed: these are transformed using the script build-ip-clearances.xml (ant script) at the top level of the uima-website svn trunk checkout. I too noticed that some of the images didn't appear.
(Don't use the build.xml to "transform" these - this picks up the wrong setup - the build-ip-clearnaces script (at one point) picked up the setup used by the incubator to build these pages for the incubator. I'd guess they could be a bit out of date.)
re: mentioning the Darmstadt CCLA - I only mentioned the Colorado CCLA (in the section of the IP clearance doc that asks for refs to the "Software Grant", because the software grant from Colorado was not done separately, but rather as part of the CCLA. So, in this section I don't think we need to reference other CCLAs.