The base.xml file contains the intelligence for the xslt PDF output sheets and is the first file processed before passing it's output to the final selected xslt sheet. The primary base.xml file can be found at the root of the outputsheets directory.
*** New 5.10
Mutiple gameMode specific base.xml files are now supported. If a base.xml file is found in the root gameMode directory that file will be used for xslt output. If no base.xml file is found in the gameMode directory PCGen will default to the standard file found in the outputsheets directory.