These represent "known problems". In some cases, they represent a temporary problem that will be synched up at the point of the next release, in other cases they may represent an abject failure to communicate.
At the moment, the taglibs builds require the presence of xalan1. Xalan1's last release was in August of 2000. It has been removed from cvs, and even the backwards compatibility support has been removed from Xalan2. Xalan1 is not compatible with Xerces2. While I would recommend letting go of the Xalan1 support, at a minimum, this dependency needs to be made optional during compilation.
These represent versioning issues that will not show up in any Gump run, but you may need to be aware.
Based on inspection, I don't believe that turbine-2 and turbine-3 can coexist in a classpath. The jakarta-jetspeed, jakarta-turbine-jyve, and jakarta-turbine-orgami projects depend on turbine-2. The jakarta-turbine-flux project depends on turbine-3.
The combination of Texen, Ant 1.4 or later, and placing jars on your classpath can result in unexpected behavior. This has been isolated to a standalone test case and being investigated by the Ant development team. Meanwhile, an undocumented attribute, reverseloader, which when set to the value "true" on taskdefs which defines texen may help.
This section describes cross project compatibility issues which were:
October 2001: The Xalan team is in the process of changing an undocumented API that dbXML used. The dbXML team determined that the reason that they were using that undocumented API no longer applies. This was corrected after the second beta of dbXML - meaning that the users of their next release will be able to upgrade smoothly to Xalan 2.2 once it is released.
September 2001: in order to more closely resemble the JSR 47 API, the Level class replaced the Priority class, and the Logger class replaced the Category class. This was originally done in a manner which was thought to be backwards compatible, but there was subtle reasons why this was not the case.
December 2001: a manifest task was added to Ant which collided with the manifest task contained within xml-fop. What followed was the most impressive cooperation between projects I have ever witnessed. The fop project removed their manifest task, and the Ant project changed their code so that the manifest task that fop previous had would have overridden the one provided with Ant.