Eclipse in the ports is the 3.1 branch. The phpeclipse port installs a version (1.1.4) that is meant for use with the 3.0 branch. I have an updated Makefile and pkg-plist for the latest stable release 1.1.7.
I can mail the updated files to a commiter.
Java ports are still 'ports'; only problems with the JRE go into 'java'.
Here are said patches.
Superseded by ports/95399