These are the steps I used to get the PalmPilot Software running under Linux.
configure --prefix=/usr/local/pilot\ --mandir=/usr/local/man\ --with-java=/usr/lib/java
I used the --with-java option to get configure to run cleanly, but it doesn't appear to cause the Java bindings to be built automatically. Without this option there was an error from the configure script when it tried to find the standard Java libraries. I didn't try building the Java tools in the pilot-link package.
PATH=$PATH:/usr/local/pilot/bin export PATH
pilot-xfer /dev/cua1 -l