This is why I'd suggested a project classpath of
WT_HOME/codebase (or a jar form thereof)
WT_HOME/codebase/WEB-INF/lib/*.jar
WT_HOME/lib/*.jar
That should suffice for any server-side development.
Now if you're talking about developing a remote Java client, however,
then that's different. Then you could do something like:
WT_HOME/codebase (or a jar form thereof)
and then possibly add additional jars as needed, e.g.:
WT_HOME/codebase/wt/security/security.jar
WT_HOME/codebase/lib/WtHttpClientAddOns.jar
Instead you might reference specific existing client jars, e.g.:
WT_HOME/codebase/wtApplet*.jar
WT_HOME/codebase/ptcCore*.jar
and thus keep track specifically of which jars your client will directly
need (there may be indirect runtime dependencies, of course) to run.
For most cases, however, you're talking about server-side development
and things are quite simple.