I have a question regarding how to set up Eclipse to develop Cytoscape
plug-ins.  I've followed the directions in the tutorial here:
http://csresources.sourceforge.net/docs/eclipse.html.  I know this is
from 2005 but I can't find any other relevant documentation.

I have set up everything as the tutorial says and the plug-in loads
and is accessible in Cytoscape, but I think it is only reading the jar
file in the plug-ins directory and not my source code in eclipse.
(The tutorial instructs to put a copy of the jar file in the plug-ins
directory so Cytoscape will "know it is there", but that it will
actually use the source code being developed in Eclipse)  I’ve tried
to test this by changing menu titles and adding debugging print
statements, but these do not appear when executing the plugin through
eclipse—only the original version of the plug-in (the jar in the plug-
ins directory supplied as an argument) seems to be running despite
changes.