All Cytoscape code is available under an open source license. See this
page for how to check it out from our public repository:
http://www.cytoscape.org/documentation_developers.html
If you are developing a plugin for Cytoscape 2.8+, all you need is the
cytoscape.jar file that comes with the distribution (i.e., when you
install the latest release). If you (for some reason) are developing
for an older version of Cytoscape, you can find all the jars in the
lib folder, again, in the distributed installation.
- Alex