As part of packaging Gephi for Debian/Ubuntu, I've found that some files in Flamingo 4.2 are missing a license header. The Flamingo 5.0 release actually still has one license header missing, but I've got an email from the author confirming that it's licensed under the BSD license. He doesn't support the project any more, and 5.0 was deemed to be the stable release.
Ideally Gephi should be updated to use Flamingo 5.0 which you can get from https://flamingo.dev.java.net/servlets/ProjectDocumentList?folderID=11909
The package names have changed, but other than that I didn't need to make any source changes. The Debian/Ubuntu version will use Flamingo 5.0, and it would be easier if the main release could follow suit at some point, maybe before the first 0.9 release?
I update the lib to Flamingo 5, seems to work properly. No source change indeed :-)