I also ran into this problem.
IClasspathEntry of kind CPE_PROJECT is not handled.
I added a switch-case for this which iterates over the dependent projects recursively and adds their output path(s) and their library dependencies, but not their source folders (only output-folders for source-folders), to avoid having analyzed all those other projects, too.
It does not handle any access rules, but i think these can be ommited safely for analyzing purposes.
My patch by the way also fixes an issue, that project-local library references are not resolved correctly.
eg. project A references a library x.jar within project A's lib folder.
This currently gets resolved to "/A/lib/x.jar".
I added a project and workspace lookup which tries to find the library within project or workspace and returns the path to that member. This can then be resolved to an absolute filesystem path.
I don't know if there is a simpler way to do that.
I tested my changes with our production setup, which contains around 60 OSGI projects and lots of third party libs. I think this covers about every possible setup you can imagine