i have the same issue and the only things i do are:
if you use the maven plugin, on each project, choose the maven option
disable workspace resolutionthe other project will not refers anymore those in the workspace.
apparently this is a known bug and you can find some more solution like rebuilding the maven indexes here.
maven in command line:
another option i choose is to use the maven on command line (it's not perfect but in the environment i work in it is the best solution) and use the option "offline" in the maven preferences. this is due to proxy which is not working from eclipse but work from command line (my setup).
personally i use both option but this is due to a very strict proxy which is not friendly; i think this is a good setup for osgi as trying to resolve all dependencies could be very long.
another point: try to see if you have circular dependencies, it can happens very quickly in osgi environment and i guess that can also make the compiler to be mad.
on my machine the vaadin designer scanned each projects of my workspace (in my case about 100 bundles), and this took very long (eclipse mars.2 and neon)
hint: open visualvm - connect to eclipse pid; create a thread dump and analyze the worker threads of eclipse.
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