Eclipse doesn't care about target/generated-sources being a source folder 
(as long as it is not also the output folder, but the output folder is 
usually target/classes). 
If, when you say that "the sources ... are created by my maven plugin", 
you mean that you wrote the maven plugin yourself, then your change your 
maven plugin so that it adds as many extra source directories as you want. 

And finally: mvn eclipse:eclipse can generate the eclipse project files 
for you, and it will include all source directories added/injected up to 
the phase "generate-sources".

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