look in the plugin marketplace for a free plugin called m2e-wtp. that will take care of the provided scope issues. as for classes not being deployed, the usual places i look at are the deployment assembly and/or java build path. make sure that the entries (and the dependent modules) are all there and located in the right place.
the answer quoted from @vsplit
the problem was solved by adding maven with wtp deployment. no performance problems ... and i don't activate serve modules without publishing
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