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If a pom includes a system dependency and an existing dependency with a missing pom (so jar exists in repo, pom does not) then m2e (0.12.0) complains about not being able to resolve the system dependency. See enclosed pom. In my case the jar for springmodules:springmodules-cache:0.9 is present in my repo.
Created attachment 195332 [details] Small pom showing the problem described.
I am not able to reproduce the problem with a recent 0.13 build. Attached sample project imports successfully and both springmodules-cache and com.sun:tools are resolved as expected.
I installed a recent 0.13 build on Indigo M7. I found out what is causing this. If settings.xml contains a reference to a legacy repository the error manifests itself.
Actually, it was a reference to a legacy repository that recently got removed from the nexus I am connecting to. Removing the reference from my settings.xml solved the issue.
Moved to https://github.com/eclipse-m2e/m2e-core/issues/