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git://github.com/bimargulies/m2e-groovy-0.13-attempt.git is an m2e configurator plugin (a pure eclipse build) If you install it, and try to import the project from: git://github.com/bimargulies/m2e-groovy-configuration-test-project.git there will be no java nature. Without the groovy configurator, the java nature sets up normally. And of course m2e is upset about the unmapped groovy goals.
The problem here is that the groovy configurator pointed to here will add nonexistent source folders, and then eclipse gets more and more unhappy. This is probably not an m2e issue.
Closing as per the last comment. Feel free to reopen if you think m2e could handle this project better, provide better diagnostics, more logs, etc.
Moved to https://github.com/eclipse-m2e/m2e-core/issues/