m2e-apt
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Turning off annotation processing for a project should delete the .factorypath file
I had to do that manually to recover from https://github.com/jbosstools/m2e-apt/issues/19
m2e-apt's code is now included in https://github.com/eclipse-m2e/m2e-core , please consider reporting issue to https://github.com/eclipse-m2e/m2e-core/issues if it's still relevant.