I asked the same question on the m2e-users mailing list and got the following answer ( link for those who want to get the full stream):
Basically, you need to manually configure (e.g. using the aforementioned hibernation tutorial) eclipse to use the generator and configure the same directory that uses maven (for me it was target / generated sources / annotations) as the output directory.
According to the m2e committers, the project does not currently modify these eclipse files, and therefore it will not be undone from them.
The problem I ran into was that this information is lost (and therefore manual change is required again) when using GIT and switching between branches, since I don't want to transfer any eclipse related files to SCM. <w> This is currently an acceptable solution, and I hope m2e can add this missing feature.
Update
Information lost, at least in my experience, is identifying the target/generated-sources/annotations folder as the source folder. Just like FYI.
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