Try to delete the .m2 folder on your computer and clean up the project, then it will automatically create it.
Next, check that the settings below are in the .project file

Next, check the settings in the .classpath file. 
If nothing works above. Try using the version of Eclipse Luna, it will work. I had a problem with maven 3.5 with kepler, then I tried to use luna, it worked for me.
I hope this helps you!
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