The only files you need to submit are NBody.java and README.txt. If for some reason you create other classes NBody depends on (this is neither necessary nor recommended), submit those as well.
Make sure when you submit, all of the following are present and functional:
Class: NBody
public double distance(double, double, double, double)
public double force(double, double, double)
public double[][] positions(Scanner, int, int)
Make sure to submit your README in order to receive any credit.