Copy comm flags in make_alike

[atmyers]

Need to make sure these are preserved (we use them as IO flags in WarpX)

The proposed changes:

• fix a bug or incorrect behavior in AMReX
• add new capabilities to AMReX
• changes answers in the test suite to more than roundoff level
• are likely to significantly affect the results of downstream AMReX users
• include documentation in the code and/or rst files, if appropriate

[ax3l]

Nice, good catch!