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Using numgroup as suggested by @swails on amber mailing list

(cherry picked from commit 200f4cb42744926a027e30393e56d315f24cd535)

Before this fix, amber was working correctly with multiple
replicas but not working correctly with a single replica.

Now both situations should be ok.

Notice that I used a hack to detect if replicas are present
or not in sander. Probably this should be cleaned up in
some way

(cherry picked from commit 0b7dc44635708e821e14ed6f1156317807e6db7d)

It should now work properly

(cherry picked from commit 6f96353a8a7975f7429426bce3777fb555deed65)

[makedoc]

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They were giving warnings with cppcheck

repeated assignment

initialization list

check for empty container

[almost]

[almost]

In commit f4ac1cf2 I forgot to also change plumed.dat.0 file.
I fix this now, so as to decrease mismatches in regtests

[makedoc]

close #124

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closes #123

tutorials: fixes

@gtribello please check before I merge!

This highlights bug #123

I suspect a problem in v2.1 with DRMSD cutoff.

This test is working properly in v2.0

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