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This is related to the closed issue #162

I think that with standard usage of PLUMED all the actions should be
active at step zero, and so all the masses and charges should be requested
to codes like NAMD or OPENMM. Anyway,this fix will double check for it
adding an overhead only at the first simulation step.

Some time ago I made one build allowed to fail.
After c9e9c366
(see also #183) it looks like the issue is solved,
so I put the build back in place.

for DEBUG logActivity and logRequestedAtoms

There was an assert checking that a stopwatch is not
started more then once. I replaced it with a counter
that, if a stopwatch is started N times, ignores the first
N-1 pause signals. This makes it possible to used Plumed.cmd
recursively. In practical terms, this makes it possible to use
DEBUG logRequestedAtoms
that was previosuly crashing the code.

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Fixed small bug in moments vessel - this would not work if you were calculating MOMENTS and MEAN simultaneously

Related to #183

This barrier is apparently useless since it comes
just before a Bcast.

Anyway, it looks like it is solving an issue that appeared on
TRAVIS (at least on my laptop) so I add it here.

Related to #183

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This regtest is failing on travis from time to time, in an
irreproducible way. I took note of the problem at issue #183

I temporarily change this regtest by:
1. moving COLVAR.reference to COLVAR.reference.dontcheck
2. adding HILLS.reference so that at least one file is checked.

Notice that this is not a solution of the problem, just a way
to avoid random failures on travis.

As soon as someone is willing to fix this, just put COLVAR.reference
back in place and push it to travis

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Before this fix, using cmd() with an erroneous string was triggering
no error. Now this is fixed.

Notice that this is an old bug (introduced in 0a46f15d).
It should be harmless when using MD codes with proper interfaces,
but could be very dangerous if there is a typo in a cmd string.

now remove trailing "/" which could lead to troubles in "#ifdef"

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