A couple of fixes in the developer doc
Slighlty optimized MSD

Reference coordinates are saved already shifted to their average.
Weights are stored already normalized.

A regtest has been fixed (it contains numerical derivatives which
slighlty changed with this commit)
Addresses #40

It just prints a meaningful error.
Updated changelog
added --help in the help section to get the help for commands
CS2Backbone: fixed error in the documentation of the keywords
Made it so help message is output for bad input to simplemd. closes #40
Merge branch 'v2.0' of github.com:plumed/plumed2 into v2.0
Added comment so that online manual is not misleading
A couple of fixes in doc
Added possibility to use replica exchange from fortran

The interface to set replica communicator from fortran was missing.
Now crashes when setting COM or CENTER with zero atoms
Moved cmd("setStopFlag") to be after cmd("init")

I think this is more coherent with other cmd() calls.
Additional test case for HISTOGRAM

This test shows a problem in reweighting (discussed in #48).
In particular, histoA and histoB in this regtest should not
come out identical as they do.
Fixes #48

(should be checked by GT)
Typo in manual
Merge branch 'fix-48' into v2.0
changelog
Merge branch 'fix-48' into v2.0
Fixed stopflag in Driver

I fixed the usage of stopflag in driver so that it is clearer
that the program stops at the end of the present step and not
at the beginning of the following. This is obviously equivalent,
but shows that scope of the flag can be reduced to be defined
at the inner of the MD loop.

Even if this is not a bux fix, I consider it as paired with fix #47
and I merge it to v2.0