Secondary structures CVs were not writing correctly in the log
file the residues they use.
Merge remote-tracking branch 'origin/v2.0' into v2.0
A couple of fixes in the developer doc
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