Modified use of neighbor list in COORDINATION

It solves a known problem with the calculation
of acceptance in replica exchange with COORDINATION
and NLIST.

Notice that it changes the behavior of neighbor list
in the first two steps of a simulation. Previously,
during those steps full pair list was used. Now,
first step is equivalent to any other step
multiple of NL_STRIDE. Because of this, I updated
a couple of regtests.
Added regtest for neighborlists

This is to probe correctness with replica exchange
Merge branch 'v2.0'
Fixed warnings

clang -Wextra-semi
Fixed warning

clang -Wdangling-else
Merge branch 'v2.0'
misdeclaration in FuncSumHills
Merge branch 'v2.0'
BACKBONE -> RESIDUES in the doxygen of Secondary Structures
Fixed warnings

clang -Wdocumentation
Removed explicit action list on log

(suggested by Paolo Raiteri)
Merge branch 'v2.0'
Replaced VolumeSubcell with VolumeAround

The old VolumeSubcell did not have translational invariance.  This
has been resolved in around by adding a reference atom about which
we integrate the density. VolumeSubcell has been removed as it is not
yet working.  Also changes were required in vesselbase
to make the numerical derivatives of these "bridged" quantities work.
Central atoms are now always in cartesians

This was a bit of flexibility that I was using in VolumeSubcell.  I
would like to remove it as I think it conceals what you are doing.
In other words it causes you to make mistakes
Fixed local average and optimized volume density calculations
Sorted regtests for ActionVolume
Made user manual nicer and ready to put online
Added nicer formatting to developer docs
Added davide's pigeon
Changed picture of developer pigeon