to reflect the implementatin of INTERVAL and ALPHABETA

and added the doxygen part

also with grid but without splines (automatically deactivated).

Now the stride for the neighbor lists in the path implementation
are in timesteps. By now this means that PATHMSD and PROPERTYMAP are
defined with e.g. NEIGH_STRIDE=5

Now, for consistency, the time units of SIGMA in METAD for the
ADAPTIVE=DIFF scheme is in timesteps to be consistent with the rest of
the program. Documentation, printout and regtests are done.

uninitialized variable (from last commit)

Now the code crashes in the following cases:
1. An exchange is attempted on a step where neighbor list for COORDINATION
(or DHENERGY) are not updated
2. An exchange is attempted and neighbor list for PATHMSD or PROPERTYMAP are enabled.

The second should be fixed better to allow using strides for lists which are
divisor of the stride between steps. The better thing will likely come later, at least
the code is safe now.

(suggested by candrewn@gmail.com)

(unused variable)

This allows a clean build also without a fortran compiler

There was a bug when reading cubic cells

(Pointed out by Sergio Decherchi)

It was wasting space (especially the developer one) and anyway improperly
formatted. Could be readded later if we fix formatting.

It is now possible to install plumed with "make install".

Installation is done just copying most files (e.g. obj needed
for patching) and fixing hardcoded paths. The advantage is
that it is possible to fix a location with environment variables
PLUMED_PREFIX (e.g. /opt/local/) and a suffix with
PLUMED_LIBPREFIX (e.g. 2.0.0). This will help in installing multiple
plumed versions in the same path.

Moreover, also include files are copied to e.g.
/opt/local/include/plumed, so that it is possible to use the plumed
tools library as a normal system library

cppcheck

For some reason on my local linux machine doxygen does not
replace the variables $extrastylesheet and $relpath in the
PlumedUserHeader.html file.  As we are not using these variables
I deleted them from the header files.  I think this will cause problems
if we ever choose to use a custom css file for the documentation or if
we use the CREATE_SUBDIRS option.  I cannot imagine that we will ever
use these options but I thought I would mention these problems in the
log.

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

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.

(suggested by Paolo Raiteri)

clang -Wdocumentation

clang -Wdangling-else