This is a huge commit, applying indentation to the whole
code. Notice that this commit is made on master branch
after having merged with -s ours from branch v2.3

See #215

This is a huge commit, applying indentation to the whole
code.

See #215

addresses #213

[makedoc]

Fix #209

driver-float was not documented

Added option in driver to evaluate forces due to a bias numerically so that they can be compared with the analytical forces evaluated by plumed

When using driver with --trajectory-stride 0
the number of the step is read from the xtc/trr file.

Notice that this only works when reading with xdr library
(--ixtc or --itrr) and not with the molfile plugins

I added the possibility to personalize charge and mass units
in the same way as length, energy, and time units were treated so far.

Notice that since two new cmd() strings have been added to set
units from an MD code, it is necessary to increase the API version
to 4.

I also added the appropriate developer documentation.

Fixes #179

This change makes the driver less error prone

It requires a lot of regtests to be fixed,
mostly adding an mc file when required or replacing
COM with CENTER

This makes these options consistent with others.

THIS REQUIRES ./configure AGAIN!!

[makedoc]

I added the possibility to dump the 9 components of the virial
from the driver.

[makedoc]

This allow amber formats to be properly read

I added a new action DUMPMASSCHARGE and a new flag for driver --mc

Fix #112

Notice that I did it differently wrt what I wrote in the issue.
Namely, I write mass and charges with an action (DUMPMASSCHARGE)
and I make the driver capable of reading them (with --mc)

Since now plumed can write xtc/trr files, in a multi replica
framework I think it makes more sense to add the replica suffix before
the extension. That is, with DUMPATOMS FILE=test.xtc, we get
files such as test.0.xtc and not test.xtc.0

The same happens for trajectories read from the driver.

Notice that this was already true for .gz files, and now applies
for .xtc and .trr files. All other extensions are still ignored
for backward compatibility.

Now driver can read using --ixtc and --itrr with the xdrfile library.
This is an alternative to molfile, and provides better support
for cells of arbitrary shape.

Now all the types and functions declared in the
local version of molfile plugins are properly wrapped
in a namespace.

Possibly fixes #110

(cherry picked from commit 3f296491)

Changes to the code are there so that I can reference the atoms
page in the descriptions of keywords that read atom numbers.  I also
changed the input to multicolvar functions.  I stopped using the ARG
keyword in these actions and used DATA instead because you are refering
to the data calculated in a multicolvar as opposed to a scalar quantity
calculated by a particular action.

Sorry for this - on linux/intel it was compiling properly