This makes it compatible with the standard behavior of GNU tools.

PLUMED_PREFIX still works but is now deprecated and dumps a warning.
I will convert it to an error in a later version (2.3).

Conflicts:
	configure

This fixes an issue on periodicity of values.

Now all the values are brought within their periodic boundaries.

I do it since an error in the last digit was making the
*next* commit fail. I first change the regtest to make it clear
that it is not changing

travis is very picky and does not understand "allow_failure"
if there is a wrong number of spaces

Conflicts:
	.travis.yml

cppcheck is installed from its github when needed

Notice that the travis test doing cppcheck also does a normal g++ check.
I did to avoid too many if's in the travis script, but should be fixed perhaps
so that the last travis test only does cppcheck

I set this test as "allowed_failures", so that is just gives a warning now

I invoke cppcheck from an external script that makes the reporting better.

In particular, I show "fatal" errors at the end, where "fatal" means
all reported issues with the exclusion of "style" issues and issues
in molfile sourcecode.

(goes with 9e7b8c15)

Before this fix, the PLUMED_KERNEL env var was erroneously not
containing the LIBSUFFIX value.

This fix is relevant only if one use at the same time PLUMED_LIBSUFFIX
*and* loads the module file, which is unlikely.

Related to: e1b845b4

Now the type is defined with a typedef so that it is easier to change it.

I also set the type to size_t instead of unsigned long long.
This should be more portable.

removed condition that seemed to create very large support
in sum hills calculation and resulting into a very large computational
time. Credits to Carolyn Phillips from the mailing list.

gromacs-5.1.0 beta patch

[makedoc]

This reverts commit b148b715.

This should go with a94b94b2

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