this is required to avoid name clashes

Now command line shortcuts such as plumed-patch
follow the same rule as plumed executable to set PLUMED_ROOT
as it was implemented in 1b20cb90

Namely, they have an hard coded value that can be replaced
setting the PLUMED_ROOT variable before launching the tool

Sometime there was problem with inconsistent on/off files. Now:

whenever all/none/reset is found, all on/off files are removed.
whenever one module is enabled, on file is added and off file is removed
the opposite when it is disabled

this should enforce consistency of on/off files.

Conflicts:
	src/maketools/update-plumedroot.sh
	user-doc/Installation.txt

Using "_" instead of "-" to avoid clashes.

Actually, the problem was that doing
make install PLUMED_SUFFIX=2
make install
The second install would have canceled the executables installed
by the first install. This is because install assumes names such as
plumed-* to be scripts installed for cross compiling

[makedoc]

There was an error in passing masses from NAMD to PLUMED.

Found by Glen Hocky.

Fixes #162

Now plumed should work if built on a directory which has a space in the path.
Notice that install directory should still not contain spaces.
This is because of some difficulties in making the
src/lib/Makefile rules compatible with names with spaces.

Addresses #157

to doxygen 1.8.7

[makedoc]

Notice that autoconf already implements --enable-openmp.
I removed the one added by hand, so that it does not appear
twice in ./configure --help

Also accepts "manyrestraint+imd" (without colon).

[makedoc]

[makedoc]

When MPI was requested and not found configure was erroneously
reporting that PLUMED was compiled with MPI support

\issue{123} to get #123 and a link at the github issue page

\branch{v2.1} to get v2.1 and a link at the github branch page

In 311f3e0b I forgot to rename
the link in Cambridge tutorial

This is necessary because of an internal bug on g++-4.2 on my mac

I changed from , to : separator which is more standard
(e.g. in PATH)

This is replaced by ./configure --enable-modules

Added an option to ./configure to choose modules.

./configure --enable-modules=all
enables all optional modules

./configure --enable-modules=none
disables all optional modules

./configure --enable-modules=reset
reset default modules

./configure --enable-modules=+manyrestraints,-colvar
enables manyrestraints and disables colvar

./configure --enable-modules
maps to ./configure --enable-modules=reset

./configure --disable-modules
maps to ./configure --enable-modules=none

I removed the sentence saying that 2.2 will crash.

We should likely make it fail on travis-ci so that
we remember to add the documentation, but I cannot
do it know as one regtest basic/rt44b in v2.2
would fail.

Here we test for sum_hills using variables
that are sub-components. This triggers
the warning about non-registered components in FAKE,
that should be fixed someway