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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

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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).

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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

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