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

to doxygen 1.8.7

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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

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.

[makedoc]

This should show "master" instead of "2.3" in
online doc-master

Includes statistics of (style) warnings.
Can be used to see if the number of warnings decreases.

[makedoc]

closes #147

[makedoc]

closes #141

Before fix the master branch was installed
Now we explicitly ask for 1.69

Now $HOME/opt has the priority. This allows properly
overriding already installed programs.

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In 84ad8d2a a bug was introduced and
manual was not correctly pushed from travis-ci

[makedoc]

(cherry picked from commit b6ea36c1)

Actually, this was a workaround I found on the web for MSC,
but looking at the code I don't think it should work.
Probably, it has never been tested, so better remove it.