I think the inclusion of numpy headers was related to non used variables
forgotten from an intermediate implementation.
I just removed them. In this manner it is not necessary that numpy is
already installed when plumed extension is compiled.

Numpy would be anyway required to run our test.

This include dir is used when using not-installed plumed.
Before this fix, using
./configure --prefix=$PWD
was leading to problems related to the overlap between
installed include files and this directory.
After this fix, it will be possible to configure plumed with
./configure --prefix=$PWD

Fixes #332

Added documentation on --enable-rpath

Removed all examples mentioning matheval

I renamed all files from .txt to .md so that they can be
visualized on github.

In addition, I renamed all files to have a name consistent with the content.
This makes manual portions easier to find.

Notice that I left the original labels (e.g. "Syntax" instead of "Getting Started")
not to break direct links to manual, though I think we should rationalize these names
as well.

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I think this fixes #143

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Clarification on one option that does not work on BG/Q

Now when plumed is installed the scripts are placed in
lib/plumed/
instead of
bin/

This makes it more robust the installation of several versions with suffixes

I only left in place the script "plumed-patch" which is likely
the most used.

I added plenty of messages at the end of ./configure and make install
+ I explained it in the user doc

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

We usually allowed users to customize the name of the plumed
library using env var PLUMED_LIBSUFFIX. I changed it to the
standard autoconf behavior, that is using
--program-suffix
--program-prefix
at configure time.

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

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).

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