Added documentation on --enable-rpath

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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A section was not properly shown

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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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Added PDF manual. I had to reorganize a bit the documentation to make
it more linear. In particular, I assigned each of the previously
"dangling" pages as subpage of another one (e.g. DEBUG keyword).
Additionally, I changed a bit the way MD-specific instructions are linked
and added some comment about the PDF manual in the introduction.

The most important change is that I am not using the Layout anymore since
it was difficult to keep it in sync. Now, in the html version, only
the left-side tree is visible, and the tabs disappeared. I don't think
this is a big issue but we might try to solve it.

PDF manual is still a bit buggy: some links are not properly resolved
and images are not shown. I think we can solve these issues later.

Addresses #101

Changes to the code are there so that I can reference the atoms
page in the descriptions of keywords that read atom numbers.  I also
changed the input to multicolvar functions.  I stopped using the ARG
keyword in these actions and used DATA instead because you are refering
to the data calculated in a multicolvar as opposed to a scalar quantity
calculated by a particular action.

I have noticed that on some machines one needs to add  -lgfortran
to link blas and lapack correctly (manual updated).