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

changed ref to subpage and added comment on FIT_TO_TEMPLATE

(no real change, the relevant files where not modified in gmx)

Added possibility to remove checks such as
"-ansi" and "-Wall" (--disable-basic-warnings)

Changed name of temporary files from test... to conftest...
(consistent with autoconf behavior)

plumed core can be compiled without these.

With this change it is necessary to solve a but in the script building the
list of modules to be tested. I took the occasion to simplify it.
Now, all the optional modules are checked, but if a directory is
not present in regtest/ that module is ignored.

Conflicts:
	src/vesselbase/ActionWithVessel.cpp

(cherry picked from commit ab117d79)

Conflicts:
	src/vesselbase/ActionWithVessel.cpp

This is for vessels.  Basically you now can't create a FunctionVessel
without adding a description to the manual of the quantity it
calculates

This test is very sensitive to numerical errors and is thus
not a good test of the code.  The functionality that is
being tested here is tested elsewhere.

Note changes to many regtests are because of changes in labels of
components

A component called "bias" is needed for replica exchange to work properly

Notice that latex cannot be used in captions

Conflicts:
	src/tools/BiasRepresentation.cpp