Conflicts:
	VERSION

Blue Gene was not correctly resolving some template.
I think that this fix makes the code more robust
(a posteriori, I do not understand how g++ was able
to solve the template...)

std::floor should only be used with double. With int it makes no sense
and do not compile on blue gene

Do not install the full user-doc source (it is much bigger now
with latex directory)

An encoding command was returning an error on my workstation,
I made a workaround

(Asked by GT)

(backported from 2.1)

(cherry picked from commit d523213f)

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.