PDF manual

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
Merge branch 'v2.1' into v2.1-pdfmanual
Allow "make docs" besides "make doc"

(Asked by GT)
Added better info version to the manual
Fixed latex

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

Do not install the full user-doc source (it is much bigger now
with latex directory)
Fixed changelog for 2.1
Fixed changelog for 2.0.4
Merge branch 'v2.0' into v2.1-pdfmanual
fixed changelog for 2.1
Note to PDF manual
Fixed underscore for lapack/blas
Fixed std::floor

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