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
Fixed issue on Blue Gene

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...)
Fixed regtests
Version tag (2.0.4)
Merge branch 'v2.0' into v2.1

Conflicts:
	VERSION
Tag (2.1.0)
Added notice about sudo -E
RDC: small change in svd