Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.

Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.

Also, some of the software versions were also updated after some checks
with their webpages.

This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).

All occurances of "pipeline" have been chanaged to "project" or "template"
withint the text (comments, READMEs, and comments) of the template. The
main template branch is now also named `template'.

This was all because `pipeline' is too generic and couldn't be
distinguished from the base, and customized project.

Until now we weren't including the citation for FFTW (one of the template's
optional packages). With this commit, it is added.

Until now, the files where the people were meant to change didn't have a
proper copyright notice (for example `Copyright (C) YOUR NAME.'). This was
wrong because the license does not convey copyright ownership. So the name
of the file's original author must always be included and when people
modify it (and add their own copyright-able modifications).

With this commit, the file's original author (and email) are added to the
copyright notice and when more than one person modified a file, both names
have their individual copyright notice.

Based on this, the description for adding a copyright notice in
`README-hacking.md' has also been modified.

Until now, even though `file' was a dependency of `gcc', it was still
listed as a `top-level-programs'. Also, we weren't including the new
`tex/dependencies' in the distribution tarball (with `make dist').

With this commit, both issues are solved and also, as a cosmetic change,
the GCC prerequisites of the same line-length were ordered alphabetically.

Until now, there was a single `tex/src/references.tex' file that housed the
BibTex entries for everything (software and non-software).

Since we have started to include the BibTeX entry for more software, it
will be hard to manage the large (sometime unused) BibTeX entries of the
software in the middle of the non-software related citations in the text of
the paper.

Therefore, with this commit, a `tex/dependencies' directory has been made
which has a separate BibTeX entry file for each software that needs
one. After the software is built, this file is copied to the new
`.local/version-info/cite' directory. At the end, the configure script will
concatenate all the files in this directory into one file which will later
be used with `tex/src/references.tex' by BibLaTeX.

This greatly simplifies managing of citations. Allowing us to focus on the
software-building and paper-writing citations separately/cleanly (and thus
be more efficient in both).

Some recent corrections that were done by Raul are now merged into the
pipeline. There weren't any conflicts.

Until now, we did not have `file'.  It was in other project, where a
problem with `Astrometry-net' software, ends up with the necessity of
having `file' into the pipeline.

With this commit, we add `file' to the project. Since it is a low level
program, it is set in `dependencies-basic.mk' as a prerequisite of GCC.

Until now, the Scipy citation was only one paper and not the correct one
(it was the online manual).

With this commit, Scipy is properly cited using the two papers. Also
some modifications in the `tex/src/references.tex' have been done
(remove last page number).

Until now, name and version of all Python packages were indicated in the
final paper, but not the main paper of them (if it exists).

With this commit, some Python packages (Cython, Matplotlib, Numpy and
Scipy) are now properly acknoledged by citating the source paper.
`mpi4py' is also cited although this package is not yet included into
the pipeline.