Better management for .tex directories to build from tarball

In order to collaborate effectively in the project, even project members
that don't necessarily want (or have the capacity) to do the whole analysis
must be able to contribute to the project. Until now, the users of the
distributed tarball could only modify the text and not the figures (built
with PGFPlots) of the paper.

With this commit, the management of TeX source files in the pipeline was
slightly modified to allow this as cleanly as I could think of now! In
short, the hand-written TeX files are now kept in `tex/src' and for the
pipeline's generated TeX files (in particular the old `tex/pipeline.tex'),
we now have a `tex/pipeline' symbolic-link/directory that points to the
`tex' directory under the build directory.

When packaging the project, `tex/pipeline' will be a full directory with a
copy of all the necessary files. Therefore as far as LaTeX is concerned,
having a build-directory is no longer relevant. Many other small changes
were made to do this job cleanly which will just make this commit message
too long!

Also, the old `tarball' and `zip' targets are now `dist' and `dist-zip' (as
in the standard GNU Build system).

8 files changed, 20 insertions, 13 deletions

diff --git a/tex/delete-me-demo.tex b/tex/src/delete-me-demo.tex
index 65aa1c7..8174bc8 100644
--- a/tex/delete-me-demo.tex
+++ b/tex/src/delete-me-demo.tex
@@ -3,7 +3,7 @@
   %% The displayed WFPC2 image.
   \node[anchor=south west] (img) at (0,0)
        {\includegraphics[width=0.5\linewidth]
-         {\bdir/tex/delete-me-demo/wfpc2.pdf}};
+         {tex/pipeline/delete-me-demo/wfpc2.pdf}};
 
   %% Its label
   \node[anchor=south west] at (0.45\linewidth,0.45\linewidth)
@@ -25,7 +25,7 @@
       ]
     \addplot [const plot mark mid, fill=red]
     table [x index=0, y index=1]
-    {\bdir/tex/delete-me-demo/wfpc2-hist.txt}
+    {tex/pipeline/delete-me-demo/wfpc2-hist.txt}
     \closedcycle;
   \end{axis}
 
diff --git a/tex/delete-me.tex b/tex/src/delete-me.tex
index 32be11c..fc1a1f9 100644
--- a/tex/delete-me.tex
+++ b/tex/src/delete-me.tex
@@ -11,7 +11,7 @@
 
     %% A particular plot.
     \addplot+[scatter, only marks]
-    table {\bdir/tex/delete-me/data.txt};
+    table {tex/pipeline/delete-me/data.txt};
 
   \end{axis}
 \end{tikzpicture}
diff --git a/tex/preamble-biblatex.tex b/tex/src/preamble-biblatex.tex
index b0660a9..bd99502 100644
--- a/tex/preamble-biblatex.tex
+++ b/tex/src/preamble-biblatex.tex
@@ -7,7 +7,7 @@
 %% just be copied there and used.
 %%
 %% USAGE:
-%%  - `tex/references.tex': the file containing Bibtex source of each
+%%  - `tex/src/references.tex': the file containing Bibtex source of each
 %%     reference. The file suffix doesn't have to be `.bib'. This naming
 %%     helps in clearly identifying the files and avoiding places that
 %%     complain about `.bib' files.
@@ -41,7 +41,7 @@
     backend=biber,natbib]{biblatex}
 \DeclareFieldFormat[article]{pages}{#1}
 \DeclareFieldFormat{pages}{\mkfirstpage[{\mkpageprefix[bookpagination]}]{#1}}
-\addbibresource{tex/references.tex}
+\addbibresource{tex/src/references.tex}
 \renewbibmacro{in:}{}
 \renewcommand*{\bibfont}{\footnotesize}
 \DefineBibliographyStrings{english}{references = {References}}
diff --git a/tex/preamble-header.tex b/tex/src/preamble-header.tex
index eb83c27..eb83c27 100644
--- a/tex/preamble-header.tex
+++ b/tex/src/preamble-header.tex
diff --git a/tex/preamble-necessary.tex b/tex/src/preamble-necessary.tex
index bef5a2f..e6ac18e 100644
--- a/tex/preamble-necessary.tex
+++ b/tex/src/preamble-necessary.tex
@@ -1,4 +1,4 @@
-%% Some (commonly) necessary LaTeX packages.
+%% Necessary (independent of style) macros for this project.
 %%
 %% These are a set of packages that have been commonly necessary in most
 %% LaTeX usages. However, if any are not needed in your work, please feel
@@ -8,6 +8,13 @@
 
 
 
+%% Values from the analysis.
+\input{tex/pipeline/macros/pipeline.tex}
+
+
+
+
+
 % Macros for to help in typing, remove them if you don't need them, but
 % this can help as a demo on how you can simply writing of commonly used
 % words that need special formatting (like software names).
diff --git a/tex/preamble-pgfplots.tex b/tex/src/preamble-pgfplots.tex
index 26b98d6..4999656 100644
--- a/tex/preamble-pgfplots.tex
+++ b/tex/src/preamble-pgfplots.tex
@@ -33,12 +33,12 @@
 %%    present in the location LaTeX is run).
 %%
 %%  - Use `\includetikz{XXXX}' to make/use the figure. If a `makepdf' LaTeX
-%%    macro is not defined, then it will simply assume a `XXXX.pdf' file
-%%    exists in the `\bdir/tex/build/tikz' directory and simply import
-%%    it. If `makepdf' is defined, then TiKZ/PGFPlot will be called to
-%%    (possibly) build the plot based on `tex/XXXX.tex'. Note that if the
-%%    contents of `tex/XXXX.tex' hasn't changed since the las
-%%    build. TiKZ/PGFPlots won't rebuild the plot.
+%%    macro is not defined, then \includetikz will assume a `XXXX.pdf' file
+%%    exists in `tex/tikz' and simply import it. If `makepdf' is defined,
+%%    then TiKZ/PGFPlot will be called to (possibly) build the plot based
+%%    on `tex/XXXX.tex'. Note that if the contents of `tex/src/XXXX.tex'
+%%    hasn't changed since the last build. TiKZ/PGFPlots won't rebuild the
+%%    plot.
 
 
 
@@ -69,7 +69,7 @@
 \newcommand{\includetikz}[1]{%
   \ifdefined\makepdf%
     \tikzsetnextfilename{#1}%
-    \input{tex/#1.tex}%
+    \input{tex/src/#1.tex}%
   \else
     \includegraphics[width=\linewidth]{tex/tikz/#1.pdf}
   \fi
diff --git a/tex/preamble-style.tex b/tex/src/preamble-style.tex
index fb08df7..fb08df7 100644
--- a/tex/preamble-style.tex
+++ b/tex/src/preamble-style.tex
diff --git a/tex/references.tex b/tex/src/references.tex
index b3998a2..b3998a2 100644
--- a/tex/references.tex
+++ b/tex/src/references.tex