IMPORTANT: Added publication checklist, improved relevant infrastructure

Possible semantic conflicts (that may not show up as Git conflicts but may
cause a crash in your project after the merge):

   1) The project title (and other basic metadata) should be set in
      'reproduce/analysis/conf/metadata.conf'. Please include this file in
      your merge (if it is ignored because of '.gitattributes'!).

   2) Consider importing the changes in 'initialize.mk' and 'verify.mk' (if
      you have added all analysis Makefiles to the '.gitattributes' file
      (thus not merging any change in them with your branch). For example
      with this command:
        git diff master...maneage -- reproduce/analysis/make/initialize.mk

   3) The old 'verify-txt-no-comments-leading-space' function has been
      replaced by 'verify-txt-no-comments-no-space'. The new function will
      also remove all white-space characters between the columns (not just
      white space characters at the start of the line). Thus the resulting
      check won't involve spacing between columns.

A common set of steps are always necessary to prepare a project for
publication. Until now, we would simply look at previous submissions and
try to follow them, but that was prone to errors and could cause
confusion. The internal infrastructure also didn't have some useful
features to make good publication possible. Now that the submission of a
paper fully devoted to the founding criteria of Maneage is complete
(arXiv:2006.03018), it was time to formalize the necessary steps for easier
submission of a project using Maneage and implement some low-level features
that can make things easier.

With this commit a first draft of the publication checklist has been added
to 'README-hacking.md', it was tested in the submission of arXiv:2006.03018
and zenodo.3872248. To help guide users on implementing the good practices
for output datasets, the outputs of the default project shown in the paper
now use the new features). After reading the checklist, please inspect
these.

Some other relevant changes in this commit:

  - The publication involves a copy of the necessary software
    tarballs. Hence a new target ('dist-software') was also added to
    package all the project's software tarballs in one tarball for easy
    distribution.

  - A new 'dist-lzip' target has been defined for those who want to
    distribute an Lzip-compressed tarball.

  - The '\includetikz' LaTeX macro now has a second argument to allow
    configuring the '\includegraphics' call when the plot should not be
    built, but just imported.

1 files changed, 16 insertions, 1 deletions

diff --git a/reproduce/software/shell/configure.sh b/reproduce/software/shell/configure.sh
index 5cf813b..789ddd5 100755
--- a/reproduce/software/shell/configure.sh
+++ b/reproduce/software/shell/configure.sh
@@ -1046,6 +1046,21 @@ tikzdir=$texbdir/tikz
 if ! [ -d $tikzdir ]; then mkdir $tikzdir; fi
 
 
+# If 'tex/build' and 'tex/tikz' are symbolic links then 'rm -f' will delete
+# them and we can continue. However, when the project is being built from
+# the tarball, these two are not symbolic links but actual directories with
+# the necessary built-components to build the PDF in them. In this case,
+# because 'tex/build' is a directory, 'rm -f' will fail, so we'll just
+# rename the two directories (as backup) and let the project build the
+# proper symbolic links afterwards.
+if rm -f tex/build; then
+    rm -f tex/tikz
+else
+    mv tex/tikz tex/tikz-from-tarball
+    mv tex/build tex/build-from-tarball
+fi
+
+
 # Set the symbolic links for easy access to the top project build
 # directories. Note that these are put in each user's source/cloned
 # directory, not in the build directory (which can be shared between many
@@ -1054,7 +1069,7 @@ if ! [ -d $tikzdir ]; then mkdir $tikzdir; fi
 # Note: if we don't delete them first, it can happen that an extra link
 # will be created in each directory that points to its parent. So to be
 # safe, we are deleting all the links on each re-configure of the project.
-rm -f .build .local tex/build tex/tikz .gnuastro
+rm -f .build .local .gnuastro
 ln -s $bdir .build
 ln -s $instdir .local
 ln -s $texdir tex/build