Consolidate document creation scripts and fix bugs

Replace the individual new_knitr_document, new_tex_assignment, and
new_tex_letter scripts with a single new_tex_document script that takes
a document type as its first argument. Fix bugs present in all scripts:
unquoted variables, TMPDIR name collision, missing existence checks, and
mktemp running unconditionally. Add cdsc_tex_aliases.sh for backwards
compatibility with old script names. Add rename_tex_to_dirname script
(moved from ~/bin). Update README and wiki page to reflect new setup.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

README

@@ -1,50 +1,130 @@
 ================================
-=== LaTeX Custom Scripts ======
+=== CDSC LaTeX Templates =======
 ================================
 
-Copyright (c) 2009-2025 Benjamin Mako Hill <mako@atdot.cc> / <makohill@uw.edu>
+Copyright (c) 2009-2026 Benjamin Mako Hill <mako@atdot.cc> / <makohill@uw.edu>
 
-This repository contains LaTeX configuration files that I use to format
-my papers. They are all released under the GNU GPL version 3 or later.
+This repository contains LaTeX configuration files and templates used to
+format papers, assignments, and letters. All files are released under the
+GNU GPL version 3 or later.
 
 The latest version can be found in git at:
 https://gitea.communitydata.science/collective/cdsc_tex
 
-As scripts and configuration files, I do not "release" these files. You
-can always check out the latest version with Git with the following
-command:
+You can check out the latest version with:
 
   git clone https://gitea.communitydata.science/collective/cdsc_tex.git
 
-Bug reports, comments, questions, and patches can all be directed to:
+Bug reports, comments, questions, and patches can be directed to:
 
   Benjamin Mako Hill <makohill@uw.edu> [work]
   Benjamin Mako Hill <mako@atdot.cc> [personal]
 
+To submit a patch, clone the repository, make your changes, and use
+git format-patch to generate patch files to send by email:
+
+  git format-patch origin/master
+  git send-email *.patch
+
 ================================
 === Dependencies ===============
 ================================
 
-If you are running Debian or Ubuntu, you will first need to install the
-following packages:
+On Debian or Ubuntu, install the following packages:
 
-  * rubber
+  * latexmk
   * texlive-latex-recommended
   * texlive-fonts-extra
   * texlive-fonts-recommended
-  * texlive-bibtex-extra 
+  * texlive-bibtex-extra
 
-You can do so with the following command:
-
-  apt-get install rubber texlive-latex-recommended \
+  apt install latexmk texlive-latex-recommended \
   texlive-fonts-extra texlive-fonts-recommended \
-  texlive-bibtex-extra 
+  texlive-bibtex-extra
 
-I don't know the details of setting up these LaTeX files to work with on
-systems other than Debian or Ubuntu but imagine it will involve
-installing a full TeX Live distribution.
+On other systems, installing a full TeX Live distribution should provide
+everything needed.
 
-In my templates, I make extensive use of the following Garamond font:
+The templates make extensive use of the URW Garamond font, available from
+CTAN: https://ctan.org/pkg/urw-garamond
 
-  http://www.ctan.org/tex-archive/fonts/urw/garamond/
+================================
+=== Branches ===================
+================================
 
+This repository has two main branches:
+
+  master  Standard LaTeX templates (paper, assignment, letter)
+  knitr   Knitr/R template for reproducible research documents
+
+================================
+=== Scripts ====================
+================================
+
+new_tex_document
+----------------
+Creates a new document directory from a template. Takes a document type
+and destination directory as arguments:
+
+  new_tex_document <type> <directory>
+
+Available types:
+
+  paper       LaTeX paper template (master branch)
+  assignment  LaTeX assignment template (master branch)
+  knitr       Knitr/R paper template (knitr branch)
+  letter      LaTeX letter template (master branch)
+
+Example:
+
+  new_tex_document paper my-new-paper
+
+This creates my-new-paper/ populated with the template files, with the
+main source file renamed to my-new-paper.tex (or .Rtex for knitr).
+
+rename_tex_to_dirname
+---------------------
+Renames the single .tex file in the current directory to match the
+directory name. Useful for cleaning up a template that was set up
+manually:
+
+  cd my-paper && rename_tex_to_dirname
+
+================================
+=== Shell Aliases ==============
+================================
+
+The file cdsc_tex_aliases.sh provides aliases for the old individual
+script names, for convenience or backwards compatibility. Add the
+following to your .bashrc or .zshrc:
+
+  [[ -f ~/tex/cdsc_tex/cdsc_tex_aliases.sh ]] && \
+    source ~/tex/cdsc_tex/cdsc_tex_aliases.sh
+
+This defines the following aliases (only if new_tex_document is in PATH):
+
+  new_tex_assignment   →  new_tex_document assignment
+  new_knitr_document   →  new_tex_document knitr
+  new_tex_letter       →  new_tex_document letter
+
+================================
+=== Migration ==================
+================================
+
+The individual scripts new_knitr_document, new_tex_assignment, and
+new_tex_letter have been consolidated into new_tex_document. The old
+scripts remain in the repository but are superseded.
+
+To migrate, replace calls to the old scripts with new_tex_document:
+
+  Old: new_knitr_document mydir
+  New: new_tex_document knitr mydir
+
+  Old: new_tex_assignment mydir
+  New: new_tex_document assignment mydir
+
+  Old: new_tex_letter mydir
+  New: new_tex_document letter mydir
+
+Alternatively, source cdsc_tex_aliases.sh (see above) to keep using the
+old names without changing your workflow.