This commit fixes some of the rules in
`reproduce/analysis/make/initialize.mk` for creating
the archive type files to upload to Zenodo.

The '-committed-only' name in variables is for archiving
commands that use git and ignore any uncommitted changes.
The '-dirty' suffix is irrelevant in this case.

Some utf-8 (unicode) characters that accidentally crept
into `tex/src/references.tex` are fixed; and '\&' is replaced
by 'and' in paper.tex.

The sequence of creating/listing files for uploading to Zenodo
should be:

./project make clean-paper
./project make dist-arXiv
./project make git-bundle
./project make dist-software # Wait! typically 0.5 Gb!
ls -lt .build/data-to-publish/

In the elaphrocentre project, remember to 'touch' the initial
conditions file to prevent a new simulation from being run,
e.g.

touch --date=2010-02-03 reproduce/analysis/config/init-conditions-params.conf

unless you really do want to run a new simulation.