Pandoc is not installed including citeproc.

https://stackoverflow.com/questions/38789253/running-script-conditionally-does-not-work-in-travis-yml-why

Hopefully this solves some issues and maybe even cuts the build time

This issue suggests we could be using an old install of texlive.
Conda should be putting pandoc on the path anyway. I wonder how it
choses what tex version to use.
https://tex.stackexchange.com/questions/567050/how-can-i-install-l3backend-pdfmode-def

This packages is depreciated for modern lex releases (post 2015).
https://tex.stackexchange.com/questions/287146/how-to-use-fixltx2e-only-when-necessary

https://tex.stackexchange.com/questions/137428/tlmgr-cannot-setup-tlpdb

```
$ make install
bash /home/travis/build/tompollard/phd_thesis_markdown/install_linux.sh
(running on Debian, switching to user mode!)
/usr/bin/tlmgr: Initialization failed (in setup_unix_one):
/usr/bin/tlmgr: could not find a usable xzdec.
/usr/bin/tlmgr: Please install xzdec and try again.
tlmgr: Couldn't set up the necessary programs.
Installation of packages is not supported.
Please report to texlive@tug.org.
Use of uninitialized value $r in split at /usr/bin/tlmgr line 3882.
tlmgr: Cannot find main repository, you have to tag one as main!
Makefile:37: recipe for target 'install' failed
make: *** [install] Error 1
The command "make install" failed and exited with 2 during .
```

https://tex.stackexchange.com/questions/180230/kubuntu-texlive-manually-installed-tlmgr-not-working

You must restart your terminal window for the installation of MacTex CLI tools to take effect.
Alternatively, Bash and Zsh users can run the command:
  eval "$(/usr/libexec/path_helper)"

Linux now stuck on error I recognise from advice:

0.12s$ if [ "$TRAVIS_OS_NAME" = "osx" ]; then
    eval "$(/usr/libexec/path_helper)"
    sudo tlmgr update --self
  elif [ "$TRAVIS_OS_NAME" = "linux" ]; then
    tlmgr init-usertree
    echo on linux we cannot update apt installed texlive c.f.
    echo https://tex.stackexchange.com/questions/551383/cant-run-tex-lives-tlmgr-in-a-github-action
    echo https://tex.stackexchange.com/questions/1092/how-to-install-vanilla-texlive-on-debian-or-ubuntu
  fi

(running on Debian, switching to user mode!)
tlmgr: action init-usertree returned a warning.

...

$ make install
bash /home/travis/build/tompollard/phd_thesis_markdown/install_linux.sh
(running on Debian, switching to user mode!)
Unknown directive ...containerchecksum 57a177b65450718631f36bfd8db0f2d1bff788f3bf147137b6412714cc945c7e08832f14f9e7e659adf7e072a91f13a2ea27fe3161cd9b60313bc956f1f543c6... , please fix it! at /usr/share/texlive/tlpkg/TeXLive/TLPOBJ.pm line 210, <$retfh> line 7085.
Makefile:37: recipe for target 'install' failed
make: *** [install] Error 25
The command "make install" failed and exited with 2 during .

https://tex.stackexchange.com/questions/313768/why-getting-this-error-tlmgr-unknown-directive

I think the way forward would be to customise the install of texlive for linux.

Trying this to compare with previous build

Else we get the following stack:
```
brew
Installing Homebrew Packages
6.51s$ rvm $brew_ruby do brew bundle --verbose --global
/usr/local/bin/brew tap homebrew/bundle
==> Tapping homebrew/bundle
Cloning into '/usr/local/Homebrew/Library/Taps/homebrew/homebrew-bundle'...
remote: Enumerating objects: 101, done.
remote: Counting objects: 100% (101/101), done.
remote: Compressing objects: 100% (95/95), done.
remote: Total 101 (delta 4), reused 28 (delta 1), pack-reused 0
Receiving objects: 100% (101/101), 51.37 KiB | 2.23 MiB/s, done.
Resolving deltas: 100% (4/4), done.
Tapped (109 files, 268.1KB).
Error: Unknown command: bundle
before_install.1
0.01s$ echo $PATH
0.05s$ if [ "$TRAVIS_OS_NAME" = "osx" ]; then
    eval "$(/usr/libexec/path_helper)"
    sudo tlmgr update --self
  elif [ "$TRAVIS_OS_NAME" = "linux" ]; then
    tlmgr init-usertree
    echo MSG FROM JO:
    echo on linux we cannot update apt installed texlive
    echo next steps to fix see commit msg: tompollard@85fd9e7
    echo c.f. https://tex.stackexchange.com/questions/551383/cant-run-tex-lives-tlmgr-in-a-github-action
    echo and https://tex.stackexchange.com/questions/1092/how-to-install-vanilla-texlive-on-debian-or-ubuntu

  fi

sudo: tlmgr: command not found
```

Added:
* Troubleshooting
* More info to "how does it work"?

Also added comments re updating all

* Section references - chapter 1
  * Uses plain LaTeX \ref{...} to indicate how to refer to each section.
* Use of URL links - chapter 1

Still todo:
* footnotes
* label arbitrary sections like it was an equation (e.g. the code snippet)

I think this makes sense, given that we are tracking both thesis.pdf (a large
binary file), and thesis.html (a file which refers to these images).

Debatable whether this is really required. I do it for completeness. I don't
know if we will be able to track changes the the file i.e. will it stay the same
if we generate from the same markdown?