Xnos & shortcaption integration + Dockerization

[dendrondal]

This PR contains all features outlined in #87 and also adds a Docker container with these changes, outlined in #72 . Please let me know if you would like me to split the commits by feature and pull request with each individually.

[tompollard]

Great, thanks @dendrondal. It looks like the tests are failing on Travis at the moment. I've posted the error below and will take a look if you don't get it to me beforehand:

$ make pdf
pandoc  \
	--filter=pandoc-shortcaption \
	--filter=pandoc-xnos \
	"/Users/travis/build/tompollard/phd_thesis_markdown/source"/*.md \
	-o "/Users/travis/build/tompollard/phd_thesis_markdown/output/thesis.pdf" \
	-H "/Users/travis/build/tompollard/phd_thesis_markdown/style/preamble.tex" \
	--bibliography="/Users/travis/build/tompollard/phd_thesis_markdown/source/references.bib" 2>pandoc.log \
	--csl="/Users/travis/build/tompollard/phd_thesis_markdown/style/ref_format.csl" \
	-V fontsize=12pt \
	-V papersize=a4paper \
	-V documentclass=report \
	--pdf-engine=xelatex \
	--verbose
make: *** [pdf] Error 83
The command "make pdf" exited with 2.
0.01s$ cat pandoc.log
[INFO] Running filter pandoc-shortcaption
Error running filter pandoc-shortcaption:
Could not find executable pandoc-shortcaption
The command "cat pandoc.log" exited with 0.
0.17s$ make html
pandoc "/Users/travis/build/tompollard/phd_thesis_markdown/source"/*.md \
	-o "/Users/travis/build/tompollard/phd_thesis_markdown/output/thesis.html" \
	--filter=pandoc-shortcaption \
	--filter=pandoc-xnos \
	--standalone \
	--template="/Users/travis/build/tompollard/phd_thesis_markdown/style/template.html" \
	--bibliography="/Users/travis/build/tompollard/phd_thesis_markdown/source/references.bib" \
	--csl="/Users/travis/build/tompollard/phd_thesis_markdown/style/ref_format.csl" \
	--include-in-header="/Users/travis/build/tompollard/phd_thesis_markdown/style/style.css" \
	--toc \
	--number-sections
Error running filter pandoc-shortcaption:
Could not find executable pandoc-shortcaption
make: *** [html] Error 83
The command "make html" exited with 2.

Please let me know if you would like me to split the commits by feature and pull request with each individually.

I'd definitely prefer a set of smaller pull requests, by feature, if you have time to do this, but I understand that you might not! Separate PRs are a little easier and quicker to review.

[dendrondal]

The Travis build failing makes sense, since Xnos and Shortcaption aren't defined in the yaml. Will have to add that.

I'll cherry-pick groups of commits by features and submit those as PRs. I'll do the Dockerization one after, because what I specify there depends on what's accepted.