pandoc/markdown support

[crmackay]

• add support for a markdown -->pandoc --> pdf workflow
• this allows for easier writing, and easier reference management

[crmackay]

so this ups the dependencies a bit, but would be a metadata.yaml file, series of markdown files, and a .bib bibliography database.

Using a python script to orchestrate everything, the yaml file would be read to order the chapters, then everything is streamed to pandoc, along with ummsthesis-template.latex pandoc template, and umms-thesis.lua custom pandoc writer.

├── metadata.yaml (author, title, readers, date, chapter file names, etc.)
├── acknowledgements.md
├── dedication.md
├── abstract.md
├── chapter-project-one.md
├── project-two.md
├── introduction.md
├── bibliography.bib
├── ...
├── ...
└── figures/
|   ├── western-blot.pdf
|   ├── qpcr.pdf
|   └── gene-pile-up.pdf
└── resources/
    ├── ummsthesis.lua                   (custom writer for pandoc)
    ├── ummsthesis-template.latex        (custom template for pandoc)
    ├── nih-citation-styles.csl          (citation styles format....not decided on this yet)
    └── compile                          (python script that pulls everything together and 
                                          sends it to pandoc, and then saves the pdf properly)

so in order for it to work you need:

• a TeX distribution (MacTeX, or MikTeX, or TeXLive)
• pandoc (crossplatform, compiled---from haskell)
• pandoc-citeproc (a python filter for pandoc)
• highlighting-kate (a code highlighting utility, available compiled)
• python (2 for now, but really should start using 3 at this point)

... is this too much stuff?