Docs, make, cleanup (#18)

* Update PUBLICATIONS.md

* Add markdown docs

* Clean up the make build

* Fix make include path bug

* Small docs fix

* Update docs source to Markdown

* Jekyll yaml config no longer needed

Implementation of sea ice: reduce wind input and wave dissipation in …

…presence of sea ice.

Implementation of sea ice: starting point

Implementation of sea ice: namelist options and parameters; reading s…

…ea ice from files and time interpolation