Markdown Conversion for the rest of documentation files

[danlwill]

Still work in progress

Changes:

• \grad converted to \nabla, \Bkappa to \kappa
• \underbrace removed and equations separated out
• converted tables to markdown syntax
• removed \ forced indent because of incapability, instead just created a new {align} space
• Changed title headers and sub headings to markdown syntax
• Removed LaTeX bibliography space and replaced with manual writing
• Changed links to link syntax
• Manually cited equations and sections when they are referenced (markdown does not support equation labels and citation)
• Changed bold and italics to markdown syntax
• Wrapped all equation spaces with $$

[landinjm]

Closes #189