[Documentation] Small formatting fixes for ReadTheDocs

[AlexandraLivadas]

Small formatting changes to a few of the markdowns so that they appear correctly in Read the docs. Updated the mkdocs.yml file to point to the correct document links. Updated the API documentation symlink docs/wiki/99_Developers/LORIS-REST-API-0.0.3-dev.md to point to the updated v0.0.4 version. Not shown here but multiple wiki links were updated to point to RTD.

Testing instructions

Checkout this branch on your fork and test how it appears on RTD. Please check that all the links are pointing to the correct document and that all formatting changes are appearing correctly. See this document for more information on setting up RTD and testing.