Change doxygen tags to markdown + enhancements

Renamed Documentation.h files to README.md.
Reorganized general documentation and split into smaller chunks.
Change documentation syntax, delete legacy files
Change most remaining Doxygen tags

Moved some docs to README.md files as well.
Fix inline equations spanning two or more lines
Fix remaining @p tags
Remove @file tags
Fix plug-in docs, remove features plug-in
Fix build order issues with parallel make
Merge documentation, refactor socket classes

Merged remote-tracking branch documentation to qml-interface.

Finished refactoring socket classes. This commit compiles, but hasn't
been thoroughly tested yet.