Reorganization of manual source files

I renamed all files from .txt to .md so that they can be
visualized on github.

In addition, I renamed all files to have a name consistent with the content.
This makes manual portions easier to find.

Notice that I left the original labels (e.g. "Syntax" instead of "Getting Started")
not to break direct links to manual, though I think we should rationalize these names
as well.

[makedoc]