Markup, links, typos, more comprehensive version history

I cleaned markup and some typos.
I also fixed missing or broken links.
I noticed the changes per version were documented but inconsistently, and it was hard to tell what the current version was. I documented all the version changes (using the freedesktop.org commits as reference up to 0.0.5) (and making them consistently use Sphinx's version history directives) (and counting !2 (merged) as incrementing the version from 0.0.5 to 0.0.6), and made index.rst indicate the version.

If I was unsure about the meaning of anything in the specification, I left it unchanged here.