- Removed multiple conf.py file. Only a single file at top-level

directory. If neccessary, this can be symlinked to other folders as
well.
- Cleanup in index.rst to make sure whole document build as whole one.
- Cleanup toplevel index.rst. Removed non-existing entries.
- Section numbers is currently disabled. It can be enabled in top-level
`index.rst` file by putting `:numbered:` in ::toc.