Markdown-ify of top-level doc readme

- Replaced doc/README.txt with doc/README.md and markdown-ified.

- Rearranged for clarity, separating the config files from the subdirectory list.

- Introduced separate build section and reordered in the correct order.

In my opinion, the screenshots (pyplots directory) have a dubious status; but in any case pyplots should be e.g. inside users, as should glossary. I am not sure if this will break something, so I haven't done these moves myself.