Improve user guide text for command line interface

Improve user guide text for command line interface

- Restructure the tools.rst to have all the content on a single page.
- Correct inaccuracies in the information about common options and
  general behavior, and extend the text to cover more cases.
- Include the list of common options on the HTML pages (somewhat ugly
  still).
- Restructure the Sphinx input for easier management and
  understandability: all pages generated from the gmx binary is now
  under onlinehelp/, and all rst fragments (whether generated or not)
  are under fragments/ to make it easy to apply the same rules to all of
  them.

Change-Id: I2d55281bfba7dc781afcc2b09a9fef843730de5f