Update manual analysis section

- Reference tools as 'gmx <tool>' instead of the old names.
- Expand the section on selections now that there actually are some
  tools that can use the full power.
- Rewrite sections that were referencing obsolete tools (g_bond and
  g_sgangle).
- Remove references to tools that aren't there.

Change-Id: Iee99f69e2d4effa585d98930ef1d78c1367e2ec0