As identified in #1091, Helmert implementation in PROJ 5.0 and 5.1 is confusing.
It happens that by default it used the coordinate_frame convention, contrary to
the position_vector convention used traditionaly for +towgs84. The documentation
of Helmert was also wrongly specifying that the default convention was
position_vector.

This commit:
- bans the confusing +transpose parameter
- removes the concept of a default convention, since in practice both are
  equally found, and requires +convention as soon as a rotational term parameter
  is present.
  For translation only, convention is ignored and optional, as having no effect.
- fixes all the identified uses of proj=helmert in code, doc and tests

This is obviously a breaking change:
- users will have to adapt their pipeline expressions
- in particular, init files that would use helmert must be adapted

However, as designed, the break will be explicit, and not silent.

The 'Applications' chapter is moved to the top level of the website in
order to make it easier for users to find the pages quickly instead of
having to search through sub-sections in other chapters.

The doc pages are reformatted to better use the features of the Sphinx
documentation system. All four pages has been formatted such that they
can serve as the basis for both the website and UNIX man-pages. This
will make it easier to keep the man-pages aligned with the main
documentation in the future.