Move some methods into FijiTools

They were in the Main class only out of historical reasons.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Use the shiny new ij1-patcher way to initialize

We have a new and improved way to initialize the legacy environment. The
code has been factored out into its own project, ij1-patcher, and we use
that, plus ij-legacy.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>
Document fiji.Main

While at it, deprecate a bunch of stuff.

Signed-off-by: Johannes Schindelin <johannes.schindelin@gmx.de>