Add .merlin file, until assemblage is maybe able to bootstrap one.
Move commands (formerly tools) to their own module.

First step towards exposing them as cmdliner terms.
Rewrite bootstrap procedure.

More convenient if a new compilation unit is added and no longer uses
ocamlbuild (since it will be forked off the compiler). First
build/rebuild is now 0.9s/0.9s vs 4.2s/0.6s with ocamlbuild on my
machine.