Coq_makefile: -extra[-phony] correction + doc
Coqdep: update include strategies

-I is (only) the ml one
-I -as is fixed
-Q is understood
-R is not a recursive ml include anymore

$COQENV, user_contrib, ... are not recursively included

coqlib/theories and coqlib/plugins are still recursively included (for now). (This
may deserves an option)

Closes Bug 2910: If there is a "Require a." in a b.v and a a.vo in path but no a.v,
coqdep does not complains about a missing a.v.
coqc is -Q aware
Coq_makefile takes advantages of -I -Q -R cleanup
refresh INSTALL