In general, you do not want to do make clean before make depend. make depend needs to have a number of things already built in order to work: the runtime runtime/ocamlrun (so that it can run boot/ocamlc to compute dependencies), and also it needs to be able to build all generated files so that dependencies are accurate. Some of these generated files are built themselves with boot/ocamlc, so again the runtime needs to be available.
This seems about right. Note that in the current trunk dependencies for C files are no longer stored in the repository, so there is no need to do make depend in the runtime directory anymore.
No.
This is again because make clean should not be used before make depend. In general you want to be in a stable state (ie after a successful make) before doing make depend.
Best wishes,
Nicolás