Small fix in Makefile

The current Makefile does not correctly handle dependencies and you may have to run ```make clean``` before running ```make```.

The main reason is missing ```-I core -I solver ...```  as parameters of ```ocamldep```. This PR reintroduces these parameters and call ```ocamldep``` through ```ocamlfind``` in order to avoid
broken dependencies on ```+ocamlgraph/persistent.mli```.

This PR also introduces ```.mli``` for all source files. This is a bit annoying (e.g. for ```core/opamTypes.mli``` or ```core/opamGlobals.mli```) but this avoids a strange interaction with the current  usage of OCamlMakefile where some files were recompiled 5 or 6 times.