> Still my question remains, how one should configure a project
 > that consists of several libraries and one binary, together
 > with ocamlbuild. E.g.,
 >
 > +- prof.dir/
 > +-+- A/
 > | +- a.mllib
 > | +- a1.ml
 > | +- ...
 > | +- aN.ml
 > |
 > +-+- B/
 > | +- b.mllib
 > | +- b1.ml
 > | +- ...
 > | +- bN.ml
 > |
 > +-+- Main/
 >   +- main.ml (depending on a.cma and b.cma)

Well, is it a problem to compile using:
	ocamlbuild -Is A,B,Main main.byte

If you really want to build libraries independently then maybe you could 
build the cma files, copy them in a "lib" directory which won't be 
included by ocamlbuild (because of "sanitization" restrictions) and then 
use the "-lib" option to use "lib/a.cma" and "lib/b.cma"...

The script would look like this, supposing B depends on A and Main 
depends on A and B (not tested):

#!/bin/sh
ocamlbuild -I A a.cma
cp _build/A/a.cma lib
ocamlbuild -lib lib/a -I B b.cma
cp _build/B/b.cma lib
ocamlbuild -libs lib/a,lib/b -I Main main.byte

-- 
Romain Bardou