Creating an OCaml Project in Multiple Directories

I have a medium-sized OCaml project (13K lines, 85 source files) that is built using OCamlMakefile, but it has a slightly overgrown OCamlMakefile: instinctively, I would prefer to split it into three or four directories and put the files in it like libraries, not last but not least, since some parts of the overall project must be separate projects in their own right.

What is the recommended way to do this in 2012? OCamlMakefile imposes a number of simplifications that interfere with what would be considered normal code organization in most other software environments.