Merge: Loader refactor

A big refactorization of the loader

This include cleanup, renaming and documentation of the existing code.

The major change is the removal of `ModulePath` used to designate an identified module that is not yet loaded. This caused major issues since once the module was loaded, the MModule object has to be used instead.
Now, genuine `MModule` are used to also represent modules identified in the file system but not yet loaded.
This simplify the code of the loader, nitls and nitcatalog.

By the way, the option `-d` (and `-M`) of nitls that was broken by the previous changes in the loader is now fixed.

Another change is the introduction of `scan_full` that is a high-level method to be used by clients like nitls or nitcatalog that just need to identify packages, groups and modules in the filesystem without loading them.

By the way, nitcalatog works on directories of projects now. eg. `nitcatalog ../lib)

Note, because this PR introduces a lot of interrelated changes, It was hard to come up with nice commits. The alternative was to have a single big commit.

Pull-Request: #1750
Reviewed-by: Alexis Laferrière <alexis.laf@xymus.net>
Reviewed-by: Lucas Bajolet <r4pass@hotmail.com>

diff --cc contrib/online_ide/sources/nit/pnacl_nit.nit
Simple merge