Implement abstraction over dependency kinds

This commit implements the abstraction over the dependency kinds and
deprecates the methods that were used to register files and their
dependencies.

Dependencies are now divided into two categories : Internal and
External dependencies. Moreover, each internal or external dependency
has a Context, which describes what introduced the dependency (for
instance, a dependency may be introduced by member reference or by
inheritance).

Dependencies must now be registered using the method `addSource` in
`Analysis` and in `Relations`. This method has the advantage of being
independent from the existing dependency contexts. That is, its
signature does not need to be modified whenever a new dependency
context is introduced.