Refactor ModuleGraph interface

The 'ModuleGraph' abstraction represents the relationship and strucutre
of the modules being compiled. This structure is meant to be constructed
once at the start of compilation, and never changed again.

However, it's exposed interface was confusing and exposed too many
footguns which led to inneficient usages of the ModuleGraph. This commit
improves significantly the exported interface of ModuleGraph, taking
into consideration the recent improvements around reachability queries.

Since the ModuleGraph graphs and related structures (HPT, EPS) are
performance critical in the sense that somewhat simple mistakes can
cause bad leaks and non-linear memory usage, we want to have proper APIs
that guide efficient usage. This is a good step in that direction.