Clean up file paths for new module hierarchy
This updates comments only.
This patch replaces file references according to new module hierarchy [1][2].
For files under the compiler/ directory, I replace them as
module paths instead of file paths. For instance,
GHC.Unit.State instead of compiler/GHC/Unit/State.hs [3].
For current and future haddock's markup, this patch encloses
the module name with "" [4].