Renamed lib/parse to lib/reader.

Includes all of the necessary rewrites. This naming change is inspired
by the fact that lib/parse actually handles all of the manifest file
reading, not just the parsing of a token stream. There was a kind of
redundancy in the path spec lib.parse.parse . Hopefully, this will be
clearer.
Renamed lib.settings.settings to lib.settings.config

This change accomodates the fact that the settings package may be used
in the future to handle dynamic alteration of settings in an interactive
context. Although there are no plans for this at present, the new name
is somewhat more appropriate.
Merge branch 'refactor/naming-cleanup-1' into dev