major refactor of analysis files, now wired up to registry

ultimately this is make it more convenient for us to wire up
different elements of the analysis pipeline, without having to
preload everything into memory before we need it

separately the index layer now has a mechanism for storing
internal key/value pairs.  this is expected to be used to
store the mapping, and possibly other pieces of data by the
top layer, but not exposed to the user at the top.