Removed extra files

Realized \newpage works from markdown in pandoc (no tex necessary). Deleted intermediate files that can be generated anytime.
update sh

Now a single one generates final copy.
Updated manuscript

Without all the extra .tex files.
Commit addresses minor comment #2 from reviewer 2
Revised intro to address comment 1 from reviewer 2.
Merged two copies of same repo

One has revisions to ms and the other was just used for cleaning up files (i.e. removing all the .tex dependencies).
Moved figures to separate folder

All in preparation to finalize the repository for permanent archiving.