Changed bzr ls to git ls-tree

I need to update the commands to make an archive file after changing version control software.
Add external packages as submodules

- dbframe package
- oosanalysis package
Move bibtex to external submodule
Update submodules
Update ignore list
Add date generation to makefile

Added code to the makefile to display the date of the commit, the branch, and
the commit SHA (all automatically generated by `make ver`) in the date field
and as a running header on every page.
Update theorem and lemma numbering

Switches from Section.number to just number (at editor's request).
Update location of latexmk
Tweak prereqs for versioning info