update br chapter

add summary outline and fix error from lacheck
small changes to dc chapter
fix lacheck errors in macros chapter
minor changes to thesis.latex

- fix lacheck errors
- update title
- add acknowelegements
add acknowledgements.latex
2nd pre-draft of betterrnaseq.latex
2nd pre-draft of dynamiccond.latex
add a lot of stuff to bib
update todo
pre-draft txomevar.latex
discussion outline
intro outline
add more papers to bib
forgot to add intro to txomevar chapter
yet more refs
add some more papers to bibiliography