remove unused files

well... I *think* they're all unused. we shall see
stash before ditching autoconf

this is both hilarious and an extraordinarily accurate depiction of my
experience in stochhmm:

http://freecode.com/articles/stop-the-autoconf-insanity-why-we-need-a-new-build-system

my favorite part is where I have to run

% make  # wait for it to crash half way through
% sed $stuff  # because make rewrote its own makefile to remove my -std=c++0x
% make
woooooo holy shit it builds with sons

already! that was easy
work on switching to tclap
lots of clean up and renaming
more renaming and cleanup
hm, well, got the namespaces sorted out

not sure what was wrong that broke it, but it's in the stashes
and... remove std:: from stochMath
rename and cleanup stochMath
change readmes
oops wrong dir
more renaming
add yaml-cpp!

haven't tested yet, but it compiles
yaml functioning inside stochhmm

doesn't yet do anything useful... time to first add yaml support to hmmwriter
stash partial yaml conversion
maybe yaml is working?

it doesn't fail... but now it's time to rewrite the stringify()
functions so I can see what the hell I'm doing
yamlized! &#!@er is totally yamlized!

well, still testing it of course, but it seems to work
renaming things