change the output of clade.freq to just a df

instead of returning the tip labels too
cumulative.freq now uses slide.freq.table

and should be a lot faster
slide.freq speed ups

we never analyse all the trees at once, just the windows. This speeds
up the code a lot.
Deleted leftover code from slide.freq

Just stuff that was left behind when changing to the fast method.
fixed errors, added mean and sd
added code to strip mean and sd from slide table
Merge branch 'dan_messing_with_fast_slide' into fast_slide
removed unnecessary print statment

and some whitepace too
tab cleaning

like Tab Clear from the 80's, but better.
whitespace in plawty
added plot.cladeprobs function

this is really just a clone of the current plawty function, but a bit
more efficient in how it melts the input data. I also changed the look
of the plot, and made it default to all clades, just to see what it
looks like.
added plot.cladevar function

this plots the absolute variation in posterior probabilities over time.
I.e. for each clade that's seen, we want to know how much it comes and
goes. I think there's a better way to do this, but it's a rough proof
of principle right now.
added gitignore file
moved test data to testdata folder

and updated the test_RWTY.R accordingly
added test data from hox genes

some ~100MB files from mr bayes.
added new tests based on hox data
fixed bug in cumulative.freq

which occurred only when passing in a slide.freq.table. Solution is to
use NULL as default, not NA.
fixed tests
added TODO to cumulative.freq
added phangorn as dependency