reCOGnizer is called without ".py"

Now called as "recognizer"

reCOGnizer was always called through the shell as recognizer.py. Now, is called with recognizer.

Now removes intermediate folders

Unused directories - tmp, rpsbproc, et al, whose files were removed, are now themselves removed.

Also, several fixes

Fixed conversion COG2KO.
Fixed future warning - xlsx_report.save() to xlsx_report.close().

Updated documentation

Added a nice interactive krona plot.
Also corrected the parameters, and talked about the taxonomy thing.