added derived/TNRS/web_app/protocol/

moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).

derived/biengeo/README.txt: updated geoscrub.sh runtime

derived/biengeo/load-geoscrub-input.sh: allow the caller to override $DATAFILE in the environment, to use a file named other than "geoscrub-corpus.csv"

derived/biengeo/load-geoscrub-input.sh: updated $DATA_URL for new input filename

/run geoscrub_input/make(): include a header on the CSV file, so that the column names don't risk getting spliced from the data (and to shorten the CSV filename, which had to contain the column names instead). this requires changing the geoscrubbing scripts to accept a CSV header.

Added an output CSV file option to geoscrub.sh.

Added notes on running biengeo scripts to README.

Added biengeo script options for data directories.

Added GADM and geonames.org data dir options to
update_validation_data.sh scripts.
Added geoscrub input data dir option to geoscrub.sh scripts.

Added update options to biengeo update_validation_data.sh

Added options to update only GADM data, only Geonames.org data, or
neither. In every case, the geonames-to-gadm scripts are always run.