download-all.pl: use Getopt::Long;

Also require setting of users file and assignment root path on the
command line.
download-all.pl: change users file format

Fields must be tab-separated; can use # for comments.
build-table.pl: use Getopt and new users format

See the earlier changes to the download script.
update.sh: use command-line opts for build-table
download-all: only recompute oracle with results

Don't try to recompute the oracle-best for the alignment assignment if
the assignment2 scores don't exist yet.

As a minor bugfix, we now actually use the assignment-root variable.
download-all: set files to find on command line
update.sh: set +r on newly-created table