Option is off by default and can be turned on by using the flag -include_duplicates

Formatting.

Add penalty when source and target are not on the same seq_region
(currently halves the score).

that I remmeber where I'm at tomorrow... or the next day.

sorex_araneus

just as is done for adding source.

If the table (either xref or object_xref) is empty, $max_val will be
undefined.  Make sure that we substitute 1 for it in this case when
calling add_meta_pair().

Use -s to determine if a file previously fetched is not only there but
also if it's non-empty.  If the file is empty, unlink it and fetch it
again.

Also, clean-up.

schema version to 64 too.

the is_current field is not updated.

fix for errors in getting a database connection when in disconnect_when_inactive set and is being called to0 fast for the system to keep up with