added cleanup_tmpfiles(), create_tmpdir() can set directory, only create files that don't exist already

Changed to use gene tree homologies, and to only use homologies of type "ortholog_one2one" and "apparent_ortholog_one2one". Should avoid many-many etc.

Also set status of the gene's transcripts.

First patch file for 38->39. Adds 'KNOWN_BY_PROJECTION' to enumerations for status in gene and transcript.

Note new patch file naming convention.

Added code to remove anything in parens from the RefSeq entry sequence line. E.g. s/Oryza sativa (ssp. japonica)/Oryza sativa/

Added logic_name option, get_mysql_command method, and a warning in direct_xref if the source does not map to an entry in the target database external_db table