fixing bug due to updated cat files

[jsemple19]

A few suggested fixes:
Necessary ones:

1. There was a bug in the worm_cat_fun since the default value was an annotation file that no longer existed in the package data. I updated the default in the function and also modified the code so that if the file is not found in the package data, it will treat the file name as a path to a file outside the package. This makes it possible to use more up to date files or even custom files.
2. The function documentation was confusing as it referred to "Wormbase ID" and "Sequence ID" but if you don't use "Wormbase.ID" or "Sequence.ID" then the table join breaks.

Useful ones:
3) worm_cat_fun will not try to create the output_dir unless it doesn't exist - makes it easier to rerun jobs and overwrite results.
4) added option to worm_cat_fun to turn off creating a zipped archive (default behavior is the same as before)