How to handle duplicate .module files that live in 2 places?
There shouldn't be a job.module in the includes directory at all, your module files for your job module should all be in sites/all/modules/jobs.

You generally shouldn't put anything in (or modify anything in) the includes directory or you will make it harder for yourself to upgrade drupal core in future.

I would say you should:


check for any differences between the two files.
If they are different determine whether or not anything in includes/jobs.module should be in sites/all/modules/jobs/jobs.module. If so add it.
Delete includes/jobs.module