Anon:
A provisional patent application will never publish so you should not fear including details about your invention for that reason. Provisional patents should include as much detail as is necessary to allow one of ordinary skill in the art to practice your invention. In other words, it must enable the invention. If it does not, it is useless as the basis for the filing of an eventual non-provisional application. Claims, however, are not necessary for provisional patents and therefore need not be included.
With many inventions, there is an intersection between what is disclosed to meet the requirements for patentability and what information might be kept as a trade secret. You should seek appropriate legal counsel to discuss this issue in greater detail and how it relates to your "secret ingredients". You should also consider copyright protection for software.
A few extra tips from a pro - put a copyright notice into the code (that's the "C" in a circle with a date and a phrase such as "All rights reserved"). Also, insert a few misspelled words here and there. This is a simple method of catching someone who has wrongfully copied your code.
This information should not be considered legal advice for your specific circumstances and are offered only as general information on the topic.
Philip Braginsky, Sills Cummis and Gross, http://www.sillscummis.com/practice/practice_group.asp?id=28
Answered on Aug 10th, 2011 at 6:58 PM