1st scenario (Ag/Commercial loan): You are correct. This is not reported for HMDA. First, ALL ag loans are exempt. If non-Ag, commercial purpose, then only if it is used to purchase, refinance or improve a dwelling. Since this is a business operating loan, it is NOT reported (the first time). IF you were to refinance this loan, it would be reported (as a refinance).
2nd scenario (credit card): You are correct. This is reported as an other purpose.
3rd scenario (existing lien replaced to pay down a loan). Let's break this apart.
If it's for Ag purposes, it is not reported. ALL ag loans are exempt.
It would be repotted if the purpose was for Commercial or consumer reasons. You have an existing, dwelling secured loan, that you are replacing with a new, dwelling secured loan. The purpose of those funds won't matter (unless it was an exempt reason - like all Ag loans).
Concerning Ag loans: §1003.3(c)(9) tells us not to report any applications for loans or lines primarily for agricultural purposes. Also, Comment #1 to this section tells us not to report any loans where there's a dwelling on land that is used primarily for ag purposes (a farm).