How to Version a Deck
To version a deck, simply click on Versions.
Click Tag This to create a new version of the deck.
Enter any text you think is appropriate for the new version.
When you click on a version in the Versions pane, you'll get a comparison with the current version of the deck. You can see that comparison here.
If you want to compare two different versions, you'll need to make one of them the active version. You start by clicking on the version that you want to make active.
Then, click Use.
Now you can open the Versions pane again and compare the active version (that you just replaced) against any other version.
If the current version is not tagged, Amaranth will warn you.
Seeing Your Deck Over Time
As I mentioned at the beginning, it can be really interesting to review a deck over the course of its lifetime. I invite you to check out Undue Art Scam. You'll notice that the name is no longer accurate: the deck doesn't even contain any Art Scam any more. If you review the deck, it gone from 90 card down to 60 and back up again. The crypt is rather different, including having Maldavis (ADV), at one point.
Do you have a deck with a long history? How drastically has it changed?