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So I just saw ProJared play this game and I it honestly got me a little bit excited. It's been ages since I've played magic and the Shandlar game seems like a good place to get back into the game. I remember having found memories of the Klans of Takir and fate reforged per-releases; the latter being where I clocked my first and currently only tournament win. So that got me thinking, if the current manalink features (presumably) all the cards from these sets, is it currently possible to set which expansions' cards are available ingame? I'd love to play though it with just Klans of Takir cards and the 2015 base set as a challenge, but at the same time, I don't want to have to go through and remove the card data manually. If not, consider this a suggestion.

Manalink3.0 patches doesn't support shandalar and they are two different projects Manalink3.0 is gauntlet, duels, challlenges, etc and shandalar has the adventure part.
If you don't have a modified shandalar by Korath your other choices are Microprose Magic the Gathering 2010 Custom Installer ISO which doesn't have any changes from original or Shandalar 2012 Revisited with UI changes only.
If you do have a modified shandalar by Korath take a look at shandalar.ini it can give you more or less what you want except for AI decks which you have to change to fulfill your needs.

Okay, I do have a modded version of Shandlar.
So under sets I entered;
Promo -- Vintage Masters= disable
Magic 2015 -- Dragons of Tarkir = enable
Modern Masters 2015 Edition -- Aether Revolt = disable

And immediately got the desired result, so thank you very much!