We tried playing a map ( http://www.minecraftmaps.com/game-maps/sorcerers-book-2 ) in vanilla Minecraft, it worked flawlessly.
Now we're testing whether it works on Spigot. Sadly, on none of our testing servers the main mechanic of unlocking spells really works.

Here are our current configs (we tested a few, see "Description" for more):
Commands.yml:

command-block-overrides:
- '*'
unrestricted-advancements: true
aliases:
 icanhasbukkit:
 - version $1-

Spigot.yml:
    Default except: 

commands:
 tab-complete: 0
 log: true
 spam-exclusions:
 - /skill
 silent-commandblock-console: false
 replace-commands:
 - help

    (And we changed mobranges.)

Bukkit.yml:

<default>

What is supposed to happen:
1. You open the book you have in your first hotbar slot form the beginning.
2. You type the short tag aka symbol of a spell (e.g. "BAL") into the book.
3. You click on "Cast spell" (if you have the texture pack enabled. If not, click the right button.)
4. You get a message in chat that your spell is unlocked and you get a new hotbar item to cast it.

What happens instead (even with all the configs mentioned above):
1. You open the book in the first hotbar slot.
2. You type e.g. "BAL" into the book. (we tested many spells).
3. You click on "Cast spell".
4. Nothing.

Even if you are OP nothing happens. What I first suspected when testing this is that advancements test for permissions and as Spigot has its own system it could have gone wrong there. Sadly, even with the right configs and even if all players are OP none of the commands in the advancement reward function get triggered. 

We tested:

• Players aren't OP with default Spigot config.
• Players are OP with default Spigot config.
• Players aren't OP with changed Spigot config (as seen above).
• Players are OP with changed Spigot config (as seen above).

My conclusion:
Somehow commands in the advancement reward function, more specifically the function itself, doesn't get triggered at all.

The log doesn't say anything (all commands being executed and shown in the chat/log by us were executed through manual input in chat), I'll attach it anyways. Also attached our own copy of the map in a zip file, though you can download a fresh copy on your own, both won't work.

Edit 1: I've recieved a small function/advancement zip with only one example of advancement rewards and it works. So Sorcerers Book 2 isn't working on Spigot, though the newly attached file is working.
Edit 2: We tested again, the Sorcerers Book 2 works on Vanilla Minecraft 1.12.2. It's really just breaking in the Spigot context. Meaning maybe advancements aren't even what is broken here, but something is!