thaumcraft 6 cannot begin without a Thaumonomicon. Mining an Air Crystal, Fire Crystal, Water Crystal, Earth Crystal, Order Crystal, Entropy Crystal, or Flux Crystal will yield this. A message encouraging the player to sleep in a Bed will be sent to them after that.
After the player has settled into a bed (the server does not require them to sleep through the night), they will be given a book called Strange Dreams with instructions on how to use Salis Mundus on a Bookshelf to get the Thaumonomicon.
A comprehensive thaumaturgical reference book is The Thaumonomicon. It gives a sense of how much more there is to learn by listing all of the discoveries made up to this point.
The player can go through the discoveries and click on them to get more information, as well as any addenda they've found and any associated crafting instructions.