Hi,
Yes thats correct. The manual was never updated from the looks of it, sorry its fixed now. Resources/tk2d/* can be reconstructed but it should be checked in.
> Also, in the "After updating..." section of the Manual, is that referring to after updating the version of the 2D Toolkit asset, or after pulling any changes related to sprite collections, animations, etc.?
After updating refers to pull / merge (in git parlance) or or otherwise changing any sprite collection assets externally from unity.