Seperately track every different source of exercising an attribute, with diminishing returns for repeated use of the same exercise source until that attribute changes value, which resets it. This prevents you from spamming an easy-to-do exercise source such as pushing boulders around or writing Elbereth, and makes you diversify your sources of exercise.

Possibly weight the different exercise sources (e.g. successfully finishing studying a spellbook should be worth more for Wisdom exercise than successfully casting that spell is).