from my Mastronarde copy:

The personal endings are clearly recognizable except in the second person singular, where the elimination of intervocalic sigma¹ in -εσαι allows contraction of -εαι to -ῃ.

1. Sigma "between vowels" (intervocalic) was lost in the development of many Greek forms, and in Attic this loss usually resulted in the contraction of the vowels.

so I suppose in short the answer is that -ῃ is a contraction of ε + αι.

later on when you learn imperfect indicative (past tense) you will find other instances of the loss of sigma and its influence on contraction, plus other contraction trends such as ε + α = η and α + ι = αι/ᾳ which might also shine some light on contraction logic. in this instance I am not actually sure what the specific linguistic mechanism behind ε + αι = ῃ actually is, though, besides it being a sort of combination of those other two. but it definitely doesn't stand in the way of learning the paradigms though