[refactor/fix] remove extra cpitch in layout_dense

Cummulative pitches were kept up to the total storage size of the
layout, even though our code never uses this information. Remove a bug
due to bad array size arithmetic, and remove the extra element in the
array too.

This patch also removes the pitches provided by the user from the
6 jobs for cpitch-rework in 8 minutes and 21 seconds (queued for 1 second)