AlgoScan

Instead of calling replaceBytes once per ref and then walking all stored
positions each time, collect all changes first, sort them, and apply them
in one left-to-right scan that builds the new program bytes and a cumDelta
array simultaneously. cumDelta[p] records the total size shift from all
replacements whose replaced region ends at or before p, so any stored
position can be adjusted with a single array lookup in any order.

Complexity goes from O(k*n + k*m) to O(n + k + m), where k = number of
refs, n = program size, m = total stored positions.