I haven't looked in detail at the code, but I'd put the block comments into pod blocks. In the short term they are easier to edit and in the longer term there are nice tools for pulling the pod out into various documentation formats. Consider:

=head3 adjust_fillstate

   my $rects = adjust_fillstate( $quadrant_bit );

This function extracts all the non-overlapping rectangles in the tree,
returning their coordinates separated by : in sets separated by |.

=cut
[download]

which renders in HTML as:

• adjust_fillstate

---

adjust_fillstate

   my $rects = adjust_fillstate( $quadrant_bit );

This function extracts all the non-overlapping rectangles in the tree, returning their coordinates separated by : in sets separated by |.