Split up annotations by top-level elements in one
go, instead of doing the filtering per top-level
element (which necessarily makes things quadratic,
or rather O(n*m) with n top-level elements and m
size of annotation map). The fixed version should
be O(log n * m), and log n is negligible.
Previously, if the input did not end with a newline
character and config had 'ppconf_hackAroundIncludes = True'
then due to using unlines/lines the output contained an
additional newline.