redesigned save_segments_and_their_sections

We have some elf files where a section (.ARM.exidx) is located in multiple segments.
To keep this property it is necessary to keep track of the emitted sections.
Furthermore, the correct sequence for the segment emission has to be determined.
This is done by postponing segments which are actually a subsequence of another segment.

Additionally the alignment is not considered as part of the file size of a segment anymore.