`odgi flip`: avoid introducing useless edges and losing edges from the original graph

[AndreaGuarracino]

This PR introduces a different way to construct the flipped graph:

• copy all edges from the input graph
• flip paths
• check missing edges (due to flipped paths)
• add missing edges (if any)

In the first tests, this avoids introducing edges that are not used in the flipped paths and avoids losing edges that are present in the input graph.

[anshumanmohan]

Thanks for this, @AndreaGuarracino! I can recreate the fact that it now (correctly) does nothing for the graph LPA.gfa. However, it now does the same fishy thing for note5.gfa.

When I run flip on note5, the only meaningful change is that L 3 - 4 + 0M becomes L 4 - 3 + 0M. The paths, segments, and other links remain the same.

If I understand flip correctly, the correct behavior for this graph is to do nothing.