Pre-index non-alt paths to fix #3054 #3068
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Changelog Entry
To be copied to the draft changelog by merger:
vg addnow supports overlapping reference paths, as in Cactus graphsDescription
We assumed in
vg addthat modifications based on one reference path wouldn't make it impossible to safely position-index a different reference path later. That turns out not to be true, so we need to build all our position indexes before we modify any paths.This will fix #3054.