Reduce excessive path indexing

[adamnovak]

Changelog Entry

To be copied to the draft changelog by merger:

• vg find -Q/--paths-named is now deprecated due to its partial-Protobuf output
• vg find will now index its target paths but not other haplotype paths.
• vg should no longer position-index haplotype paths unnecessarily in commands using the PathPositionOverlayHelper.

Description

This should fix cases where using the PathPositionOverlayHelper was making us index all haplotype paths.

I'm not sure if more commands need to be patched like vg paths to send along the names of haplotype paths they're actually interested in, to let queries on haplotype paths work. But we've only been indexing all the paths for a few months, and before that I think the behavior before that was for those queries to mysteriously give wrong answers.

[adamnovak]

I think we might need to fix vg stats --snarl-sample; I'm not sure it's under test with non-reference samples.

[adamnovak]

This uses vgteam/libbdsg#241 in libbdsg.