Fix limit arg

[faithokamoto]

Changelog Entry

To be copied to the draft changelog by merger:

• If vg index --snarl-limit has a threshold equal to a snarl's size, it no longer counts as an automatic snarl
• Hint to the user what value they might need to increase --snarl-limit to

Description

Take two! While previously I'd fixed the temporary distance index so that it now performs pairwise distance calculations when N=size_limit, those calculations were all wasted because the same off-by-one error existed when transferring distance values over from the temporary index to the final index. Poked my head into libbdsg to fix that: vgteam/libbdsg#228

Also, I added that max snarl size hint I mentioned in the previous PR, since I had to play with libbdsg anyhow.

@adamnovak help I don't know how to get the submodule update to play nice :( I think I did it wrong.