census node per lineage, not segment: closes #2540

[petrelharp]

I think this was a conceptual error: all segments in a given lineage at a given time point in the simulation are in the same genome (=node=haplosome), and hence in doing a census event we should assign a single node to each lineage, not each segment.

If we agree, this needs an update to the CHANGELOG (and maybe another test? I'm not sure if we've a good way to test this).

Also note the test that triggers #2540 (but this - I think - fixes).

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##             main    #2541   +/-   ##
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  Coverage   93.81%   93.81%           
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  Branches     2250     2250           
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  Misses        574      574           
  Partials      181      181           

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[petrelharp]

Verification that (after fixing it) the new test catches the bug without this fix:

$ git checkout main lib/msprime.c
$ make
$ uv run pytest tests/test_demography.py::TestCensusEvent::test_census_at_end_time
=========================================================================================== test session starts ===========================================================================================
platform linux -- Python 3.13.12, pytest-9.1.1, pluggy-1.6.0
rootdir: /home/peter/projects/tskit-dev/msprime
configfile: pyproject.toml
plugins: xdist-3.8.0, cov-7.1.0
4 workers [1 item]      
Fatal Python error: Aborted

[petrelharp]

What does this affect? So I think it definitely is a bug, in that we're calling things different nodes that aren't really; but this only affects census nodes: it's not going to change anything about the subsequent simulation. So, it's a pretty minor bug. It'd only affect people who wanted to see how many distinct ancestors there were at a given time using a census event

I got curious: how big of an effect is this? Here's a jupyter notebook:
census_edges.ipynb
(run with uv run --with plotnine --with jupyterlab jupyter lab),
and in this simulation of 100 samples from rho=0.01 there's a lot of census nodes that have more than one segment (like, a third of them): here is all the edges below census nodes (of which there are 154), and the color is how many distinct segments a given parent census node has (55 have > 1):

[petrelharp]

(Note: one might naively hope that adding census nodes literally does not change the output of the simulation, seed-by-seed, except for the census nodes, but this turns out not to be true; I'm not actually sure why.)