Don't remove msprime mutations in the recaptiation region

[petrelharp]

so if you keep the initial slim generation in the tree sequence
ie don't simplify
then you can always tell which muts happened in the slim period versus in the recapitation period
so you should only thin mutations in the slim period
so only mutations for which the parent of the edge on which the mutation occurred lived since the start > of the slim period
can efficiently get that out of the tables

[mufernando]

Can you help me craft a solution to this? The existing code to remove the mutations is in greatapes_sims/overlay.py

[mufernando]

Fixed with commit fff9f61

Pretty sure this does the right thing, but would be good to have a code review (@petrelharp ?)

[petrelharp]

Looks good!