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If I simply would package libpll-2 in the very place where libpll was packaged and I keep that name (without the -2) this would be pretty convenient since its not a new Debian package and does not need any new processing. Do you think this is the correct way to go?
Yes, I think this is the way to go.
In fact, in the next major raxml-ng release, both libpll-2 and pll-modules will be superseded by the new lib coraxlib:
https://codeberg.org/Exelixis-Lab/coraxlib
This should hopefully solve the long-lasting historical name confusion.
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