Hi Andreas,
I'm not very happy with the rename of the binary to "plink2" for this version. I speak with upstream about this [1] and he suggest me to not rename plink 1.9 to "plink2" because the real plink 2 will break more things and will be distributed under the "plink2" name.
So the options are:
1. Stay with the rename to "plink2" for the version 1.9. But with possible breaks when the real plink2 will be released.
2. As suggest by upstream, stay with "p-link" for the version 1.9 with a Breaks or Conflicts field in d/control for the plink 1.07. Not possible to use both versions (1.07 and 1.9) at the same time, so not ideal to replicate results obtained from plink 1.07.