The app-emulation/basiliskII and app-emulation/basiliskII-jit both install a file at /usr/bin/BasiliskII as their main binary, and if both packages are emerged one of them will be overwritten. Proper solution would seem to be to rename app-emulation/basiliskII-jit's binary to /usr/bin/BasiliskII-JIT. Reproducible: Always Steps to Reproduce: 1. Emerge app-emulation/basiliskII 2. Emerge app-emulation/basiliskII-jit 3. Observe 4. If desired, unmerge app-emulation/basiliskII-jit and note breakage
Thanks for reporting. Fixed in -r1.