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I think, that is because every release is associated to a git tag, which points to the commit for the release. In this repository, the tags are conventionally called "bee-1.2.24" etc. while, for example, in the mxq repository, the tags are convetionally called "0.30.8" etc. The root directory in the archive is REPOSITORY-TAG, which here resolve to e.g. "bee-bee-1.2.24".
If we change the tags to version-only, this would be fixed. On the other hand, it is also a disadvantage to change the customs. If you know, that you current tag ist "1.2.400" and you want review something in version 1.2.24 you might wrongly conclude that the tag for that version must be "1.2.10" when in fact it is "bee-1.2.24". But who needs to look something up in old version?
Another nice thing with the longer tag is, that the generated URL for that release , https://github.molgen.mpg.de/mariux64/bee/archive/refs/tags/bee-1.2.24.tar.gz would produce a file bee-1.2.24.tar.gz on download per default. Otherwise you might end up with an ugly '1.2.24.tar.gz' or need to fix the name one way or another.
as said before...
tar file has weird directory root...
bee-bee-1.2.24/
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