True, they were concerned because offering plain compressed binary packages is one of the methods currently for getting Linux software. Since these formats of course contain no data about where the files should be placed, it'd be difficult to have the package manager deal with them in the way they were supposed to be installed, but it still could deal with them. The package manager could offer to deal with the file, and it could store them in a special place for simple uncompressed binaries, and could either ask the user for a name for the program or just use the name of the compressed file. That way, the user could "uninstall" them from the manager interface. I don't know, just an idea, but of course a much better solution is that a standard package format/container replaces this compressed program distribution system.
Unless the package manager was just a simple program which listened to a universal configuration file which told managers where the user wanted files placed, and if package managers dealt with dependency resolution issues in the same way because they and the package format had all the information necessary to cope with anything thrown at them (within a confined scope of some standard packaging API), then yes they could cope side by side I think.
I'd love it if things become that modular, but I think just making each package manager able to read multiple package formats would hopefully be enough.
Actually I think .bin is used for binary files sometimes, but now I can't find any examples of it. >.< Oh and don't forget .run files. I don't know if a package manager could deal with all of these, well, I'm sure it could be done but perhaps it wouldn't be that appropriate. At the very least, any files which are based on scripts will be replaced with proper package formats, like .run and such, since there's no need to make a jerry-rigged script to accomplish what a simple package format will do and make much easier.
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