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For every problem, how many times did package management work flawlessly?None. It built a massive teetering edifice of fragile interdependencies that incurs staggering human cost in maintenance, and has almost singlehandedly stood in the way of progress by third-parties that would benefit from working outside that system -- from commercial software vendors to OSS vendors that would prefer to be able to release versions on their own schedule.
If it wasn't for package managers making it possible to maintain fragile dependencies in lockstep, Linux distributions would have been forced to confront simple issues like ABI and API compatibility, third-party distribution, and other basic facets of producing a user-friendly and vendor-friendly OS ... we may have even had a "year of Linux on the desktop" by now.
Instead, we keep throwing humans at the problem of keeping the teetering pile of dependencies operational, largely because of people like you that cargo cult the ideas out of some strange combination of stockholm syndrome and a lack of vision for how things could be better.
Why was anyone was surprised that Google threw away the entire Linux user-space when developing Android?
> So, the user tried to somehow bypass the official distro package management.
... because that's the only way to achieve perfectly reasonable goals as a user.
If I want to install Chrome, guess what it does? It adds an external repository that broke in strange ways when I updated Ubuntu.
> If you open up your microwave oven and electrocute yourself, is that because of a basic flaw of microwave ovens?
Your microwave doesn't refuse to operate unless you only buy food that has been prepackaged by your microwave vendor, that can only be mixed with other food also repackaged by that vendor, and only if all the food has been pre-certified to work together in that exact combination.