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Even PHP manages to get this right - Composer uses the Packagist repository as a default but just about any git or svn repo with a URL will do.

npm supports git urls, too (or the even shorter user/project#tag if it is from github)

Composer also supports namespacing

Does apt allow you to have multiple packages with the same name from different repositories? I don't see how it solves this issue otherwise.

No, it does not.

But I don't use the vast majority of apt repos.

I use a handful of well-curated ones with high-quality software, plus a handful for one-off packages.

In contrast, there's basically no limit to how much debris you can upload to npm.

There's a lot of problems with APT. :)