fix: remove recently added deno.json node_modules aliasing #25542
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This was initially added in #25399 in order to make transitioning over from package.json to deno.json more easy, but it causes some problems that are shown in the issue and it also means that the output of
deno install
would have different resolution thannpm install
. Overall, I think it's too much complexity to be smarter about this and it's probably best to not do it. If someone needs an aliased folder then they should keep using a package.jsonCloses #25538