fix(prune): Handle `patchedDependencies` for bun (#11027)
~~`bunfig.toml` is basically bun's `.npmrc` file. Needs to be copied to
handle options like `linker = hoisted`~~
Prune was already correctly pruning the `patchedDepenedencies` in the
lockfile for bun, but it wasn't pruning them from `package.json` which
was causing `bun install` to complain that the patches were missing.
In addition, it was not copying the patch files for packages that
weren't pruned
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Co-authored-by: Anthony Shew <anthonyshew@gmail.com>
