wrangler: 3.80.1 -> 4.16.0

[ezrizhu]

Fixes #409155
Fixes #381980
Fixes #376947

Relates to #352287 but I think we should have a closer look to address the comments in a future commit.

Closes #377334

Upstream Changelog: https://github.com/cloudflare/workers-sdk/releases/tag/wrangler%404.16.0

Besides the version update, I also resolved two issues that prevented us from updating wrangler (context in the update request issue).

• Broken symlinks: nixpkgs build now checks for broken symlinks, this PR adds all the relevant directories back to the out dir so all symlinks are intact.
• Missing npm: wrangler specifies an older version of pnpm than the one in pnpm_9 as used in the build process, this PR patches the package.json to remove the pnpm version so pnpm_9 doesn't attempt to change it's version resulting in a pnpm binary not found error. (with help from @cameronraysmith)

Things done

• Built on platform(s)
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
  • sandbox = relaxed
  • sandbox = true
• Tested, as applicable:
  • NixOS test(s) (look inside nixos/tests)
  • and/or package tests
  • or, for functions and "core" functionality, tests in lib/tests or pkgs/test
  • made sure NixOS tests are linked to the relevant packages
• Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
• Tested basic functionality of all binary files (usually in ./result/bin/)
• Nixpkgs 25.11 Release Notes (or backporting 24.11 and 25.05 Nixpkgs Release notes)
  • (Package updates) Added a release notes entry if the change is major or breaking
• NixOS 25.11 Release Notes (or backporting 24.11 and 25.05 NixOS Release notes)
  • (Module updates) Added a release notes entry if the change is significant
  • (Module addition) Added a release notes entry if adding a new NixOS module
• Fits CONTRIBUTING.md.

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[ryand56]

All tested and works in my flake as well, LGTM
Thanks for all your work on this!

[nixpkgs-ci]

Backport failed for release-25.05, because it was unable to cherry-pick the commit(s).

Please cherry-pick the changes locally and resolve any conflicts.

git fetch origin release-25.05
git worktree add -d .worktree/backport-409572-to-release-25.05 origin/release-25.05
cd .worktree/backport-409572-to-release-25.05
git switch --create backport-409572-to-release-25.05
git cherry-pick -x 515e5fe4cc7e102199988d4010de70ccbbb7b1bb c332cf3d2935fd8bedae280158e2ce742c8596d1