[Bug?]: yarn up incorrectly updates dependencies using the link protocol

[mskelton]

Self-service

• I'd be willing to implement a fix

Describe the bug

When using the link: protocol for linking local packages (as described in the protocols docs), I noticed that running yarn up will incorrectly swap these dependencies for their registry equivalents.

I would expect yarn up to ignore dependencies listed with the link: protocol.

To reproduce

const {promises: {readFile}} = require(`fs`);

await packageJsonAndInstall({
  dependencies: {
    [`fixtures`]: `link:./fixtures`,
  }
});

await yarn(`up`, `fixtures`);

const pkgJson = JSON.parse(await readFile(`package.json`, `utf8`));
expect(pkgJson.dependencies.fixtures).toBe(`link:./fixtures`);

While this example is not a real world use case since I'm explicitly updating the dependency, this also occurs when using a wildcard such as yarn up '*' which is a real world use case for updating all deps.

Environment

System:
OS: macOS 10.15.7
CPU: (12) x64 Intel(R) Core(TM) i9-8950HK CPU @ 2.90GHz
Binaries:
Node: 14.17.1 - /private/var/folders/jh/s3v_qtkx501g98yxct1x4g3r634gd_/T/xfs-00f87514/node
Yarn: 2.4.2 - /private/var/folders/jh/s3v_qtkx501g98yxct1x4g3r634gd_/T/xfs-00f87514/yarn
npm: 6.14.13 - ~/.local/share/nvm/v14.17.1/bin/npm

Additional context

No response

[yarnbot]

This issue reproduces on master:

Error: expect(received).toBe(expected) // Object.is equality

Expected: "link:./fixtures"
Received: "^0.0.2"
    at module.exports (evalmachine.<anonymous>:13:39)
    at async /github/workspace/.yarn/cache/@arcanis-sherlock-npm-2.0.2-91650a2501-627bee24a7.zip/node_modules/@arcanis/sherlock/lib/executeRepro.js:56:13
    at async executeInTempDirectory (/github/workspace/.yarn/cache/@arcanis-sherlock-npm-2.0.2-91650a2501-627bee24a7.zip/node_modules/@arcanis/sherlock/lib/executeRepro.js:17:16)
    at async Object.executeRepro (/github/workspace/.yarn/cache/@arcanis-sherlock-npm-2.0.2-91650a2501-627bee24a7.zip/node_modules/@arcanis/sherlock/lib/executeRepro.js:24:12)
    at async ExecCommand.execute (/github/workspace/.yarn/cache/@arcanis-sherlock-npm-2.0.2-91650a2501-627bee24a7.zip/node_modules/@arcanis/sherlock/lib/commands/exec.js:25:38)
    at async ExecCommand.validateAndExecute (/github/workspace/.yarn/cache/clipanion-npm-2.0.0-rc.16-b9444aaf89-91cf93ba72.zip/node_modules/clipanion/lib/advanced/Command.js:161:26)
    at async Cli.run (/github/workspace/.yarn/cache/clipanion-npm-2.0.0-rc.16-b9444aaf89-91cf93ba72.zip/node_modules/clipanion/lib/advanced/Cli.js:74:24)
    at async Cli.runExit (/github/workspace/.yarn/cache/clipanion-npm-2.0.0-rc.16-b9444aaf89-91cf93ba72.zip/node_modules/clipanion/lib/advanced/Cli.js:83:28)

[merceyz]

Duplicate of #1492