perf(node-modules): remove redundant semver instance from bundle

[merceyz]

What's the problem this PR addresses?

There is an instance of semver@^6.0.0 in the CLI that we don't need as it's just used to check if node is >= 10.12.0

$ yarn why semver -R
[...]
├─ @yarnpkg/plugin-node-modules@workspace:packages/plugin-node-modules
│  ├─ @zkochan/cmd-shim@npm:4.3.0 (via npm:^4.3.0)
│  │  └─ make-dir@npm:3.1.0 (via npm:^3.0.0)

How did you fix it?

Update @zkochan/cmd-shim which removes the version of make-dir that drags in semver@^6.0.0

 Bundle size
- 1 999 317 bytes
+ 1 978 490 bytes

Checklist

• I have read the Contributing Guide.
• I have set the packages that need to be released for my changes to be effective.
• I will check that all automated PR checks pass before the PR gets reviewed.