fix: honor never/only-built-dependencies in workspace setup

[alvis]

Fix #7135 #5407

In the current implementation there are 2 bugs that prevent pnpm.neverBuiltDependencies and pnpm.onlyBuiltDependencies to work under a workspace that doesn't share a single lockfile

1. The argument passed to some getOptionsFromRootManifest calls are wrong. They were incorrectly passed the project manifest instead of the intended root project manifest.
2. Both neverBuiltDependencies and onlyBuiltDependencies settings are not implemented in the recursive logic.

This PR provides a fix to the bugs above.

[welcome]

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[zkochan]

Thanks, I'll review it later.

[alvis]

@zkochan any idea about the patching errors in the CI tests? Not sure where do they come from

[zkochan]

That is a new error for sure. I haven't seen it in the past.

[alvis]

@zkochan Seems like the error is caused by the recent 8.8.0 release while the code was based on 8.7.6. I've rebased the branch and please approve the CI test again

Update:
There is another separate issue related to the 8.8.0 release that causes the ERR_PNPM_SOME_CODE  some error error in the test (which also happen in other recent commits) but it is red herring because it won't fail the test (which is another separate issue)

The reason of the test failure is due to the change in the argument supplied to getOptionsFromRootManifest as explained below

[alvis]

@zkochan so the patching error is due to the earlier proposed change (opts.rootProjectManifest ?? {} instead of opts.rootProjectManifest ?? manifest in the latest update).

In the latest update, I uses the project manifest as a fallback instead of an empty object.
Now the tests will pass as you can see those in mine:
https://github.com/alvis/pnpm/actions/runs/6338054374

The change is harmless but I guess there is a bug in the test because the earlier proposed logic is identical to the usage in other places in the codebase, and it makes more sense than using the project manifest e.g.

pnpm/pkg-manager/plugin-commands-installation/src/link.ts

Line 178 in a5fff1c

...getOptionsFromRootManifest(config.rootProjectManifest ?? {}),

pnpm/pkg-manager/plugin-commands-installation/src/remove.ts

Line 175 in a5fff1c

...getOptionsFromRootManifest(opts.rootProjectManifest ?? {}),

Regardless, I'm looking forward to your review and get it merged.

[welcome]

Congrats on merging your first pull request! 🎉🎉🎉