feat(core): support reading projects under new pnpm workspaces entry + skip writing empty nx property to pacakge.json for non-root projects

[jaysoo]

This PR is a prerequisite to removing nx property from package.json files in the new TS setup. It fixes two issues:

1. We always write nx property in package.json even if it is empty. This should be done for root projects.
2. Adding an entry to pnpm-workspace.yaml is not picked up because readProjectConfiguration only reads the file from disk, not from virtual Tree

This is the next PR to remove the property: #29705

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☁️ Nx Cloud last updated this comment at 2025-01-21 22:02:14 UTC

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