refactor: initial project layout

[arendjr]

Summary

Fixes #2475.

With this PR, we get a first version of our ProjectLayout that we will be able to expose through a service to lint rules that want to do more complex analysis. For now, the only thing it contains is the NodeJsPackage which has been updated from the previous NodeJsProject that was stored on ProjectData directly.

This is enough to fix noUndeclaredDependencies in monorepos.

The biome_project crate has also been renamed to biome_package.

As part of this refactoring, clients no longer manually set the manifest. Instead, they call scan_project_folder(), and the manifests are discovered and put into the ProjectLayout when the scanning is done.

Later I want to use a similar mechanism for resolving package-level configs, but I think I better wait with that until @ematipico is done with #4845.

Test Plan

Added tests.

[codspeed-hq]

CodSpeed Performance Report

Merging #4846 will not alter performance

_{Comparing arendjr:initial-project-layout (470952e) with next (24c8256)}

Summary

✅ 97 untouched benchmarks

[dyc3]

LGTM