Add all package folders to index

[citizenmatt]

This PR changes what non-project files are indexed:

• All packages are indexed. This includes the contents of the Packages folder, as well as any cached, read only/referenced packages, and any file: or git based packages.
• Removes non-project root folders from the index. This can have a huge impact on the file index if e.g. a backup copy of the Library folder is made to avoid a lengthy reimport all, or a player project is built into the root folder of the Unity project
• It also fixes a few edge cases where the Packages Explorer nodes would resolve incorrectly (e.g. editing the Packages/manifest.json file to add a package that hasn't yet been resolved by Unity).

Note that the contents of these folders will only show up when the "Include non-solution items" checkbox is selected in Find in Files.

The code will keep the index up to date as packages are added/removed/updated, and root folders are added/removed and when the project model is reloaded (meaning packages are correctly resolved).

This fixes RIDER-25340 as well as reducing the indexing time for projects that include extra folders at the root.