fix(plugin-pnpm): various improvements

[paul-soporan]

What's the problem this PR addresses?

• The PnpmLinker didn't install transitive dependencies in such a way that they can require themselves
• The PnpmLinker didn't support running binaries of soft links
• The PnpmLinker didn't remove the scope folder (e.g. node_modules/@yarnpkg) after removing a scoped dependency
• The PnpmLinker didn't remove folders that looked like scopes

How did you fix it?

• Made it copy the package sources to node_modules/.store/<hash>/node_modules/<ident> and use that as the symlink source so that self-references work. There is a special edge-case though: when a package depends on a different version of itself. Both pnp and nm get that right (though pnpm doesn't), so I made it skip generating self-references in that case (i.e. made it keep copying the sources to node_modules/.store/<hash> so that the dependency can be put inside node_modules/.store/<hash>/node_modules/<ident>. The sources will now be copied to node_modules/.store/<hash>/node_modules/<ident> and dependencies will be symlinked to node_modules/.store/<hash>/node_modules/<ident>/node_modules.
• Made it persist packageLocations (now renamed to pathByLocator) inside the install state and made findPackageLocation query that
• Made it remove those
• Made it remove those

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.

[edvardchen]

I saw this PR when I was going to submit my own PR. It seems that all issues I encountered will be fixed by this PR. Look forward to it!