Fix generate with Workspace.swift

[fortmarek]

Resolves #6038

Short description 📝

If you have a Workspace.swift with the projects: ["./**"], we would match also packages in the .build/checkouts and the Package.swift in the Tuist directory since we added direct support for SPM packages.

How to test the changes locally 🧐

Run generate on the project in the attached issue. You should no longer get a crash.

Contributor checklist ✅

• The code has been linted using run mise run lint:fix
• The change is tested via unit testing or acceptance testing, or both
• The title of the PR is formulated in a way that is usable as a changelog entry
• In case the PR introduces changes that affect users, the documentation has been updated

Reviewer checklist ✅

• The code architecture and patterns are consistent with the rest of the codebase
• Reviewer has checked that, if needed, the PR includes the label changelog:added, changelog:fixed, or changelog:changed, and the title is usable as a changelog entry