Fix generation of SPM packages when some resources are missing

[fortmarek]

Resolves #6019

Short description 📝

We skip adding globs where the base folder doesn't exist at all for external dependencies as we shouldn't be stricter than SPM.

How to test the changes locally 🧐

You should be able to generate and build the app_with_spm_dependencies project

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