[FIX] Issue where the presence non-whitelisted flags would remove all other flags detected from .pc files

I recently encountered an issue (link to forum question) when trying to use the SDL 2 from Swift : I had to manually specify flags that were already present in the corresponding .pc file.
There are additional details in my pull request including links to similar issues that were reported on bugs.swift.org.

This is my first pull request ever to Swift, I'd love to get some feedback from the Swift PM authors and contributors both on possible improvements to the PR and on why Swift PM behaved this way.

Thank you !

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Thanks for submitting a PR! I'll take a look in the morning.

Thank you!