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Issue Description:

• DESCRIPTION:
  If I load an SPM package into Xcode that includes a target that uses the `sources` parameter to define where to find source files any files that are inside the path for the target but not inside any of the sources folders are considered unhandled.

• OTHER INFORMATION:

Please list the steps you took to reproduce the issue:
Open the Package.swift from the attached project and view the error messages.

What did you expect to happen?
Given I have told the target where to look for files via the `sources` parameter it shouldn't be warning about files outside of those folders.

What actually happened?
I get the warning “found 1 file(s) which are unhandled; explicitly declare them as resources or exclude from the target”.