Fix generation failure when package test resources overlap with source folders

Projects that depend on a local Swift package with a test target using resources: [.copy(".")] now generate correctly. Previously, Tuist tried to add a test source file to a build phase that did not exist in the generated project, causing tuist generate to fail with an error about a missing build phase. Tuist now tracks folder references separately from logical file groups, allowing copied resource folders to coexist with nested source file references at the same path.