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patch: improve tracking of applied patches
Each applied patch is tracked individually. This has the benefit of being able to handle situations where multiple patches touch the same file. Also remove the check if the patch is still applied. This proved to be unreliable, especially if multiple patches touch the same file. We now solely rely on the tracked applied patches and compare them to the desired ones. If they match, the class will assume the patch is still applied. Fixes #55. Fixes #180.
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