transformFiles no in-place

[cvogt]

trafficstars

currently transformFiles and transformFilesOrError operate in-place https://github.com/cvogt/cbt/blob/e760ee9e4c4c3b3f39e2bb2dfd47d2b142e12a53/stage2/Lib.scala#L539

Let's make them not operate in-place and take Seq[File,File] instead. And have transformFilesInPlace and transformFilesOrErrorInPlace wrappers, which simply do (files zip files).

[cvogt]

cc @shanedelmore