Improve usage of targetLocation if renameFiles and flattenFiles is used

[MCMicS]

• targetLocation is used if flattenFiles and renameFiles is used (see fileOperations - fileCopyOperation: targetLocation variable ignored when renameFiles: true #101)
• add Sample to Source Capture Expression
• add note to doc that sub-directories are preserved if includes path not handled in regex

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• Ensure that the pull request title represents the desired changelog entry
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[jonesbusy]

Thanks for your PR!

[MCMicS]

Thanks for merging so the issue #101 is maybe also closed with new doc and improved handling isn't