Change LayerEntry to be more like TarArchiveEntry.

[coollog]

A LayerEntry should be a tuple of (Path, extractionPath) rather than (List<Path>, extractionPath). extractionPath will be the exact location of the file in the container file system rather than the directory to extract the source file to. This way, a LayerConfiguration becomes a list of LayerEntrys, each with its own source file and target path in the container file system.

The benefits of these are:

• Simplifies LayerConfiguration to not be a list of lists
• Does not hide the directory-walking logic within ReproducibleLayerBuilder - each file must be explicitly added
• Allows files to be renamed (to fix Error build a project with the same module and submodule name #810)
• Allow adding only select files in a directory (to fix Limitation of LayerConfiguration.addEntry() #957)

Fixes #957