Keep subdirectory structure when compiling a manifest file

Keep the subdirectory information for assets when writing a manifest
file. The logical path in the manifest now represents the original
location in the filesystem and the fingerprinted asset will reflect
the original directory structure.

See bug reports #14, #17 for details.
Merge pull request #19 from pirxpilot/manifest-subdirectories

Keep subdirectory structure when compiling a manifest file [Fixes #14, #17]