Add a `--preserveDirs` flag

[dacharyc]

By default, Bluehawk's snip command dumps all files in the root of the output directory.

Bluehawk's copy command copies all files to the output directory, preserving the directory structure.

For a new use case, we would like to add an optional flag to the CLI for the snip command to preserve the directory structure in the output. i.e. --preserveDirs to output a file from examples/aggregation/filter to outputDir/aggregation/filter.