Recover from manifest.json failures gracefully.

This PR addresses Issue #36. 

Three changes:
1. Removes the root directory from the snap_paths since the root directory will not have a manifest.json.
2. Skips through the directories that don't have a manifest.json and moves to the next path in the list. (Warning message is logged).
3. Skips the manifest.json if it fails to parse correctly. (Error message logged).