Feature Request: Support directories in bundles

[thoughtrealm]

Currently, you can only bundle a single file or input. Need to support bundling whole directories. User would reference the directory in the bundle request.

Requirements:

• Add a flag "--inputs" to the bundle command. This flag will be a comma separated list of files and directories. References will be
  checked if they are a directory or file and handled accordingly.

• Add a flag "--input-list" to the bundle command. This will point to a text file that has a list of directories and files. It would be something like this:
  input-list.txt
  =====================
  file-ref
  file-ref
  directory-ref
  directory-ref

• Directories will be scanned and their whole tree and related files will be included in the bundle. This should include empty paths.

• Any file references will be added to the root of the tree, so later open commands will emit them to the root of the output path.

• Each node in the tree will contain some properties for the file at that node. This should include:
  Name
  Date and Time
  Any attributes?

• For command open, if the bundle is a directory or multiple files, they just provide flag "--output-path" or we will write out everything to the current working directory. If they supply the flag --output-file, indicate an error that this is a directory bundle.