Update CLI

[thclark]

Redesign CLI to a single CLI, instead of a mechanism that defines a new CLI for every app.

• give an app path argument to specify which app to run
• allow user to specify a --data-dir argument which, on instantiation of Analysis(), gives a hint to the location of sources which aren't specified on the command (allowing use straight from the terminal)
• get version from git or from setup.py to remove the need for @octue_version decorator
• remove deprecated logs directory
• add CLI usage instructions to README

[cortadocodes]

Requirements:

1. We need to be able to find input and configuration datasets (i.e. a data path)
2. We need to know where to write output datasets (i.e. a data path)
3. We need to be able to read the manifest data (for configuration and inputs) from a src, which can be a file or raw json
4. We need to be able to write the output manifest to a file (and need to know where that is)
5. We need to be able to write the output_values to a file (and know where that is)

[cortadocodes]

Based on conversation on 2020-10-31, I've removed this part of the issue: give input sources arguments (e.g. src can be a data path or a json string