Update Readme

### Acceptance Criteria
1. Readme no longer has references to IODocs
1. Readme has instructions for adding a new cookbooks submodule
1. Readme doesn't mention customizing the application namespace
1. Readme is re-ordered to flow with how users should approach setup
1. Readme includes notes about how to access the project and lively
1. Readme includes notes about all @todo placeholder references to be updated

### Tasks
- None

### Additional Notes
- None