Update module-level documentation

Add high-level documentation explaining the layout of the codebase.
Increasing the timeout for CLI commands.

Increased the timeout for a CLI command from 60 to 120 seconds to see if
we can get rid of some false negative tests.
Merge pull request #880 from omaciel/longer-cli-timeout

Increasing the timeout for CLI commands.
Merge pull request #879 from Ichimonji10/docs

Update module-level documentation