Review of error/exceptions and code documentation

This PR updates all error reporting in the system tree to use suitable exceptions and updated all code docblocks

| Q             | A
| ------------- | ---
| Bug fix?      | no
| New feature?  | no
| BC breaks?    | no
| Deprecations? | no
| Tests pass?   | yes
| Fixed tickets | 
| Refs tickets  | 
| License       | MIT
| Doc PR        |