Handle TODOs and commented code

This PR will need all ACK before merge.

The TODOs is listed on the diff and should be added inline comments if some of them should not be remove. Also if a TODO will not be deleted then an issue will be created to track that.

Was found and removed only two lines of commented code.

During the search for TODOs was done small fixes like adding testimony tags and removing `# noqa` and  `# pylint` comments.

Related to #577