Fix undefined names

[woutdenolf]

First commit are fixes after the CLI refactoring related to 'undefined names': #1198

The other commits fix more undefined names found with flake8 --select=F821. I did not fix the ones that had no clear solution.

[sergey-yaroslavtsev]

I checked - everything seems OK.
However some code which was corrected is actually a "dead" code (see comments) because it goes after "if 0:" or after "return" or after "elif 1: / else:". I do not know if it should be cleaned in this PR or in a different one.

[sergey-yaroslavtsev]

Contain some "dead" code but it does not affect workability,

[woutdenolf]

Contain some "dead" code but it does not affect workability.

Yes the project is full of dead code but I did not introduce the dead code, I fix it because it exists.