Make --analyze_all optional

If users want to perform the full analysis, they have to type `--analyze_all` (or add as many `--analyze_` options as desired).

Can't we make this flag optional, and set by default?
When users want only one part of the analysis, this flag would become disabled instead.

Start by locating the command-line parsing and the existing --analyze_all handling. Check how individual --analyze_ options are detected, then define completion as full analysis running without --analyze_all while selecting one analysis disables the default. Verify the behavior with the available CLI checks or tests.

Written by the indexing model from the issue text.