refactor: update on security logic and adjustments on CLI interface + error correction and CLI optimization

[Palodeaza]

Description

Fixes #575
Refactor from long functions into consice ones, helping the separation of responsabilities and making the code more readable. Also, decreasing the warning count!

Type of Change

Refactor
Changes on cli.py and cli_util.py: adjustments on the calls to the scanning logic function to ensure the compatibility with all the structure. Also, minor refactoring to enhance the readability and to ensure params validations.

Testing

All tests passed, before and after changes.

Checklist

• Code is well-documented
• Changelog is updated (if needed)
• No sensitive information (e.g., keys, credentials) is included in the code
• All PR feedback is addressed

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