Fix various issues, improve log messages, update documentation, and add regression tests

[davidallendj]

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Description

This PR adds documentation that about using --insecure with scan after changing the default value to false. It also adds more log messages to find these related issues and fixes an issue related to closing the secrets file too early, and adds regression tests.

Fixes #(issue)

Type of Change

• Bug fix
• New feature
• Breaking change
• Documentation update

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[davidallendj]

Still need to add the regression tests before merging.