refactor: better integration of the parser into Trivy

[knqyf263]

Description

Leftover of #6094

• Unify the logging package
• Unify the io package

Related PRs

• chore(deps): merge go-dep-parser into Trivy #6094

Checklist

• I've read the guidelines for contributing to this repository.
• I've followed the conventions in the PR title.
• I've added tests that prove my fix is effective or that my feature works.
• I've updated the documentation with the relevant information (if needed).
• I've added usage information (if the PR introduces new options)
• I've included a "before" and "after" example to the description (if the PR is a user interface change).

[DmitriyLewen]

LGTM