Add comprehensive test coverage & Protect credentials file permissions for cbrain_cli

[RafsanNeloy]

Contributor checklist

• This pull request is on a separate branch and not the main branch
• I ran pre-commit run --all-files and/or pytest as appropriate (see Tests in the README). A clean Ruff/pre-commit run is necessary but not sufficient—behavior still needs tests and review.
• If CLI output changed intentionally, I updated capture_tests/expected_captures.txt
• If command behavior changed, I checked normal, --json, and --jsonl output modes (or noted why not applicable)
• Data-layer modules do not add direct print() calls for user-visible output
• Public command names, flags, and default behavior remain compatible unless this PR explicitly documents a breaking change
• No credentials, tokens, or session data appear in code, fixtures, logs, or this PR description

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Type of change

• Bug fix
• New feature or command behavior
• Documentation
• Tests only
• Other (describe below)
  Protect credentials file permissions

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Description

This PR fixes task 9 and task 11 from plan.md. Added credential management for file permission also added pytest test coverage for the CLI.

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Test plan

pytest --cov=cbrain_cli --cov-report=term-missing

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Related issue

-Partially Closes #47

[dlq]

I removed calling lint twice in two workflows - but otherwise this looks good!