Improve permissions checking when dealing with existing files

[cole-h]

Description

Fixes #266.

Also explicitly checks if the path was a file.

Checklist

• Formatted with cargo fmt
• Built with nix build
• Ran flake checks with nix flake check
• Added or updated relevant tests (leave unchecked if not applicable)
• Added or updated relevant documentation (leave unchecked if not applicable)
• Linked to related issues (leave unchecked if not applicable)

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[Hoverbear]

Other than my comment (which I would consider a blocker -- users should get valid commands suggested to them) this looks great!