Replace leaanthony/clir with spf13/cobra across all command packages.
This provides better subcommand handling, built-in shell completion,
and a more widely-used CLI framework.
Changes:
- Update cmd/core.go with cobra root command and completion support
- Convert all subcommand packages to use *cobra.Command
- Use init() functions for flag registration instead of inline setup
- Maintain all existing functionality and flag behaviors
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>