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This PR refactors the command structure to decouple subcommands from the root command, improving modularity and testability. **Key Changes:** - Move `internal/cli` to `cmd/internal`. Being in a `internal` folder, other packages outside of `cmd` will not be able to import them. - Encapsulated I/O: Introduced a new IOStreams struct to standardize in, out, and errOut handling. - Shared Dependencies: Extracted shared fields (including IOStreams, Logger, ServerConfig, and various Tools paths) from the root `Command` into a new `ToolboxOptions` struct. This also includes moving `cmd/options.go` to be part of `ToolboxOptions`. - Logic Migration: Moved setup logic, such as `Setup()` and `LoadConfig()`, into `ToolboxOptions`. Removing the need to import `rootCmd` to subcommands. - Package Reorganization: - Relocated PersistentFlag and ToolsFiles to the cli package to remove base command dependencies. This removes dependencies on the base command, allowing subcommands to consume these utilities independently. - Moved all side-effect registration to the `cmd/internal` package, enabling other packages to import it safely for unit tests. **Testing Improvements:** - Subcommand packages can now be tested in isolation without relying on the base command package. - Added `TestSubcommandWiring()` to the base command tests to verify proper subcommand registration.