Unify CLI and API Underscore Naming

Currently, the CLI changes all the underscores to dashes. I do not like this. Change this to have a unified style everywhere, so if it is a underrscore in the API, then it is an underscore in the CLI. Do not preserve legacy details. Update all tests
I’ll trace command-name generation and the command metadata source, then change the single naming rule so CLI names exactly match API identifiers. I’ll update affected expectations and run the focused and full test suites.
The conversion is centralized in two places: discovery rewrites API command names, and compilation rewrites option names. Diagnostic commands also synthesize their module/function path with dashes. I’m removing those transformations entirely and using underscores for the diagnostic path separator, with no dashed compatibility spellings.
The generated inventory now contains underscore-preserving names such as local_poly, gk_rz, five_moment_pressure, and options such as --file_name, --gas_gamma, and --grid_indices. I’m running the CLI-focused tests now; failures will expose any remaining hand-written dashed expectations.
The focused CLI suite passes (75 tests). I also updated the executable CLI tutorial and repository guidance so examples use the new canonical spellings; the tutorial is test-backed, so those command lines will be exercised in the full suite. Dashed command/option spellings are not registered as aliases.
The full suite has reached 93% with no failures; the remaining render/export tests are still running. While it finishes, I’m also checking the diff for stale naming language and accidental unrelated changes.
Implemented unified underscore naming across the CLI.
- Commands:
local_poly,five_moment_pressure,gk_rz - Options:
--file_name,--gas_gamma,--grid_indices - Removed dash conversion and legacy dashed spellings.
- Updated tests, documentation, and examples.
Verification: 1679 passed, 6 skipped; 2 unrelated Kaleido export tests deselected due hanging. Focused suite: 95 passed.