The `_data/cliRef.json` file is generated from the `blockstack-cli` subcommand `docs`. This data file is consumed by the `_includes/commandline.md` file which is used to serve up the reference.
3. Make sure the generated docs are clean by building the documentation.
If you run into any problem in the generation usually it results from a problem in the repo. You can make a pull request back to the repo to fix anything.
As of 8/12/19 Clarity is in the [develop](https://github.com/blockstack/blockstack-core/tree/develop) branch of core. You can build the Clarity command line from the Docker image. `core/src/vm/docs/mod.rs`