Now if you run npm run build-keycloak-theme it will generate the JAR in dist/apps/keycloak-theme.
When you want to use the keycloakify CLI commands you can either cd into your keycloakify sub app directory or use the --project option of the Keycloakify CLI.
Like for example if you want to run add-story you can do either:
cd apps/keycloak-theme && npx keycloakify add-story
OR
npx keycloakify add-story -p apps/keycloak-theme from the root of your monorepo
To go beyond the base configuration you might want to explore what build options are available. Starting with with keycloakVersionTargets to make sure that you only generates the JARs file you need.