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docs(skill): document --name and --secret-key flags, fix api ls example
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‎skills/clerk-cli/SKILL.md‎

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## Core commands at a glance
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| Command | Purpose | Key flags |
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| -------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------- |
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| `clerk init` | Scaffold Clerk into a project, or emit an agent handoff with `--prompt`. | `--framework`, `--pm`, `--prompt`, `--starter`, `-y`, `--no-skills` |
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| `clerk auth login` | OAuth browser login (stores token). Agent mode: no-op if already logged in, else prints guidance. | — |
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| `clerk auth logout` | Clear stored credentials. | — |
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| `clerk whoami` | Print the logged-in email. | — |
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| `clerk link` | Link this repo to a Clerk app. | `--app <id>` |
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| `clerk unlink` | Remove the link. | `--yes` |
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| `clerk env pull` | Write publishable + secret keys to `.env.local` (merge, not clobber). | `--app`, `--instance`, `--file` |
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| `clerk config pull` | Fetch instance config JSON. | `--app`, `--instance`, `--output`, `--keys` |
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| `clerk config schema` | Fetch the JSON Schema for the instance config. | `--app`, `--instance`, `--output`, `--keys` |
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| `clerk config patch` | Partial update (PATCH) of instance config. | `--file`, `--json`, `--dry-run`, `--yes`, `--destructive` |
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| `clerk config put` | Full replacement (PUT) of instance config. Pass `--destructive` to actually delete removed sub-resources rather than resetting them to defaults. | `--file`, `--json`, `--dry-run`, `--yes`, `--destructive` |
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| `clerk apps list` | List Clerk applications. | `--json` |
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| `clerk apps create <name>` | Create a new Clerk application. | `--json` |
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| `clerk open [subpath]` | Open the linked app's dashboard in a browser. Agent mode: prints a JSON descriptor instead of opening. | `--print` |
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| `clerk doctor` | Health check. | `--json`, `--spotlight`, `--verbose`, `--fix` |
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| `clerk api [path]` | Authenticated HTTP to Backend/Platform API. | `-X`, `-d`, `--file`, `--dry-run`, `--yes`, `--include`, `--app`, `--instance`, `--platform` |
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| `clerk api ls [filter]` | Discover endpoints from the bundled OpenAPI catalog. | `--platform` |
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| `clerk completion [shell]` | Print a shell completion script (`bash`, `zsh`, `fish`, `powershell`). | — |
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| `clerk skill install` | Reinstall the bundled `clerk-cli` skill. Run after upgrading the CLI so the skill matches the new binary. | `-y`, `--pm` |
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| Command | Purpose | Key flags |
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| -------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------ |
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| `clerk init` | Scaffold Clerk into a project, or emit an agent handoff with `--prompt`. | `--framework`, `--pm`, `--name` (with `--starter`), `--prompt`, `--starter`, `-y`, `--no-skills` |
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| `clerk auth login` | OAuth browser login (stores token). Agent mode: no-op if already logged in, else prints guidance. | — |
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| `clerk auth logout` | Clear stored credentials. | — |
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| `clerk whoami` | Print the logged-in email. | — |
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| `clerk link` | Link this repo to a Clerk app. | `--app <id>` |
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| `clerk unlink` | Remove the link. | `--yes` |
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| `clerk env pull` | Write publishable + secret keys to `.env.local` (merge, not clobber). | `--app`, `--instance`, `--file` |
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| `clerk config pull` | Fetch instance config JSON. | `--app`, `--instance`, `--output`, `--keys` |
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| `clerk config schema` | Fetch the JSON Schema for the instance config. | `--app`, `--instance`, `--output`, `--keys` |
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| `clerk config patch` | Partial update (PATCH) of instance config. | `--file`, `--json`, `--dry-run`, `--yes`, `--destructive` |
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| `clerk config put` | Full replacement (PUT) of instance config. Pass `--destructive` to actually delete removed sub-resources rather than resetting them to defaults. | `--file`, `--json`, `--dry-run`, `--yes`, `--destructive` |
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| `clerk apps list` | List Clerk applications. | `--json` |
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| `clerk apps create <name>` | Create a new Clerk application. | `--json` |
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| `clerk open [subpath]` | Open the linked app's dashboard in a browser. Agent mode: prints a JSON descriptor instead of opening. | `--print` |
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| `clerk doctor` | Health check. | `--json`, `--spotlight`, `--verbose`, `--fix` |
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| `clerk api [path]` | Authenticated HTTP to Backend/Platform API. | `-X`, `-d`, `--file`, `--dry-run`, `--yes`, `--include`, `--app`, `--secret-key`, `--instance`, `--platform` |
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| `clerk api ls [filter]` | Discover endpoints from the bundled OpenAPI catalog. | `--platform` |
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| `clerk completion [shell]` | Print a shell completion script (`bash`, `zsh`, `fish`, `powershell`). | — |
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| `clerk skill install` | Reinstall the bundled `clerk-cli` skill. Run after upgrading the CLI so the skill matches the new binary. | `-y`, `--pm` |
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**`clerk <command> --help` is the source of truth for flags.** This table is a hint, not a spec. Before running an unfamiliar command or flag combination, run `clerk <command> --help` once per session. Every command also defines `setExamples([...])` in source, which `--help` renders as a copy-pasteable Examples block, so you rarely need to guess syntax.
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‎skills/clerk-cli/references/agent-mode.md‎

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```sh
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clerk api ls users # discover available user endpoints
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clerk api ls -- --platform apps # platform-side endpoints
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clerk api ls --platform apps # platform-side endpoints
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```
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### Surface doctor remedies to the user

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