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docs: document missing CLI flags and json-schema command in cli.md (#64596)
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‎docs/src/content/docs/setup/cli.md‎

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@@ -598,7 +598,7 @@ gh aw audit 1234567890 --runtime cloud-hypervisor # Skip run unless sandb
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The `--repo` flag accepts `owner/repo` format and is required when passing a bare numeric run ID without a full URL, allowing the command to locate the correct repository.
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The `--artifacts` flag selects which artifact sets to download (default: `all`). Valid sets include `activation`, `agent`, `all`, `detection`, `evals`, `experiment`, `firewall`, `github-api`, `graders`, `mcp`, and `usage`. Use `all` to download the full artifact set. Unlike `gh aw logs`, which defaults to `usage`, `audit` defaults to `all` for comprehensive analysis. The `--experiment` flag filters to runs that include the named experiment; `--variant` further restricts to a specific variant value and requires `--experiment` to be set. The `--output/-o` flag overrides the output directory.
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The `--artifacts` flag selects which artifact sets to download (default: `all`). Valid sets include `activation`, `agent`, `all`, `detection`, `evals`, `experiment`, `firewall`, `github-api`, `graders`, `info`, `mcp`, and `usage`. Use `all` to download the full artifact set. Unlike `gh aw logs`, which defaults to `usage`, `audit` defaults to `all` for comprehensive analysis. The `--experiment` flag filters to runs that include the named experiment; `--variant` further restricts to a specific variant value and requires `--experiment` to be set. The `--output/-o` flag overrides the output directory.
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Logs are saved to `.github/aw/logs/run-{id}/` with filenames indicating the extraction level. Pre-agent failures (integrity filtering, missing secrets, binary install) surface the actual error in `failure_analysis.error_summary`. Invalid run IDs return a human-readable error.
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@@ -898,7 +898,9 @@ gh aw env update defaults.yml --scope org --org my-org --dry-run
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gh aw env update defaults.yml --scope ent --enterprise my-enterprise --yes
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```
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**Options:** `--scope` (required), `--repo/-r`, `--org`, `--enterprise`, `--yes/-y`, `--dry-run`
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**Options:** `--scope` (required), `--repo/-r`, `--org`, `--enterprise`, `--visibility`, `--yes/-y`, `--dry-run`
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The `--visibility` flag sets access for newly created org or ent variables (`all`, `private`, or `selected`; default: `all`). Existing variables keep their current visibility. The flag is rejected with `--scope repo`.
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For repository scope, `--repo` currently accepts `owner/repo` only. To target GitHub Enterprise Server, select the host via `GH_HOST` rather than prefixing the repository with `[HOST/]`.
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gh aw mcp add workflow server --tool-id my-server # Override the tool ID
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```
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**`mcp list-tools` options:** `--server` (required)
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**`mcp inspect` options:** `--check-secrets`, `--inspector`, `--server`, `--tool`
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**`mcp add` options:** `--transport`, `--registry`, `--tool-id`
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**Options:** `--json/-j`
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When no workflow is specified, lists all workflows with a summary of allowed and blocked domain counts. When a workflow is specified, lists all effective allowed and blocked domains including domains expanded from ecosystem identifiers (e.g., `node`, `python`, `github`) and engine defaults.
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When no workflow is specified, lists all workflows with a summary of allowed and blocked domain counts. When a workflow is specified, lists all effective allowed and blocked domains including domains expanded from named domain sets (e.g., `node`, `python`, `github`, `copilot`) and engine defaults.
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### Utility Commands
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Includes all frontmatter fields, imported workflow frontmatter (BFS traversal), template expressions containing `env.` or `vars.`, and version information (gh-aw, awf, agents).
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#### `json-schema`
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Print the JSON Schema for structured command output.
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```bash wrap
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gh aw json-schema audit # Schema for gh aw audit --json
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gh aw json-schema logs # Schema for gh aw logs --json
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gh aw json-schema logs-jsonl # Schema for each gh aw logs --cached-jsonl line
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```
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**Schema arguments:** `audit`, `logs`, `logs-jsonl`. The schema is written to stdout. See [JSON output schemas](/gh-aw/reference/audit/#json-output-schemas).
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## Shell Completions
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Enable tab completion for workflow names, engines, and paths. After running `gh aw completion install`, restart your shell or source your configuration file.

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