ory-permissions-onboarding

name	ory-permissions-onboarding
description	Onboard a fresh install onto Ory Permissions for AI agent tool calls. Use when the user has just installed the Ory plugin and wants to enforce per-tool authorization without first getting blocked by missing tuples. Walks through observe-mode observation, idempotent tuple bootstrap, and promotion to enforce mode.

Onboard onto Ory Permissions for Agent Tool Calls

You are helping a user move a freshly-installed Ory agent plugin from "permissions are running but never block" (the default after install) to "permissions are enforcing" (the production posture), without the common first-run failure mode of getting every tool call blocked because no tuples exist yet.

The plugin ships with two orthogonal switches:

• auditOnly — a kill switch. When set, Ory is off entirely (no auth, no permission checks). This is for users who want only audit logging of tool invocations. Not what onboarding is about.
• permissionMode — the dial this skill is about. observe (the default) runs every permission check, logs denials, but allows the tool to proceed. enforce blocks on deny. Mode is read from ORY_PERMISSION_MODE first, then the shared config file, then defaults to observe.

The journey: install → observe → bootstrap → enforce.

Step 1: Confirm the plugin is installed and configured

Verify the plugin is wired up and pointing at the right Ory project:

npx -y -p @ory/gemini-cli ory-gemini status

What you want to see:

• Project URL: a real Ory URL or your local dev gateway (not "NOT SET").
• API Key: set (Ory Network) or unset (local Keto OSS — that's fine).
• Mode: not "audit-only" — that would mean Ory is disabled.

If any of those are wrong, fix them before continuing:

npx -y -p @ory/gemini-cli ory-gemini configure --project-url <URL> --oauth2-client-id <CLIENT_ID> [--api-key <KEY>]

--oauth2-client-id is the public OAuth2 client registered in your Ory project (needed for the per-session user login to complete its PKCE browser flow; see the Register the user OAuth2 client section of the plugin README).

Step 2: Look at the current permission posture

npx -y -p @ory/gemini-cli ory-gemini permissions status

This prints:

• The current permission mode (observe or enforce) and where it was resolved from (env / config / default).
• The subject (the user identity tuples are checked against).
• For each tool in this harness's built-in catalog, allowed / denied / errored based on a real checkPermission call against your Ory project right now.

On a fresh install you will almost always see every tool reported as denied — because no tuples exist yet for the current user. That's expected, and in observe mode it is not blocking anyone. The tool calls are running through; you are simply seeing what would be blocked once enforce mode is turned on.

If the status command prints Mode: enforce but tuples are missing, stop here: tool calls are being blocked right now. Either bootstrap (next step) or run npx -y -p @ory/gemini-cli ory-gemini permissions observe first to flip back to non-blocking.

Step 3: Bootstrap tuples for the harness's built-in tools

Grant the current user use on every tool the harness ships with:

npx -y -p @ory/gemini-cli ory-gemini permissions bootstrap

This is idempotent — Keto returns 409 on a tuple that already exists, and the command treats that as success. Safe to re-run any time (e.g. after the harness adds a new tool to its catalog).

The command writes <namespace>:<tool>#use@<userSubject> for each tool in the harness's known catalog. MCP server tools are not covered — they are discovered dynamically per session, so they need tuples added out-of-band as they come into scope.

When bootstrap can't write tuples

Two common failure modes:

1. No user identity cached. Bootstrap needs to know which subject to grant tuples to. If the user login has never completed (no PKCE login, no ORY_USER_SUBJECT_ID), the command refuses. Run the harness once (the user login runs every session) to cache a user token, or set ORY_USER_SUBJECT_ID=<id> to target a known subject.
2. Credentials lack write scope on the permission namespace. The command prints the full tuple list so you can apply them manually via keto relation-tuples create, the Ory Console's Add relationship dialog, or curl against Keto's write API. Hand the list to whoever holds write credentials.

Add tuples for non-default tools

If the harness has tools beyond the built-in catalog (MCP servers, custom commands), grant them by writing tuples directly. Use the same shape:

namespace: AgentTools           (or whatever ORY_PERMISSION_NAMESPACE is set to)
object:    <tool name>
relation:  use
subject:   <user subject id>

Re-run npx -y -p @ory/gemini-cli ory-gemini permissions status afterwards to confirm coverage.

Step 4: Promote to enforce mode

Once permissions status shows the tools you actually use are allowed, flip the dial:

npx -y -p @ory/gemini-cli ory-gemini permissions enforce

This persists permissionMode = "enforce" in the shared config file. Subsequent sessions will block any tool call that returns deny. Mode can always be flipped back:

npx -y -p @ory/gemini-cli ory-gemini permissions observe

ORY_PERMISSION_MODE, when set, overrides the config — useful for CI runs that want enforce regardless of what's persisted, or for one-off debugging sessions where you want observe without rewriting config.

Step 5: Verify a real session

Start a normal agent session and confirm:

• Allowed tools invoke without complaint.
• Denied tools (if any) are blocked with a clear "Ory: permission denied" message.
• The trace file shows permission.check spans for each tool call and tool.block spans for any denial.

If a tool is unexpectedly blocked, run npx -y -p @ory/gemini-cli ory-gemini permissions status to confirm whether the tuple exists, then add or fix tuples and re-test.

Reference: what each command does

Command	Effect
npx -y -p @ory/gemini-cli ory-gemini permissions status	Print mode + per-tool allow/deny breakdown for the current user. Read-only.
npx -y -p @ory/gemini-cli ory-gemini permissions bootstrap	Write use tuples for the harness's built-in tools. Idempotent.
npx -y -p @ory/gemini-cli ory-gemini permissions bootstrap --dry-run	Print what would be written without making any changes.
npx -y -p @ory/gemini-cli ory-gemini permissions observe	Persist permissionMode = "observe" (denies log, allow through).
npx -y -p @ory/gemini-cli ory-gemini permissions enforce	Persist permissionMode = "enforce" (denies block).

For deeper background on the authentication side of the flow (which identity is the subject, how the user gate resolves it), see ory-auth-setup and ory-login-flow.