CLI Reference — `mergen-server`

One binary operates the local runtime, the policy gate, and every recovery path. Commands below are grouped the way you'll actually reach for them: get running, operate day-to-day, manage policy, configure, and — once you're past day one — report and audit.

Run mergen-server help any time for the same list from your terminal, or mergen-server help <command> for a single command's full option list.

Get started

Command	What it does
`mergen-server`	Zero-config demo — blocks a real destructive command, no account needed
`mergen-server setup`	Installs Mergen, configures your detected AI IDE, and starts the local runtime. No questions asked.
`mergen-server setup --full`	The same, plus guided Slack, PagerDuty, GitHub, and git-hook connection
`mergen-server setup --ide cursor`	Configure one specific IDE (`cursor` \| `vscode` \| `claude-code` \| `windsurf`)
`mergen-server start`	Starts the local runtime (production mode)
`mergen-server stop`	Stops this workspace's running server — also the sanctioned recovery command if the gate is ever wedged
`mergen-server service install`	Supervises the server with your OS (launchd/systemd): starts at login, restarts on crash
`mergen-server login`	Authenticates the CLI — only needed for cloud/team features
`mergen-server dashboard`	Opens My Machine in your browser: this machine's gate activity across every connected IDE
`mergen-server governance`	Opens My Organization on mergen.app: org-wide policies, members, and billing (human-only — no agent can reach this)

Operate & recover

These work even when the gate itself is unreachable — they're recognized directly by the Claude Code hook without a network round-trip.

Command	What it does
`mergen-server status`	Live snapshot: server health, buffer size, errors, MCP activity
`mergen-server doctor`	Full health check: env vars, IDE config, integrations, orphaned processes
`mergen-server doctor --fix`	Repairs what it finds: prunes stale records, kills confirmed orphans, repairs the hook, starts a clean instance
`mergen-server doctor --security`	Hardening posture checklist — what an agent with filesystem access could forge on this install, and how to close it
`mergen-server approve <token>`	Approves a held tool call by token (honored once, for 10 minutes)
`mergen-server approve --last`	Approves the most recent pending hold — no token to copy
`mergen-server trust-reset`	Resets this session's scrutiny-tier reputation to normal, if every command is suddenly being held
`mergen-server panic on --minutes 15 --reason "..."`	Operator escape hatch: passes everything unenforced for a bounded window (max 4h), fully audited
`mergen-server exec -- <cmd>`	Runs a command through the full gate, then executes it — the explicit entrypoint for anything outside an IDE
`mergen-server gate-check -- <cmd>`	Evaluates only, no execution — this is what the Claude Code `PreToolUse` hook calls

Policy

Command	What it does
`mergen-server policies`	Lists active rules with action and trigger counts
`mergen-server promote`	Promotes the observation-window findings into active enforcement
`mergen-server policy-push`	Saves the live server's policy to `.mergen/policy.json`, for git
`mergen-server policy-pull`	Applies `.mergen/policy.json` to the live server
`mergen-server policy-diff`	Shows what would change between the file and the live server
`mergen-server policy-simulate <file>`	Replays a candidate policy against historical traffic — see what would newly block or hold
`mergen-server policy-test [file.json]`	Runs `{input, expectedVerdict}` test cases — no server required, CI-usable
`mergen-server policy-versions`	Lists restorable full-policy snapshots
`mergen-server policy-rollback <id>`	Restores a prior snapshot (immutable rules always survive)
`mergen-server scan <url>`	Scans an MCP server for injection vectors and risk signals before you connect it
`mergen-server test-safety`	Runs the adversarial bypass test suite against your live gate

See Policies for the rule format and condition fields.

Configure

Command	What it does
`mergen-server config`	Inspects every effective setting: value, source, and any ACTIVE settings that weaken enforcement
`mergen-server config set K V`	Writes an org-policy setting to the signed config file (guarded keys need `--acknowledge-risk`)
`mergen-server config modules`	Shows the core/module/integration manifest with live enabled state
`mergen-server config profile team`	Materializes a whole policy profile at once (`solo` \| `team` \| `enterprise` \| `fintech`)
`mergen-server connect <name>`	Guided integration setup — `slack` \| `pagerduty` \| `github` \| `datadog` \| `jira` \| `linear` \| `email` \| `sync-plane`
`mergen-server agent-register <id>`	Issues a signed identity token for an agent profile
`mergen-server agent-list`	Lists issued agent identity tokens on this machine
`mergen-server test`	Validates the installation end-to-end
`mergen-server test hitl`	End-to-end HITL check: synthetic hold → Slack delivery → approve round trip
`mergen-server ci`	CI smoke test (exit 0 = healthy)
`mergen-server --version`	Shows version

Full environment-variable reference (151 settings, generated, always current): Configuration Reference.

Reporting & insights

Command	What it does
`mergen-server impact-report`	Prints the board-deck metrics: autonomous resolution rate, MTTR, blocks prevented
`mergen-server export-risk-report`	Prints a CISO-facing security risk report
`mergen-server verify-log`	Verifies the Agent Blunder Log's hash chain (tamper-evident audit)
`mergen-server trace-replay <traceId>`	Reconstructs the full gate-event + blunder-log timeline for one cross-process trace

Run mergen-server help for the complete list, including advanced commands (watch, explain, guard, backfill, pr) used less often day-to-day.