Repair MCP diagnostics and gateway lifecycle

README.md

@@ -7,7 +7,8 @@ This repository is intended to become the canonical source for:
 - `nap` installer and update UX.
 - Project bootstrap and status commands.
 - Local authenticated MCP wrapper launch/update behavior.
-- Gateway command facade commands such as `nap gateway start`, `nap gateway logs`, and `nap gateway update`.
+- Gateway lifecycle commands such as `nap gateway setup`, `repair`, `start`,
+  `status`, `logs`, `terminal`, `schedule`, and `vault`.
 
 Current state:
 
@@ -20,6 +21,16 @@ Current state:
   the generated `napseer_mcp_server.py` worker between requests.
 - Gateway service compatibility remains in the worker while the standalone
   gateway image is built from the public gateway repository.
+- `nap mcp status` and `nap doctor` run a fresh stdio initialization,
+  `tools/list`, and authenticated read probe. They deliberately report an
+  existing client connection as `not_observable`; a successful fresh probe
+  does not claim that a previously opened Codex transport is connected.
+- Operator OAuth credentials remain in `.napseer/auth.json`. A repaired local
+  gateway uses a separate `.napseer/gateway-auth.json` worker identity, so
+  relay token renewal cannot rotate or overwrite the operator/MCP session.
+- CLI terminal and schedule operations call the running gateway's
+  loopback-only, CSRF-protected control API. PTYs therefore live in the daemon
+  instead of disappearing when a CLI subprocess exits.
 
 Backend discovery publishes the release manifest and exact public source
 revision used for each bundle.
@@ -30,5 +41,20 @@ Configure Codex and other long-lived stdio clients to launch:
 python3 ~/.local/share/napseer/napseer_mcp_supervisor.py
 ```
 
+For repositories that may be resumed after Codex opened a different working
+directory, add a trusted project `.codex/config.toml` override with both
+`cwd` and `NAPSEER_PROJECT_ROOT`. MCP processes inherit their launch directory;
+they cannot infer a later client workspace switch over stdio.
+
+The public operator surface is intentionally small:
+
+```text
+nap init | status | doctor | auth | project | mcp | gateway | update | version | help
+```
+
+Authentication has one recovery verb: `nap auth repair`. Normal refresh is
+automatic. `nap gateway repair` creates the separate worker identity once;
+`--replace` is required to replace an existing identity.
+
 The direct wrapper remains the `nap` CLI implementation and an isolated
 protocol-debugging entrypoint.