docs: OpenAPI and API.md cover every route; drop removed endpoints; guard config writes

- openapi-extra/run.js describes tmux pane runs only: the removed
  POST /api/run/{id}/message and stream-json run_stream/run_input_ack are gone.
- 108 operations added to OpenAPI (lanes, run, settings, reports, cc-config,
  pets, ai-proxies, tool-profiles, ai-tools, snapshots, locks, ...);
  openapi.yaml regenerated.
- docs/API.md: 74 routes added, 4 endpoints that no longer exist removed.
- Role is `developer`, not `member` (CLI.md, DATABASE.md, OVERVIEW.md);
  `agenthub update` -> `update-check`; help lists `server install-system|tools`
  and `users provision`; ARCHITECTURE.md's stale paths and names fixed.
- cc-config/codex-config writes carry sameOriginGuard (an MCP server or plugin
  is code Claude runs later), with a test; `command -v` takes its name as $1.

bin/agenthub.js

@@ -2845,12 +2845,12 @@ const COMMAND_GROUPS = [
       ],
       [
         "server",
-        "setup|off|status [--hostname name] [--admin name]",
+        "setup|install-system|tools|off|status [--hostname name] [--admin name]",
         "Server mode: logins for a shared dashboard (docs/SERVER-MODE.md)",
       ],
       [
         "users",
-        "list|add|passwd|role|disable|enable|assign|audit [name]",
+        "list|add|passwd|role|disable|enable|provision|assign|audit [name]",
         "Server mode's accounts (add: --role admin|analyst|developer)",
       ],
       [
@@ -3812,8 +3812,8 @@ const COMMANDS = (() => {
 const SUBCOMMANDS = {
   alerts: ["ack", "ack-all"],
   service: ["install", "uninstall", "status"],
-  server: ["setup", "off", "status"],
-  users: ["list", "add", "passwd", "role", "disable", "enable", "assign", "audit"],
+  server: ["setup", "install-system", "tools", "off", "status"],
+  users: ["list", "add", "passwd", "role", "disable", "enable", "provision", "assign", "audit"],
   accounts: ["list", "add", "remove", "pin", "unpin"],
   pricing: ["set", "delete", "reset"],
   webhooks: ["test"],
@@ -3905,7 +3905,7 @@ async function newPassword(label) {
   return first;
 }
 
-/** `agenthub server setup|off|status` — turn server mode on or off. */
+/** `agenthub server setup|install-system|tools|off|status` — turn server mode on or off. */
 async function cmdServer(sub, flags) {
   const { settingsEnv, auth } = serverAuth();
   const file = settingsEnv.settingsFilePath();
@@ -4062,7 +4062,7 @@ async function installSystem(flags, settingsEnv) {
     throw new Error("run this as the account that runs the dashboard, not as root (it uses sudo)");
   }
   const which = (bin) =>
-    spawnSync("sh", ["-c", `command -v ${bin}`], { encoding: "utf8" }).stdout.trim();
+    spawnSync("sh", ["-c", 'command -v "$1"', "sh", bin], { encoding: "utf8" }).stdout.trim();
   const host = os.userInfo().username;
   const { getDataDir } = require(path.join(REPO_ROOT, "server", "lib", "claude-home.js"));
   const data = getDataDir();