@topolo/cli 0.13.8 → 0.13.10

package/dist/index.js

@@ -14,7 +14,7 @@ function registerAgentPacksCommand(program2) {
       throw new Error("Exact closed smoke operation, role/case and UUID required.");
     const store = packs.opts().store ?? resolve(homedir(), "AgentPacks");
     if (options.harness === "claude") {
-      const { operateClaudeSmoke } = await import("./claude-pack-backend-3YJNKMYD.js");
+      const { operateClaudeSmoke } = await import("./claude-pack-backend-RMSOPHVQ.js");
       console.log(JSON.stringify(await operateClaudeSmoke({
         store,
         kind: "smoke-" + operation,
@@ -44,7 +44,7 @@ function registerAgentPacksCommand(program2) {
   });
   packs.command("configure").description("Qualify and configure an adopted Claude roster through its live native backend").argument("<pack>").option("--harness <name>", "Host adapter", "claude").requiredOption("--policy <path>", "Reviewed execution policy JSON").requiredOption("--endpoint <url>", "Explicit loopback main-process inspector endpoint, enabled separately with authorization").requiredOption("--pid <pid>", "Expected Claude main-process PID").option("--apply", "Apply native groups, pins, models, effort and permission modes; otherwise preflight only").action(async (pack, options) => {
     if (options.harness !== "claude") throw new Error("Native configure is currently qualified only for Claude Desktop.");
-    const { configureClaudePack } = await import("./claude-pack-backend-3YJNKMYD.js");
+    const { configureClaudePack } = await import("./claude-pack-backend-RMSOPHVQ.js");
     const result = await configureClaudePack({
       store: packs.opts().store ?? resolve(homedir(), "AgentPacks"),
       pack,
@@ -67,8 +67,10 @@ function registerAgentPacksCommand(program2) {
     "list",
     "recover",
     "doctor",
+    "open",
     "policy",
     "permissions",
+    "lane",
     "approvals",
     "remote-recover",
     "connect",
@@ -80,9 +82,40 @@ function registerAgentPacksCommand(program2) {
   for (const name of commands) {
     const command = packs.command(name).description(name === "add" ? "Add an installed or bundled pack, group, or agent" : `Run the pack ${name} operation`);
     if (name === "switch" || name === "recover") command.option("--policy <path>", "Reviewed policy for an adopted Claude roster").option("--endpoint <url>", "Explicit authorized Claude main-process inspector endpoint").option("--pid <pid>", "Expected Claude main-process PID").option("--apply", "Apply a native switch; recovery is always read-only");
-    if (name === "approvals") command.option("--intake <id>", "Exact owning native intake identity").option("--fingerprint <hash>", "Exact pending native request fingerprint").option("--response <path>", "Recorded one-request response JSON").option("--human-decision-recorded", "Assert that the exact human decision is recorded in the intake");
+    if (name === "lane") command.option("--input <path>", "Closed native lifecycle input JSON").option("--pack <name>", "Exact installed pack for Claude native lifecycle").option("--policy <path>", "Current reviewed source execution policy").option("--endpoint <url>", "Explicit authorized current Claude main-process inspector endpoint").option("--pid <pid>", "Expected current Claude native main PID").option("--connection <id>", "Exact explicit owned lane connection");
+    if (name === "approvals") command.option("--connection <id>", "Exact private dynamic lane control connection").option("--intake <id>", "Exact owning native intake identity").option("--fingerprint <hash>", "Exact pending native request fingerprint").option("--response <path>", "Recorded one-request response JSON").option("--human-decision-recorded", "Assert that the exact human decision is recorded in the intake");
     command.option("--harness <name>", "Local host adapter (codex, claude Desktop Code sessions)", "codex").option("--adapter-help", "Show every option supported by the selected adapter").argument("[arguments...]").allowUnknownOption().allowExcessArguments().addHelpText("after", name === "add" ? "\nExamples:\n  topolo agent-packs add founder\n  topolo agent-packs add founder --group specialists\n  topolo agent-packs add founder --agent strategy\n" : "\nRun topolo agent-packs <command> --adapter-help for all adapter options. Cloud commands require explicit --environment and --context-key.\n").action(async (args, options) => {
       if (!["codex", "claude"].includes(options.harness)) throw new Error(`The ${options.harness} pack adapter is not available. Supported adapters: codex, claude.`);
+      if (name === "lane" && options.harness === "claude" && !options.adapterHelp && !["status", "models-template", "models-install"].includes(args[0] ?? "")) {
+        if (options.connection) {
+          if (args.length !== 1 || !["read", "context-start", "context-read", "fixture-start", "fixture-read", "retire", "close"].includes(args[0]))
+            throw new Error("Closed existing Claude lane control operation required.");
+          const input3 = options.input ? JSON.parse(readFileSync(options.input, "utf8")) : {};
+          if (!input3 || typeof input3 !== "object" || Array.isArray(input3) || Object.keys(input3).some((k) => k !== "operationId")) throw new Error("Only an exact bootstrap/fixture operation UUID may be supplied.");
+          const { operateClaudeLaneControl } = await import("./claude-pack-backend-RMSOPHVQ.js");
+          console.log(JSON.stringify(await operateClaudeLaneControl({
+            store: packs.opts().store ?? resolve(homedir(), "AgentPacks"),
+            connection: options.connection,
+            operation: { kind: args[0], ...input3 }
+          }), null, 2));
+          return;
+        }
+        if (args.length !== 1 || !options.input || !options.pack || !options.policy || !options.endpoint || !options.pid)
+          throw new Error("Closed Claude lane operation requires --input, --pack, --policy, --endpoint and --pid.");
+        const input2 = JSON.parse(readFileSync(options.input, "utf8"));
+        if (!input2 || typeof input2 !== "object" || Array.isArray(input2)) throw new Error("Closed native lane input object required.");
+        const { operateClaudeLane } = await import("./claude-pack-backend-RMSOPHVQ.js");
+        console.log(JSON.stringify(await operateClaudeLane({
+          store: packs.opts().store ?? resolve(homedir(), "AgentPacks"),
+          pack: options.pack,
+          policy: options.policy,
+          endpoint: options.endpoint,
+          pid: Number(options.pid),
+          operation: args[0],
+          input: input2
+        }), null, 2));
+        return;
+      }
       if (name === "approvals" && options.harness === "claude" && !options.adapterHelp) {
         if (!["list", "details", "respond"].includes(args[0] ?? "") || args.length > 2)
           throw new Error("Approvals requires list, details KEY, or respond KEY.");
@@ -96,7 +129,20 @@ function registerAgentPacksCommand(program2) {
             throw new Error("Only a one-request once/deny response is supported.");
           decision = response.decision;
         }
-        const { operateClaudeApprovals } = await import("./claude-pack-backend-3YJNKMYD.js");
+        if (options.connection) {
+          const { operateClaudeLaneControl } = await import("./claude-pack-backend-RMSOPHVQ.js");
+          console.log(JSON.stringify(await operateClaudeLaneControl({
+            store: packs.opts().store ?? resolve(homedir(), "AgentPacks"),
+            connection: options.connection,
+            operation: {
+              kind: "approval-" + args[0],
+              ...args[0] !== "list" ? { key: args[1], intake: options.intake, fingerprint: options.fingerprint } : {},
+              ...args[0] === "respond" ? { decision, humanDecisionRecorded: options.humanDecisionRecorded } : {}
+            }
+          }), null, 2));
+          return;
+        }
+        const { operateClaudeApprovals } = await import("./claude-pack-backend-RMSOPHVQ.js");
         console.log(JSON.stringify(await operateClaudeApprovals({
           store: packs.opts().store ?? resolve(homedir(), "AgentPacks"),
           kind: args[0],
@@ -108,10 +154,10 @@ function registerAgentPacksCommand(program2) {
         }), null, 2));
         return;
       }
-      if (options.policy || options.endpoint || options.pid || options.apply) {
+      if (name !== "lane" && (options.policy || options.endpoint || options.pid || options.apply)) {
         if (options.harness !== "claude" || !options.policy || !options.endpoint || !options.pid || args.length !== 1)
           throw new Error("Native switch/recovery requires one Claude pack, --policy, --endpoint and --pid.");
-        const { configureClaudePack } = await import("./claude-pack-backend-3YJNKMYD.js");
+        const { configureClaudePack } = await import("./claude-pack-backend-RMSOPHVQ.js");
         const result2 = await configureClaudePack({
           store: packs.opts().store ?? resolve(homedir(), "AgentPacks"),
           pack: args[0],
@@ -129,7 +175,12 @@ function registerAgentPacksCommand(program2) {
       if (!adapter) throw new Error("This CLI installation is missing its bundled Topolo Agent Pack adapter. Reinstall @topolo/cli.");
       const store = packs.opts().store;
       const forwarded = (options.adapterHelp ? ["--help"] : args).map((value) => value === "--group" ? "--set" : value);
+      if (name === "lane" && !options.adapterHelp) {
+        if (options.input) forwarded.push("--input", options.input);
+        if (options.connection) forwarded.push("--connection", options.connection);
+      }
       if (name === "approvals" && !options.adapterHelp) {
+        if (options.connection) forwarded.push("--connection", options.connection);
         if (options.intake) forwarded.push("--intake", options.intake);
         if (options.fingerprint) forwarded.push("--fingerprint", options.fingerprint);
         if (options.response) forwarded.push("--response", options.response);
@@ -158,7 +209,7 @@ import { platform as platform2 } from "os";
 import { createInterface } from "readline/promises";
 import { stdin as input } from "process";
 
-// node_modules/.pnpm/@topolo+sdk@0.23.20/node_modules/@topolo/sdk/dist/index.js
+// node_modules/.pnpm/@topolo+sdk@0.23.21/node_modules/@topolo/sdk/dist/index.js
 function record(value) {
   return Boolean(value) && typeof value === "object" && !Array.isArray(value);
 }
@@ -523,6 +574,9 @@ function publicTopoloErrorMessage(error) {
   const code = canonicalTopoloServiceErrorCode(
     typeof error === "string" ? error : error.code ?? extractTopoloServiceErrorCode(error.body)
   ) ?? "request_failed";
+  if (code === "organization_policy_admin_permission_required") {
+    return "Organization policy administration permission is required.";
+  }
   if (/(?:organization|org).*(?:enroll|membership|member|admission)/.test(code)) {
     return "Organization or application enrollment is required.";
   }
@@ -550,6 +604,9 @@ function topoloErrorHint(error) {
   if (code === "enrollment_required" || code === "membership_required" || /(?:organization|org).*(?:enroll|membership|member|admission)|(?:enroll|membership).*(?:organization|org)/.test(code)) {
     return "The current identity is not enrolled for this organization or application. Use an enrolled identity or ask an organization administrator to complete enrollment.";
   }
+  if (code === "organization_policy_admin_permission_required") {
+    return "This action requires explicit organization policy administration permission. Ask an authorized organization administrator to review the exact grant and the published principal and workspace authorization contract.";
+  }
   if (/(?:organization|org).*(?:context|required|missing|invalid|unknown|not_found)/.test(code)) {
     return "Select a signed-in organization context, then verify the effective identity and organization before retrying.";
   }
@@ -1741,7 +1798,7 @@ var TopoloClient = class _TopoloClient {
         } catch (error) {
           const transportFailure = !(error instanceof TopoloSdkError) && !opts.signal?.aborted;
           if (!transportFailure || attempt === maxAttempts) throw error;
-          await new Promise((resolve4) => setTimeout(resolve4, 250));
+          await new Promise((resolve5) => setTimeout(resolve5, 250));
         }
       }
       throw new TopoloSdkError("network_error", "Topolo read retry loop exhausted.");
@@ -3740,7 +3797,7 @@ function createTopolo(options) {
 async function pollUntilApproved(params) {
   let interval = Math.max(params.intervalSeconds ?? 5, 1);
   while (Date.now() < params.expiresAtMs) {
-    await new Promise((resolve4) => setTimeout(resolve4, Math.min(interval * 1e3, params.expiresAtMs - Date.now())));
+    await new Promise((resolve5) => setTimeout(resolve5, Math.min(interval * 1e3, params.expiresAtMs - Date.now())));
     if (Date.now() >= params.expiresAtMs) break;
     try {
       return await params.oauth.pollDeviceToken({
@@ -3768,7 +3825,7 @@ async function pollUntilApproved(params) {
   throw new Error("Device code expired. Run `topolo auth login` again.");
 }
 
-// node_modules/.pnpm/@topolo+sdk@0.23.20/node_modules/@topolo/sdk/dist/node/credential-store.js
+// node_modules/.pnpm/@topolo+sdk@0.23.21/node_modules/@topolo/sdk/dist/node/credential-store.js
 import { mkdir as mkdir2, readFile as readFile2, writeFile as writeFile2, chmod as chmod2, lstat, readdir as readdir2 } from "fs/promises";
 import { existsSync as existsSync2, mkdirSync, lstatSync, readdirSync, readFileSync as readFileSync2, openSync, writeFileSync, fsyncSync, closeSync, renameSync, unlinkSync, rmdirSync, linkSync } from "fs";
 import { createHash as createHash2, randomUUID as randomUUID2 } from "crypto";
@@ -6521,7 +6578,7 @@ import { spawnSync as spawnSync4 } from "child_process";
 import { existsSync as existsSync6 } from "fs";
 import { readFile as readFile6, rm as rm2 } from "fs/promises";
 import { homedir as homedir5 } from "os";
-import { dirname as dirname6, join as join7, resolve as resolve2 } from "path";
+import { dirname as dirname6, join as join7, resolve as resolve3 } from "path";
 import { fileURLToPath as fileURLToPath3 } from "url";
 import { createRequire } from "module";
 
@@ -6530,7 +6587,7 @@ import { spawnSync as spawnSync3 } from "child_process";
 import { existsSync as existsSync4 } from "fs";
 import { readFile as readFile4 } from "fs/promises";
 import { homedir as homedir4 } from "os";
-import { isAbsolute, join as join6 } from "path";
+import { isAbsolute, join as join6, resolve as resolve2 } from "path";
 var SUPPORTED_AGENT_IDS = [
   "claude",
   "claude-desktop",
@@ -6570,6 +6627,18 @@ var AGENT_NAME_FOR = {
   goose: "goose",
   "amazon-q": "amazon-q"
 };
+function resolveAgentHostTarget(options) {
+  const homeDir = resolve2(options.homeDir ?? homedir4());
+  const codexHome = options.codexHome ?? (options.homeDir === void 0 ? process.env.CODEX_HOME || void 0 : void 0);
+  if (codexHome !== void 0 && (!codexHome.trim() || !isAbsolute(codexHome))) {
+    throw new Error("Codex home must be an absolute nonempty directory.");
+  }
+  return Object.freeze({
+    homeDir,
+    ...options.projectDir ? { projectDir: resolve2(options.projectDir) } : {},
+    codexHome: codexHome ?? join6(homeDir, ".codex")
+  });
+}
 var RESERVED_OPERATOR_REGISTRATION = ["topolo", "platform"].join("-");
 function isPublicRegistrationName(name) {
   return name === "topolo" || name.startsWith("topolo-") && name !== RESERVED_OPERATOR_REGISTRATION;
@@ -6585,14 +6654,14 @@ function stableNodeCommand() {
   });
   return selectStableNodeCommand(probe.status === 0 ? probe.stdout : void 0);
 }
-function agentSkillPath(agent, homeDir = homedir4(), projectDir) {
+function agentSkillPath(agent, homeDir = homedir4(), projectDir, codexHome) {
   switch (agent) {
     case "claude":
       return projectDir ? join6(projectDir, ".claude", "skills", "topolo", "SKILL.md") : join6(homeDir, ".claude", "skills", "topolo", "SKILL.md");
     case "claude-desktop":
       return join6(homeDir, ".claude", "skills", "topolo", "SKILL.md");
     case "codex":
-      return join6(homeDir, ".codex", "skills", "topolo", "SKILL.md");
+      return join6(codexHome ?? join6(homeDir, ".codex"), "skills", "topolo", "SKILL.md");
     case "cursor":
       return join6(projectDir ?? homeDir, ".cursor", "rules", "topolo.mdc");
     case "grok":
@@ -6610,10 +6679,10 @@ function agentSkillPath(agent, homeDir = homedir4(), projectDir) {
       return void 0;
   }
 }
-function agentConfigPaths(agent, homeDir = homedir4(), projectDir) {
+function agentConfigPaths(agent, homeDir = homedir4(), projectDir, codexHome) {
   switch (agent) {
     case "claude":
-      return [{ path: join6(homeDir, ".claude.json"), format: "json", rootKey: "mcpServers" }];
+      return [{ path: projectDir ? join6(projectDir, ".mcp.json") : join6(homeDir, ".claude.json"), format: "json", rootKey: "mcpServers" }];
     case "claude-desktop":
       return [{
         path: claudeDesktopConfigPath(homeDir),
@@ -6621,7 +6690,7 @@ function agentConfigPaths(agent, homeDir = homedir4(), projectDir) {
         rootKey: "mcpServers"
       }];
     case "codex":
-      return [{ path: join6(homeDir, ".codex", "config.toml"), format: "toml" }];
+      return [{ path: join6(codexHome ?? join6(homeDir, ".codex"), "config.toml"), format: "toml" }];
     case "cursor":
       return [{
         path: projectDir ? join6(projectDir, ".cursor", "mcp.json") : join6(homeDir, ".cursor", "mcp.json"),
@@ -6702,8 +6771,36 @@ function agentCliNames(agent) {
       return ["qchat", "q"];
   }
 }
-function agentConfigExists(agent, homeDir = homedir4(), projectDir) {
-  return agentConfigPaths(agent, homeDir, projectDir).some((config) => existsSync4(config.path));
+function agentConfigExists(agent, homeDir = homedir4(), projectDir, codexHome) {
+  return agentConfigPaths(agent, homeDir, projectDir, codexHome).some((config) => existsSync4(config.path));
+}
+async function assertClaudeProjectScope(homeDir, projectDir, name) {
+  const path = join6(homeDir, ".claude.json");
+  let contents;
+  try {
+    contents = await readFile4(path, "utf8");
+  } catch (error) {
+    if (error.code === "ENOENT") return;
+    throw error;
+  }
+  let config;
+  try {
+    config = JSON.parse(contents);
+    if (!config || typeof config !== "object" || Array.isArray(config)) throw new Error();
+  } catch {
+    throw new Error("Cannot verify malformed Claude scope configuration at " + path + ".");
+  }
+  const object = (value) => {
+    if (value === void 0) return void 0;
+    if (!value || typeof value !== "object" || Array.isArray(value)) {
+      throw new Error("Cannot verify malformed Claude scope configuration at " + path + ".");
+    }
+    return value;
+  };
+  const local = object(object(config.projects)?.[resolve2(projectDir)]);
+  if (Object.hasOwn(object(config.mcpServers) ?? {}, name) || Object.hasOwn(object(local?.mcpServers) ?? {}, name)) {
+    throw new Error("Claude MCP scope conflict for " + name + ": a user or local definition can override the project registration. Resolve that scope before setup.");
+  }
 }
 function claudeDesktopConfigPath(homeDir) {
   if (process.platform === "darwin") return join6(homeDir, "Library", "Application Support", "Claude", "claude_desktop_config.json");
@@ -6715,9 +6812,9 @@ function vscodeUserConfigPath(homeDir) {
   if (process.platform === "win32") return join6(process.env.APPDATA ?? join6(homeDir, "AppData", "Roaming"), "Code", "User", "mcp.json");
   return join6(process.env.XDG_CONFIG_HOME ?? join6(homeDir, ".config"), "Code", "User", "mcp.json");
 }
-async function readAgentRegistrations(agent, homeDir = homedir4(), projectDir) {
+async function readAgentRegistrations(agent, homeDir = homedir4(), projectDir, codexHome) {
   const registrations = [];
-  for (const config of agentConfigPaths(agent, homeDir, projectDir)) {
+  for (const config of agentConfigPaths(agent, homeDir, projectDir, codexHome)) {
     if (!existsSync4(config.path)) continue;
     if (config.format === "json") {
       registrations.push(...await readJsonRegistrations(config.path, config.rootKey ?? "mcpServers", agent));
@@ -6982,17 +7079,19 @@ function message(error) {
 
 // src/commands/agent-config.ts
 import { existsSync as existsSync5 } from "fs";
-import { mkdir as mkdir3, readFile as readFile5, rename as rename2, writeFile as writeFile3 } from "fs/promises";
+import { lstat as lstat2, mkdir as mkdir3, open, readFile as readFile5, rename as rename2, unlink, writeFile as writeFile3 } from "fs/promises";
+import { randomUUID as randomUUID3 } from "crypto";
 import { dirname as dirname5 } from "path";
-async function installAgentSkill(agent, source, homeDir, projectDir) {
-  const path = agentSkillPath(agent, homeDir, projectDir);
+async function installAgentSkill(agent, source, homeDir, projectDir, codexHome) {
+  const path = agentSkillPath(agent, homeDir, projectDir, codexHome);
   if (!path) return { installed: false };
   const contents = formatSkillForAgent(agent, source);
   await atomicWrite(path, contents);
   return { path, installed: true };
 }
-async function registerAgentConfig(agent, mcp, homeDir, registration, projectDir) {
-  for (const config of agentConfigPaths(agent, homeDir, projectDir)) {
+async function registerAgentConfig(agent, mcp, homeDir, registration, projectDir, codexHome) {
+  if (agent === "claude" && projectDir) await assertClaudeProjectScope(homeDir, projectDir, registration.name);
+  for (const config of agentConfigPaths(agent, homeDir, projectDir, codexHome)) {
     if (config.format === "json") {
       await registerJson(config, agent, mcp, registration);
     } else if (config.format === "toml") {
@@ -7002,8 +7101,8 @@ async function registerAgentConfig(agent, mcp, homeDir, registration, projectDir
     }
   }
 }
-async function unregisterAgentConfig(agent, homeDir, name, projectDir) {
-  for (const config of agentConfigPaths(agent, homeDir, projectDir)) {
+async function unregisterAgentConfig(agent, homeDir, name, projectDir, codexHome) {
+  for (const config of agentConfigPaths(agent, homeDir, projectDir, codexHome)) {
     if (!existsSync5(config.path)) continue;
     if (config.format === "json") {
       await unregisterJson(config, agent, name);
@@ -7016,18 +7115,39 @@ async function unregisterAgentConfig(agent, homeDir, name, projectDir) {
   }
 }
 function registrationEnvironment(agent, registration) {
+  let privateAliases = {};
+  if (registration.configPath) {
+    const prefixes = {
+      production: "TOPOLO_PRODUCTION",
+      staging: "TOPOLO_STAGING",
+      development: "TOPOLO_DEVELOPMENT",
+      local: "TOPOLO_LOCAL"
+    };
+    const prefix = prefixes[registration.environment];
+    if (!prefix) throw new Error("Cannot isolate a private profile for an unknown environment.");
+    privateAliases = {
+      TOPOLO_API_KEY: "",
+      TOPOLO_ACCESS_TOKEN: "",
+      [prefix + "_API_KEY"]: "",
+      [prefix + "_ACCESS_TOKEN"]: "",
+      TOPOLO_ENV: registration.environment
+    };
+  }
   return {
     TOPOLO_AGENT_NAME: AGENT_NAME_FOR[agent],
     ...registration.configPath ? { TOPOLO_CONFIG_PATH: registration.configPath } : {},
     ...registration.installationId ? { TOPOLO_AGENT_INSTALLATION_ID: registration.installationId } : {},
-    ...registration.context ? { TOPOLO_CONTEXT: registration.context, TOPOLO_ENV: registration.environment } : {}
+    ...registration.context ? { TOPOLO_CONTEXT: registration.context, TOPOLO_ENV: registration.environment } : {},
+    ...privateAliases
   };
 }
 async function registerJson(config, agent, mcp, registration) {
+  const before = await fileSnapshot(config.path);
   let parsed = {};
-  if (existsSync5(config.path)) {
+  if (before.contents !== void 0) {
     try {
-      parsed = JSON.parse(await readFile5(config.path, "utf8"));
+      parsed = JSON.parse(before.contents);
+      if (!parsed || typeof parsed !== "object" || Array.isArray(parsed)) throw new Error("Expected an object.");
     } catch (error) {
       throw new Error(
         "Cannot update malformed " + (agent === "claude" ? "Claude" : AGENT_LABELS[agent]) + " configuration at " + config.path + ": " + (error instanceof Error ? error.message : String(error))
@@ -7048,7 +7168,7 @@ async function registerJson(config, agent, mcp, registration) {
   if (agent === "claude" || agent === "claude-desktop" || rootKey === "servers") entry.type = "stdio";
   servers[registration.name] = entry;
   parsed[rootKey] = servers;
-  await atomicWrite(config.path, JSON.stringify(parsed, null, 2) + "\n");
+  await atomicWrite(config.path, JSON.stringify(parsed, null, 2) + "\n", before);
 }
 async function unregisterJson(config, agent, name) {
   let parsed;
@@ -7070,13 +7190,14 @@ async function unregisterJson(config, agent, name) {
   await atomicWrite(config.path, JSON.stringify(parsed, null, 2) + "\n");
 }
 async function registerToml(path, agent, mcp, registration) {
-  const existing = existsSync5(path) ? await readFile5(path, "utf8") : "";
+  const before = await fileSnapshot(path);
+  const existing = before.contents ?? "";
   const text2 = withoutMcpServerSections(existing, registration.name);
   const args = mcp.args.length ? "\nargs = [" + mcp.args.map((item) => JSON.stringify(item)).join(", ") + "]" : "";
   const environment = registrationEnvironment(agent, registration);
   const environmentText = Object.entries(environment).map(([key, value]) => JSON.stringify(key) + " = " + JSON.stringify(value)).join(", ");
   const block = agent === "grok" ? "\n\n[mcp_servers." + registration.name + "]\ncommand = " + JSON.stringify(mcp.command) + args + "\nenv = { " + environmentText + " }\n" : "\n\n[mcp_servers." + registration.name + "]\ncommand = " + JSON.stringify(mcp.command) + args + "\n\n[mcp_servers." + registration.name + ".env]\n" + Object.entries(environment).map(([key, value]) => key + " = " + JSON.stringify(value)).join("\n") + "\n";
-  await atomicWrite(path, text2 + block);
+  await atomicWrite(path, text2 + block, before);
 }
 async function registerGoose(path, mcp, registration) {
   const existing = existsSync5(path) ? await readFile5(path, "utf8") : "";
@@ -7146,11 +7267,82 @@ function formatSkillForAgent(agent, source) {
   }
   return "---\ntrigger: model_decision\ndescription: Use Topolo MCP for Topolo platform operations.\n---\n\n" + body;
 }
-async function atomicWrite(path, contents) {
+function fileIdentity(stat2) {
+  return [stat2.dev, stat2.ino, stat2.size, stat2.mtimeMs, stat2.ctimeMs, stat2.mode, stat2.nlink].join(":");
+}
+async function fileSnapshot(path) {
+  const parents = [];
+  for (let parent = dirname5(path); ; parent = dirname5(parent)) {
+    try {
+      const stat2 = await lstat2(parent);
+      if (!stat2.isDirectory() || stat2.isSymbolicLink()) throw new Error("Host destination contains a symbolic link or non-directory at " + parent + ".");
+      parents.push({ path: parent, identity: [stat2.dev, stat2.ino].join(":") });
+    } catch (error) {
+      if (error.code !== "ENOENT") throw error;
+    }
+    if (dirname5(parent) === parent) break;
+  }
+  try {
+    const stat2 = await lstat2(path);
+    if (!stat2.isFile() || stat2.isSymbolicLink() || stat2.nlink !== 1) throw new Error("Host configuration must be a single regular file at " + path + ".");
+    const contents = await readFile5(path, "utf8");
+    if (fileIdentity(await lstat2(path)) !== fileIdentity(stat2)) throw new Error("Host configuration changed while reading at " + path + ".");
+    return { contents, identity: fileIdentity(stat2), parents };
+  } catch (error) {
+    if (error.code === "ENOENT") return { parents };
+    throw error;
+  }
+}
+async function assertSnapshot(path, before) {
+  const current = await fileSnapshot(path);
+  if (current.contents !== before.contents || current.identity !== before.identity || before.parents.some((parent) => !current.parents.some((candidate) => candidate.path === parent.path && candidate.identity === parent.identity))) {
+    throw new Error("Host destination changed before write at " + path + ".");
+  }
+}
+async function atomicWrite(path, contents, before) {
+  before ??= await fileSnapshot(path);
+  await assertSnapshot(path, before);
+  if (before.contents === contents) return;
   await mkdir3(dirname5(path), { recursive: true });
-  const temporaryPath = path + ".topolo-" + process.pid + ".tmp";
-  await writeFile3(temporaryPath, contents, { encoding: "utf8", mode: 384 });
-  await rename2(temporaryPath, path);
+  const destination = await fileSnapshot(path);
+  await assertSnapshot(path, before);
+  const temporaryPath = path + ".topolo-" + randomUUID3() + ".tmp";
+  const handle = await open(temporaryPath, "wx", 384);
+  let temporaryIdentity;
+  let handleClosed = false;
+  let temporaryPending = true;
+  try {
+    const created = await handle.stat();
+    temporaryIdentity = [created.dev, created.ino].join(":");
+    await assertSnapshot(path, destination);
+    await writeFile3(handle, contents, { encoding: "utf8" });
+    await handle.close();
+    handleClosed = true;
+    await assertSnapshot(path, destination);
+    const temporary = await lstat2(temporaryPath);
+    if (!temporary.isFile() || temporary.isSymbolicLink() || temporary.nlink !== 1 || [temporary.dev, temporary.ino].join(":") !== temporaryIdentity) {
+      throw new Error("Host temporary file custody changed before rename at " + path + ".");
+    }
+    await rename2(temporaryPath, path);
+    temporaryPending = false;
+    const installed = await fileSnapshot(path);
+    if (installed.contents !== contents) throw new Error("Host configuration read-back failed at " + path + ".");
+  } finally {
+    if (!handleClosed) await handle.close();
+    if (temporaryPending && temporaryIdentity) {
+      let cleanupOwned = false;
+      try {
+        const parentsOwned = await Promise.all(destination.parents.map(async (parent) => {
+          const current2 = await lstat2(parent.path);
+          return current2.isDirectory() && !current2.isSymbolicLink() && [current2.dev, current2.ino].join(":") === parent.identity;
+        }));
+        const current = await lstat2(temporaryPath);
+        cleanupOwned = parentsOwned.every(Boolean) && current.isFile() && !current.isSymbolicLink() && current.nlink === 1 && [current.dev, current.ino].join(":") === temporaryIdentity;
+      } catch {
+      }
+      if (cleanupOwned) await unlink(temporaryPath);
+    }
+  }
 }
 function withoutMcpServerSections(text2, name) {
   const section = "[mcp_servers." + name + "]";
@@ -7171,8 +7363,8 @@ function withoutMcpServerSections(text2, name) {
 var AGENT_LABELS2 = AGENT_LABELS;
 function skillsSourceDir() {
   const here = dirname6(fileURLToPath3(import.meta.url));
-  const distCandidate = resolve2(here, "../skills");
-  const srcCandidate = resolve2(here, "../../skills");
+  const distCandidate = resolve3(here, "../skills");
+  const srcCandidate = resolve3(here, "../../skills");
   for (const candidate of [distCandidate, srcCandidate]) {
     if (existsSync6(join7(candidate, "topolo", "SKILL.md"))) return candidate;
   }
@@ -7224,14 +7416,22 @@ function resolveMcpRegistration(options) {
   };
 }
 async function installForAgent(agent, sourceDir, mcp, opts) {
+  const { homeDir, projectDir, codexHome } = opts.target;
+  if (opts.withMcp && agent === "claude" && projectDir) {
+    try {
+      await assertClaudeProjectScope(homeDir, projectDir, opts.registration.name);
+    } catch (err) {
+      return { agent, skillInstalled: false, mcp: "failed", detail: err instanceof Error ? err.message : String(err) };
+    }
+  }
   const source = await readFile6(join7(sourceDir, "topolo", "SKILL.md"), "utf8");
-  const skill = await installAgentSkill(agent, source, opts.homeDir, opts.projectDir);
+  const skill = await installAgentSkill(agent, source, homeDir, projectDir, codexHome);
   if (!opts.withMcp) {
     return { agent, skillPath: skill.path, skillInstalled: skill.installed, mcp: "skipped" };
   }
   try {
-    await registerAgentConfig(agent, mcp, opts.homeDir, opts.registration, opts.projectDir);
-    const installed = (await readAgentRegistrations(agent, opts.homeDir, opts.projectDir)).find((registration) => registration.name === opts.registration.name);
+    await registerAgentConfig(agent, mcp, homeDir, opts.registration, projectDir, codexHome);
+    const installed = (await readAgentRegistrations(agent, homeDir, projectDir, codexHome)).find((registration) => registration.name === opts.registration.name);
     const expectedEnvironment = registrationEnvironment(agent, opts.registration);
     if (!installed || installed.command !== mcp.command || JSON.stringify(installed.args) !== JSON.stringify(mcp.args) || Object.entries(expectedEnvironment).some(([key, value]) => installed.env[key] !== value)) {
       throw new Error(`Host configuration did not retain the ${opts.registration.name} MCP registration.`);
@@ -7265,12 +7465,12 @@ function resolveTargets(opts) {
   if (opts.all) return [...SUPPORTED_AGENT_IDS];
   const homeDir = opts.homeDir ?? homedir5();
   const detectBinaries = homeDir === homedir5();
-  const detected = SUPPORTED_AGENT_IDS.filter((agent) => agentConfigExists(agent, homeDir, opts.project) || detectBinaries && agentBinaryExists(agent));
+  const detected = SUPPORTED_AGENT_IDS.filter((agent) => agentConfigExists(agent, homeDir, opts.project, opts.codexHome) || detectBinaries && agentBinaryExists(agent));
   return [.../* @__PURE__ */ new Set(["claude", "codex", ...detected])];
 }
 function registerSkillsCommand(program2) {
   const skills = program2.command("skills").description("Install the Topolo agent skill + MCP server into supported agent hosts");
-  skills.command("install").description("Copy the skill file and register the topolo MCP server (credential-free)").option("--claude", "Target Claude Code only").option("--codex", "Target Codex only").option("--agent <host...>", "Target one or more hosts by id (for example cursor gemini)").option("--all", "Configure every supported local host").option("--project <dir>", "Write project-scoped host files under <dir> where supported").option("--agent-home <dir>", "Target an alternate agent home (managed installs and clean-room verification)").option("--name <name>", "Register a named pinned MCP, such as topolo-acme").option("--context <context>", "Pin the named MCP to an exact context returned by topolo context ls").option("--installation <id>", "Bind the MCP runtime to a registered external-agent installation").option("--no-mcp", "Copy the skill file but do not register the MCP server").option("--json", "Output JSON", true).option("--no-json", "Output human-readable text").action(
+  skills.command("install").description("Copy the skill file and register the topolo MCP server (credential-free)").option("--claude", "Target Claude Code only").option("--codex", "Target Codex only").option("--agent <host...>", "Target one or more hosts by id (for example cursor gemini)").option("--all", "Configure every supported local host").option("--project <dir>", "Write project-scoped host files under <dir> where supported").option("--codex-home <dir>", "Use an explicit native Codex home instead of <agent-home>/.codex").option("--agent-home <dir>", "Target an alternate agent home (managed installs and clean-room verification)").option("--name <name>", "Register a named pinned MCP, such as topolo-acme").option("--context <context>", "Pin the named MCP to an exact context returned by topolo context ls").option("--installation <id>", "Bind the MCP runtime to a registered external-agent installation").option("--no-mcp", "Copy the skill file but do not register the MCP server").option("--json", "Output JSON", true).option("--no-json", "Output human-readable text").action(
     async (opts) => {
       const mode = resolveOutputMode(opts.json);
       try {
@@ -7286,11 +7486,12 @@ function registerSkillsCommand(program2) {
       }
     }
   );
-  skills.command("status").description("List public Topolo skill and MCP registrations for each agent").option("--agent <host...>", "Inspect one or more hosts by id").option("--all", "Inspect every supported host").option("--project <dir>", "Inspect project-scoped host files under <dir>").option("--agent-home <dir>", "Inspect an alternate agent home").option("--name <name>", "Inspect one registration name").option("--json", "Output JSON", true).option("--no-json", "Output human-readable text").action(async (opts) => {
+  skills.command("status").description("List public Topolo skill and MCP registrations for each agent").option("--agent <host...>", "Inspect one or more hosts by id").option("--all", "Inspect every supported host").option("--project <dir>", "Inspect project-scoped host files under <dir>").option("--codex-home <dir>", "Use an explicit native Codex home instead of <agent-home>/.codex").option("--agent-home <dir>", "Inspect an alternate agent home").option("--name <name>", "Inspect one registration name").option("--json", "Output JSON", true).option("--no-json", "Output human-readable text").action(async (opts) => {
     const mode = resolveOutputMode(opts.json);
     try {
       const rows = await agentSurfaceStatus({
-        homeDir: opts.agentHome ? resolve2(opts.agentHome) : void 0,
+        homeDir: opts.agentHome ? resolve3(opts.agentHome) : void 0,
+        codexHome: opts.codexHome,
         name: opts.name,
         agent: opts.agent,
         all: opts.all,
@@ -7301,12 +7502,12 @@ function registerSkillsCommand(program2) {
       fail2(err, mode);
     }
   });
-  skills.command("uninstall").description("Remove the skill file and MCP registration for each agent").option("--claude", "Target Claude Code only").option("--codex", "Target Codex only").option("--agent <host...>", "Target one or more hosts by id").option("--all", "Remove from every supported host").option("--project <dir>", "Remove project-scoped host files under <dir>").option("--agent-home <dir>", "Target an alternate agent home (managed installs and clean-room verification)").option("--name <name>", "Remove one registration (defaults to topolo)").option("--json", "Output JSON", true).option("--no-json", "Output human-readable text").action(async (opts) => {
+  skills.command("uninstall").description("Remove the skill file and MCP registration for each agent").option("--claude", "Target Claude Code only").option("--codex", "Target Codex only").option("--agent <host...>", "Target one or more hosts by id").option("--all", "Remove from every supported host").option("--project <dir>", "Remove project-scoped host files under <dir>").option("--codex-home <dir>", "Use an explicit native Codex home instead of <agent-home>/.codex").option("--agent-home <dir>", "Target an alternate agent home (managed installs and clean-room verification)").option("--name <name>", "Remove one registration (defaults to topolo)").option("--json", "Output JSON", true).option("--no-json", "Output human-readable text").action(async (opts) => {
     const mode = resolveOutputMode(opts.json);
     try {
       const removed = await uninstallAgentSurfaces({
         ...opts,
-        homeDir: opts.agentHome ? resolve2(opts.agentHome) : void 0
+        homeDir: opts.agentHome ? resolve3(opts.agentHome) : void 0
       });
       emit(
         { removed },
@@ -7325,20 +7526,20 @@ async function installAgentSurfaces(opts) {
   }
   const mcp = resolveMcpCommand();
   const registration = resolveMcpRegistration(opts);
-  const homeDir = opts.homeDir ?? homedir5();
+  const target = resolveAgentHostTarget({ homeDir: opts.homeDir, projectDir: opts.project, codexHome: opts.codexHome });
+  const { homeDir, projectDir, codexHome } = target;
   const results = [];
-  for (const agent of resolveTargets({ ...opts, homeDir, project: opts.project })) {
+  for (const agent of resolveTargets({ ...opts, homeDir, project: projectDir, codexHome })) {
     results.push(await installForAgent(agent, sourceDir, mcp, {
       withMcp: opts.mcp !== false,
-      projectDir: opts.project,
-      homeDir,
+      target,
       registration
     }));
   }
   return { results, mcp };
 }
 function registerSetupCommand(program2) {
-  program2.command("setup").description("Install the Topolo skill and deterministic local MCP server for supported agent hosts").option("--claude", "Target Claude Code only").option("--codex", "Target Codex only").option("--agent <host...>", "Target one or more hosts by id").option("--all", "Configure every supported local host").option("--project <dir>", "Write project-scoped host files under <dir> where supported").option("--agent-home <dir>", "Target an alternate agent home (managed installs and clean-room verification)").option("--name <name>", "Register a named pinned MCP, such as topolo-acme").option("--context <context>", "Pin the named MCP to an exact context returned by topolo context ls").option("--installation <id>", "Bind the MCP runtime to a registered external-agent installation").option("--json", "Output JSON", true).option("--no-json", "Output human-readable text").action(async (opts) => {
+  program2.command("setup").description("Install the Topolo skill and deterministic local MCP server for supported agent hosts").option("--claude", "Target Claude Code only").option("--codex", "Target Codex only").option("--agent <host...>", "Target one or more hosts by id").option("--all", "Configure every supported local host").option("--project <dir>", "Write project-scoped host files under <dir> where supported").option("--codex-home <dir>", "Use an explicit native Codex home instead of <agent-home>/.codex").option("--agent-home <dir>", "Target an alternate agent home (managed installs and clean-room verification)").option("--name <name>", "Register a named pinned MCP, such as topolo-acme").option("--context <context>", "Pin the named MCP to an exact context returned by topolo context ls").option("--installation <id>", "Bind the MCP runtime to a registered external-agent installation").option("--json", "Output JSON", true).option("--no-json", "Output human-readable text").action(async (opts) => {
     const mode = resolveOutputMode(opts.json);
     try {
       const { results, mcp } = await installAgentSurfaces({
@@ -7360,18 +7561,20 @@ function assertAgentSetupSucceeded(results) {
   }
 }
 async function agentSurfaceStatus(options = {}) {
-  const homeDir = options.homeDir ?? homedir5();
+  const target = resolveAgentHostTarget({ homeDir: options.homeDir, projectDir: options.project, codexHome: options.codexHome });
+  const { homeDir, projectDir, codexHome } = target;
   const sourceSkill = await readFile6(join7(skillsSourceDir(), "topolo", "SKILL.md"), "utf8");
   const agents = resolveTargets({
     agent: options.agent,
     all: options.all,
     homeDir,
-    project: options.project
+    project: projectDir,
+    codexHome
   });
   return Promise.all(agents.map(async (agent) => {
-    const skillPath = agentSkillPath(agent, homeDir, options.project);
+    const skillPath = agentSkillPath(agent, homeDir, projectDir, codexHome);
     const installedSkill = skillPath && existsSync6(skillPath) ? await readFile6(skillPath, "utf8") : void 0;
-    const registrations = (await readAgentRegistrations(agent, homeDir, options.project)).filter((registration) => !options.name || registration.name === options.name);
+    const registrations = (await readAgentRegistrations(agent, homeDir, projectDir, codexHome)).filter((registration) => !options.name || registration.name === options.name);
     return {
       agent,
       skillInstalled: installedSkill !== void 0,
@@ -7384,16 +7587,17 @@ async function agentSurfaceStatus(options = {}) {
   }));
 }
 async function uninstallAgentSurfaces(options) {
-  const homeDir = options.homeDir ?? homedir5();
+  const target = resolveAgentHostTarget({ homeDir: options.homeDir, projectDir: options.project, codexHome: options.codexHome });
+  const { homeDir, projectDir, codexHome } = target;
   const name = options.name?.trim() || "topolo";
   resolveMcpRegistration({ name, ...name === "topolo" ? {} : { context: "uninstall-validation" } });
   const removed = [];
-  for (const agent of resolveTargets({ ...options, homeDir, project: options.project })) {
-    const before = await readAgentRegistrations(agent, homeDir, options.project);
+  for (const agent of resolveTargets({ ...options, homeDir, project: projectDir, codexHome })) {
+    const before = await readAgentRegistrations(agent, homeDir, projectDir, codexHome);
     const registrationRemoved = before.some((entry) => entry.name === name);
-    await unregisterAgentConfig(agent, homeDir, name, options.project);
-    const remaining = await readAgentRegistrations(agent, homeDir, options.project);
-    const skillPath = agentSkillPath(agent, homeDir, options.project);
+    await unregisterAgentConfig(agent, homeDir, name, projectDir, codexHome);
+    const remaining = await readAgentRegistrations(agent, homeDir, projectDir, codexHome);
+    const skillPath = agentSkillPath(agent, homeDir, projectDir, codexHome);
     const skillRemoved = remaining.length === 0 && Boolean(skillPath && existsSync6(skillPath));
     if (skillRemoved && skillPath) await rm2(dirname6(skillPath), { recursive: true, force: true });
     removed.push({ agent, name, registrationRemoved, skillRemoved });
@@ -7426,7 +7630,7 @@ function formatStatus(rows) {
 // src/commands/doctor.ts
 import { access } from "fs/promises";
 import { homedir as homedir6 } from "os";
-import { resolve as resolve3 } from "path";
+import { resolve as resolve4 } from "path";
 import { Client } from "@modelcontextprotocol/sdk/client/index.js";
 import { StdioClientTransport } from "@modelcontextprotocol/sdk/client/stdio.js";
 var defaultDependencies = {
@@ -7488,7 +7692,7 @@ async function verifyMcpProtocol(command, args, env = definedEnvironment(process
 }
 async function resolveInstalledDoctorTarget(options) {
   const name = options.name?.trim() || "topolo";
-  const homeDir = options.agentHome ? resolve3(options.agentHome) : homedir6();
+  const homeDir = options.agentHome ? resolve4(options.agentHome) : homedir6();
   const expected = resolveMcpCommand();
   const requestedAgents = resolveTargets({
     ...options,