@brainbase-labs/cli 0.32.0 → 0.33.0

package/dist/index.js

@@ -36018,7 +36018,7 @@ function padStart(s, n) {
 // package.json
 var package_default = {
   name: "@brainbase-labs/cli",
-  version: "0.32.0",
+  version: "0.33.0",
   description: "Pack, share, and install agent templates across harnesses (Claude Code, Codex, ...).",
   type: "module",
   bin: {
@@ -41663,6 +41663,12 @@ ${block}
 var DEFAULT_MCP_PROXY_BASE = "https://brainbase-mcp-proxy.onrender.com";
 var THREAD_ID_TEMPLATE = "${BRAINBASE_THREAD_ID}";
 var PROXY_AUTH_HEADER = "Bearer ${BRAINBASE_TOKEN}";
+function isRuntimeMcpAuth(value) {
+  if (!value || typeof value !== "object")
+    return false;
+  const auth = value;
+  return auth.version === 1 && auth.requires_oauth === true && (auth.kind === "agent" || auth.kind === "orchestration") && typeof auth.server_id === "string" && /^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/i.test(auth.server_id);
+}
 function mcpProxyBaseUrl(env = process.env) {
   const envOverride = env.BRAINBASE_MCP_PROXY_URL;
   if (envOverride) {
@@ -41675,19 +41681,31 @@ function mcpProxyBaseUrl(env = process.env) {
 function isBrainbaseTaskRuntime(env = process.env) {
   return typeof env.BRAINBASE_THREAD_ID === "string" && env.BRAINBASE_THREAD_ID.trim().length > 0 && typeof env.BRAINBASE_TOKEN === "string" && env.BRAINBASE_TOKEN.trim().length > 0;
 }
-function proxifyMcpPayload(payload, env = process.env) {
+function proxifyMcpPayload(payload, env = process.env, identity) {
   if (!payload)
     return payload;
   if (!isBrainbaseTaskRuntime(env))
     return payload;
-  if (!shouldProxy(payload, env))
+  if (typeof payload.url !== "string" || !payload.url || payload.command)
+    return payload;
+  let route = "";
+  let keepInstalledUrl = false;
+  let upstreamUrl = payload.url;
+  if (identity !== undefined) {
+    if (!isRuntimeMcpAuth(identity))
+      throw new Error("mcp_server_identity_required: incompatible runtime_mcp_auth");
+    route = `s/${identity.kind}/${identity.server_id}/`;
+    const installed = parseMcpProxyUrl(payload.url, env.BRAINBASE_THREAD_ID?.trim() ?? "", mcpProxyBaseUrl(env));
+    keepInstalledUrl = installed?.kind === identity.kind && installed.serverId === identity.server_id;
+    if (installed)
+      upstreamUrl = installed.upstreamUrl;
+  } else if (!shouldProxy(payload, env))
     return payload;
   const base = mcpProxyBaseUrl(env);
-  const upstreamUrl = payload.url;
-  const existingHeaders = payload.headers ?? {};
+  const existingHeaders = Object.fromEntries(Object.entries(payload.headers ?? {}).filter(([key]) => key.toLowerCase() !== "authorization"));
   return {
     ...payload,
-    url: `${base}/t/${THREAD_ID_TEMPLATE}/${upstreamUrl}`,
+    url: keepInstalledUrl ? payload.url : `${base}/t/${THREAD_ID_TEMPLATE}/${route}${upstreamUrl}`,
     headers: { ...existingHeaders, Authorization: PROXY_AUTH_HEADER }
   };
 }
@@ -41701,46 +41719,57 @@ function shouldProxy(payload, env) {
   if (headers && typeof headers === "object" && Object.keys(headers).length > 0) {
     return false;
   }
-  if (isMcpProxyUrl(url, env.BRAINBASE_THREAD_ID?.trim() ?? "", mcpProxyBaseUrl(env))) {
+  if (parseMcpProxyUrl(url, env.BRAINBASE_THREAD_ID?.trim() ?? "", mcpProxyBaseUrl(env))) {
     return false;
   }
   return true;
 }
-function isMcpProxyUrl(value, threadId, proxyBase) {
+function parseMcpProxyUrl(value, threadId, proxyBase) {
   let outer;
   try {
     outer = new URL(value);
   } catch {
-    return false;
+    return;
   }
   if (outer.protocol !== "http:" && outer.protocol !== "https:")
-    return false;
-  const candidatePaths = [outer.pathname];
-  try {
-    const base = new URL(proxyBase);
-    const basePath = base.pathname.replace(/\/+$/, "");
-    if (basePath && outer.origin === base.origin && outer.pathname.startsWith(`${basePath}/`)) {
-      candidatePaths.push(outer.pathname.slice(basePath.length));
-    }
-  } catch {}
-  const match = candidatePaths.map((path13) => /^\/t\/([^/]+)\/(https?:\/\/.+)$/.exec(path13)).find((candidate) => candidate !== null);
+    return;
+  const candidatePaths = [];
+  for (const trusted of [proxyBase, DEFAULT_MCP_PROXY_BASE]) {
+    try {
+      const base = new URL(trusted);
+      if (outer.origin !== base.origin || outer.username || outer.password)
+        continue;
+      const basePath = base.pathname.replace(/\/+$/, "");
+      if (outer.pathname.startsWith(`${basePath}/`)) {
+        candidatePaths.push(outer.pathname.slice(basePath.length));
+      }
+    } catch {}
+  }
+  const match = candidatePaths.map((path13) => /^\/t\/([^/]+)\/(?:s\/(agent|orchestration)\/([0-9a-f-]+)\/)?(https?:\/\/.+)$/i.exec(path13)).find((candidate) => candidate !== null);
   if (!match)
-    return false;
+    return;
   let pathThreadId = match[1];
   try {
     pathThreadId = decodeURIComponent(pathThreadId);
   } catch {
-    return false;
+    return;
   }
   if (pathThreadId !== threadId && pathThreadId !== THREAD_ID_TEMPLATE)
-    return false;
+    return;
   try {
-    const upstream = new URL(match[2]);
-    return (upstream.protocol === "http:" || upstream.protocol === "https:") && upstream.hostname.length > 0;
+    const upstreamUrl = match[4] + outer.search + outer.hash;
+    const upstream = new URL(upstreamUrl);
+    if (upstream.protocol !== "http:" && upstream.protocol !== "https:" || !upstream.hostname)
+      return;
+    return { upstreamUrl, kind: match[2], serverId: match[3] };
   } catch {
-    return false;
+    return;
   }
 }
+function mcpUpstreamUrl(value, env = process.env) {
+  const resolved = resolveMcpEnvTemplates({ url: value }, env)?.url;
+  return parseMcpProxyUrl(resolved, env.BRAINBASE_THREAD_ID?.trim() ?? "", mcpProxyBaseUrl(env))?.upstreamUrl ?? resolved;
+}
 function resolveMcpEnvTemplates(payload, env = process.env) {
   if (!payload)
     return payload;
@@ -53941,6 +53970,7 @@ var InstalledComponentSchema = exports_external.object({
   slug: exports_external.string(),
   installedPaths: exports_external.array(exports_external.string()),
   sourceChecksum: exports_external.string(),
+  runtime_mcp_auth: exports_external.unknown().optional(),
   scope: ScopeSchema.optional(),
   embeddedKey: exports_external.string().optional(),
   settingsFile: exports_external.string().optional()
@@ -59276,7 +59306,7 @@ function buildTemplateComponents(manifest, rootDir) {
     rootDir: path63.join(rootDir, c2.path),
     description: c2.description,
     target: c2.target,
-    payload: proxifyMcpPayload(c2.meta?.mcp),
+    payload: proxifyMcpPayload(c2.meta?.mcp, undefined, c2.meta?.runtime_mcp_auth),
     meta: c2.meta,
     checksum: c2.checksum,
     source: c2.source
@@ -59446,6 +59476,7 @@ async function runOnboard(cwd2, args) {
       slug: o2.slug,
       installedPaths: o2.installedPaths,
       sourceChecksum: o2.sourceChecksum,
+      ...o2.type === "mcp" ? { runtime_mcp_auth: components.find((c2) => c2.type === o2.type && c2.slug === o2.slug)?.meta?.runtime_mcp_auth } : {},
       scope: o2.scope,
       embeddedKey: o2.embeddedKey,
       settingsFile: o2.settingsFile
@@ -63542,10 +63573,462 @@ async function runUnlink(cwd2, args) {
 }
 
 // src/cli/sync.ts
+import { isDeepStrictEqual } from "node:util";
+
+// src/core/agent-diff.ts
 import path77 from "node:path";
 import fs69 from "node:fs";
-import os12 from "node:os";
 import crypto3 from "node:crypto";
+function compKey(type, slug) {
+  return `${type}/${slug}`;
+}
+function hashString(s3) {
+  return crypto3.createHash("sha256").update(s3).digest("hex");
+}
+function jsonStringAsciiSafe(s3) {
+  return JSON.stringify(s3).replace(/[\u007f-\uffff]/g, (c2) => "\\u" + c2.charCodeAt(0).toString(16).padStart(4, "0"));
+}
+function canonicalJson2(value) {
+  if (value === null)
+    return "null";
+  if (typeof value === "boolean")
+    return value ? "true" : "false";
+  if (typeof value === "number") {
+    if (!Number.isFinite(value))
+      throw new Error("Non-finite numbers are not JSON");
+    return String(value);
+  }
+  if (typeof value === "string")
+    return jsonStringAsciiSafe(value);
+  if (Array.isArray(value)) {
+    return "[" + value.map(canonicalJson2).join(",") + "]";
+  }
+  if (typeof value === "object") {
+    const obj = value;
+    const keys2 = Object.keys(obj).sort();
+    return "{" + keys2.map((k3) => `${jsonStringAsciiSafe(k3)}:${canonicalJson2(obj[k3])}`).join(",") + "}";
+  }
+  throw new Error(`Unsupported value in canonicalJson: ${typeof value}`);
+}
+function hashMcpEntry(entry) {
+  const payload = {
+    args: entry.args ?? [],
+    env: entry.env ?? {},
+    headers: entry.headers ?? {}
+  };
+  if (entry.url !== undefined)
+    payload.url = entry.url;
+  if (entry.command !== undefined)
+    payload.command = entry.command;
+  payload.is_enabled = entry.is_enabled ?? true;
+  return crypto3.createHash("sha256").update(canonicalJson2(payload)).digest("hex");
+}
+function evalWirePayload(entry) {
+  return {
+    criteria: entry.criteria,
+    enabled: entry.enabled,
+    icon: entry.icon || null,
+    judge_agent: entry.judge_agent ?? null,
+    judge_model: entry.judge_model,
+    judge_type: entry.judge_type,
+    output_shape: entry.output_shape,
+    classification_values: entry.classification_values && entry.classification_values.length > 0 ? entry.classification_values : null
+  };
+}
+function hashEvalEntry(entry) {
+  return crypto3.createHash("sha256").update(canonicalJson2(evalWirePayload(entry))).digest("hex");
+}
+function fileHash(p2) {
+  if (!exists(p2))
+    return null;
+  try {
+    const buf = fs69.readFileSync(p2);
+    return crypto3.createHash("sha256").update(buf).digest("hex");
+  } catch {
+    return null;
+  }
+}
+function componentHashFromFileHashes(fileHashes) {
+  const h2 = crypto3.createHash("sha256");
+  for (const fh of [...fileHashes].sort()) {
+    h2.update(fh);
+    h2.update(`
+`);
+  }
+  return h2.digest("hex");
+}
+function hashDirectoryAsComponent(dir) {
+  if (!exists(dir))
+    return null;
+  const fileHashes = [];
+  const walk = (sub) => {
+    let entries;
+    try {
+      entries = fs69.readdirSync(sub, { withFileTypes: true });
+    } catch {
+      return;
+    }
+    for (const e2 of entries) {
+      const full = path77.join(sub, e2.name);
+      if (e2.isFile()) {
+        const fh = fileHash(full);
+        if (fh)
+          fileHashes.push(fh);
+      } else if (e2.isDirectory()) {
+        walk(full);
+      }
+    }
+  };
+  walk(dir);
+  return componentHashFromFileHashes(fileHashes);
+}
+function readLocalComponents(cwd2, manifest) {
+  const out = [];
+  const instr = readInstructions(cwd2, manifest);
+  if (instr !== null && instr.trim().length > 0) {
+    out.push({
+      type: "instruction",
+      slug: "agent-instructions",
+      hash: componentHashFromFileHashes([hashString(normalizeInstructionBody(instr))])
+    });
+  }
+  for (const entry of manifest.skills) {
+    let parsed;
+    try {
+      parsed = parseSkillSource2(entry.source);
+    } catch {
+      try {
+        const core = parseSkillSource(entry.source);
+        if (core.type !== "inline" && core.type !== "local") {
+          out.push({
+            type: "skill",
+            slug: defaultSkillSlug(core),
+            hash: null,
+            declaredSource: entry.source
+          });
+        }
+      } catch {}
+      continue;
+    }
+    if (parsed.kind === "registry") {
+      out.push({
+        type: "skill",
+        slug: registrySkillComponentSlug(parsed),
+        hash: null,
+        declaredSource: entry.source
+      });
+    } else {
+      const abs = path77.resolve(cwd2, parsed.path);
+      const slug = path77.basename(abs);
+      out.push({
+        type: "skill",
+        slug,
+        hash: hashDirectoryAsComponent(abs),
+        declaredSource: entry.source,
+        localPath: abs
+      });
+    }
+  }
+  for (const entry of manifest.mcp ?? []) {
+    out.push({
+      type: "mcp",
+      slug: entry.name,
+      hash: hashMcpEntry(entry)
+    });
+  }
+  const pbEntries = manifest.playbooks ?? [];
+  const pbSlugs = assignPlaybookSlugs(pbEntries.map((e2) => e2.title));
+  for (let i = 0;i < pbEntries.length; i++) {
+    const entry = pbEntries[i];
+    const slug = pbSlugs[i];
+    const body = resolvePlaybookContent(cwd2, entry);
+    if (body === null) {
+      out.push({ type: "playbook", slug, hash: null });
+      continue;
+    }
+    const wireBody = assemblePlaybookWireBody(entry, body);
+    out.push({
+      type: "playbook",
+      slug,
+      hash: componentHashFromFileHashes([hashString(wireBody)])
+    });
+  }
+  for (const entry of manifest.evals ?? []) {
+    out.push({
+      type: "eval",
+      slug: entry.slug,
+      hash: hashEvalEntry(entry)
+    });
+  }
+  return out;
+}
+function threeWayDiff(input) {
+  const lockMap = new Map;
+  for (const c2 of input.lock)
+    lockMap.set(compKey(c2.type, c2.slug), c2);
+  const cloudMap = new Map;
+  for (const c2 of input.cloud)
+    cloudMap.set(compKey(c2.type, c2.slug), c2);
+  const localMap = new Map;
+  for (const c2 of input.local)
+    localMap.set(compKey(c2.type, c2.slug), c2);
+  const keys2 = new Set;
+  for (const k3 of lockMap.keys())
+    keys2.add(k3);
+  for (const k3 of cloudMap.keys())
+    keys2.add(k3);
+  for (const k3 of localMap.keys())
+    keys2.add(k3);
+  const rows = [];
+  for (const key2 of [...keys2].sort()) {
+    const lock = lockMap.get(key2);
+    const cloud = cloudMap.get(key2);
+    const local = localMap.get(key2);
+    const [type, slug] = key2.split("/", 2);
+    let localHash = local?.hash ?? null;
+    if (local && local.hash === null && local.declaredSource && lock?.source === local.declaredSource && cloud) {
+      localHash = cloud.hash;
+    }
+    const cloudHash = cloud?.hash;
+    const lockHash = lock?.hash;
+    const declaredSource = local?.declaredSource;
+    const present = {
+      local: !!local,
+      lock: !!lock,
+      cloud: !!cloud
+    };
+    let status;
+    if (present.local && present.cloud && !present.lock) {
+      status = "added-local";
+    } else if (!present.local && present.cloud && !present.lock) {
+      status = "added-cloud";
+    } else if (present.local && !present.cloud && !present.lock) {
+      status = "added-only-local";
+    } else if (!present.local && present.lock) {
+      status = "removed-local";
+    } else if (present.local && !present.cloud && present.lock) {
+      status = "removed-cloud";
+    } else {
+      const sourceChanged = !!local && local.hash === null && !!local.declaredSource && lock?.source !== undefined && lock.source !== local.declaredSource;
+      const localChanged = sourceChanged || localHash !== null && lockHash !== undefined && localHash !== lockHash;
+      const cloudChanged = cloudHash !== undefined && lockHash !== undefined && cloudHash !== lockHash;
+      const converged = !sourceChanged && localHash !== null && cloudHash !== undefined && localHash === cloudHash;
+      if (converged)
+        status = "in-sync";
+      else if (localChanged && cloudChanged)
+        status = "modified-both";
+      else if (localChanged)
+        status = "modified-local";
+      else if (cloudChanged)
+        status = "modified-cloud";
+      else
+        status = "in-sync";
+    }
+    rows.push({
+      key: key2,
+      type,
+      slug,
+      status,
+      localHash: localHash ?? undefined,
+      lockHash,
+      cloudHash,
+      declaredSource
+    });
+  }
+  return rows;
+}
+function partitionPushRows(rows, force) {
+  const toSend = [];
+  const conflicts = [];
+  const upstreamOnly = [];
+  for (const r2 of rows) {
+    switch (r2.status) {
+      case "modified-local":
+      case "added-only-local":
+      case "added-local":
+      case "removed-local":
+        toSend.push(r2);
+        break;
+      case "modified-both":
+        if (force)
+          toSend.push(r2);
+        else
+          conflicts.push(r2);
+        break;
+      case "modified-cloud":
+      case "added-cloud":
+      case "removed-cloud":
+        upstreamOnly.push(r2);
+        break;
+      case "in-sync":
+        break;
+      default: {
+        const _exhaustive = r2.status;
+      }
+    }
+  }
+  return { toSend, conflicts, upstreamOnly };
+}
+function diffAgentMeta(manifestMeta, lockMeta, cloudMeta) {
+  const eq = (a3, b4) => {
+    if (!a3 && !b4)
+      return true;
+    if (!a3 || !b4)
+      return false;
+    return a3.name === b4.name && (a3.tagline ?? "") === (b4.tagline ?? "");
+  };
+  return {
+    localChanged: !!manifestMeta && !!lockMeta && !eq(manifestMeta, lockMeta),
+    cloudChanged: !!cloudMeta && !!lockMeta && !eq(cloudMeta, lockMeta)
+  };
+}
+var WRITABLE_CAPABILITIES = ["memory", "browser"];
+var MIRRORED_CAPABILITIES = ["slack", "meeting", "github", "linear"];
+function manifestConfigState(manifest) {
+  return {
+    ...manifest.machine_kind !== undefined ? { machine_kind: manifest.machine_kind } : {},
+    ...hasOwn(manifest, "default_model") ? { default_model: manifest.default_model ?? null } : {},
+    ...manifest.capabilities?.memory !== undefined ? { memory: manifest.capabilities.memory } : {},
+    ...manifest.capabilities?.browser !== undefined ? { browser: manifest.capabilities.browser } : {}
+  };
+}
+function cloudConfigState(agent) {
+  return {
+    ...agent.machine_kind !== undefined ? { machine_kind: agent.machine_kind } : {},
+    ...hasOwn(agent, "default_model") ? { default_model: agent.default_model ?? null } : {},
+    ...agent.memory_enabled !== undefined ? { memory: agent.memory_enabled } : {},
+    ...agent.browser_enabled !== undefined ? { browser: agent.browser_enabled } : {}
+  };
+}
+function hasOwn(value, key2) {
+  return !!value && Object.prototype.hasOwnProperty.call(value, key2);
+}
+function staleConnectionMirrors(manifest, cloud) {
+  const actualByName = {
+    slack: cloud.slack_connected,
+    meeting: cloud.meeting_connected,
+    github: cloud.github_connected,
+    linear: cloud.linear_connected
+  };
+  const stale = [];
+  for (const name of MIRRORED_CAPABILITIES) {
+    const authored = manifest.capabilities?.[name];
+    const actual = actualByName[name];
+    if (authored === undefined || actual === undefined)
+      continue;
+    if (authored !== actual)
+      stale.push({ name, authored, actual });
+  }
+  return stale;
+}
+function diffAgentConfig(manifest, lock, cloud) {
+  const unsupported = [];
+  const machineSupported = cloud.machine_kind !== undefined;
+  const defaultModelSupported = hasOwn(cloud, "default_model");
+  if (manifest.machine_kind !== undefined && !machineSupported) {
+    unsupported.push("machine_kind");
+  }
+  if (manifest.default_model !== undefined && !defaultModelSupported) {
+    unsupported.push("default_model");
+  }
+  const machineMismatch = manifest.machine_kind !== undefined && machineSupported && manifest.machine_kind !== cloud.machine_kind;
+  const machineLocalChanged = manifest.machine_kind !== undefined && machineSupported && (lock?.machine_kind !== undefined ? manifest.machine_kind !== lock.machine_kind && manifest.machine_kind !== cloud.machine_kind : manifest.machine_kind !== cloud.machine_kind);
+  const machineCloudChanged = lock?.machine_kind !== undefined && machineSupported && lock.machine_kind !== cloud.machine_kind && manifest.machine_kind !== cloud.machine_kind;
+  const machineConverged = manifest.machine_kind !== undefined && machineSupported && manifest.machine_kind === cloud.machine_kind && (lock?.machine_kind === undefined || lock.machine_kind !== cloud.machine_kind);
+  const defaultModel = threeWayField(defaultModelSupported, manifest.default_model, cloud.default_model, lock, "default_model");
+  const memory = threeWayField(hasOwn(cloud, "memory"), manifest.memory, cloud.memory, lock, "memory");
+  const browser = threeWayField(hasOwn(cloud, "browser"), manifest.browser, cloud.browser, lock, "browser");
+  if (manifest.memory !== undefined && !hasOwn(cloud, "memory")) {
+    unsupported.push("memory");
+  }
+  if (manifest.browser !== undefined && !hasOwn(cloud, "browser")) {
+    unsupported.push("browser");
+  }
+  return {
+    unsupported,
+    machineMismatch,
+    machineLocalChanged,
+    machineCloudChanged,
+    defaultModelLocalChanged: defaultModel.localChanged,
+    defaultModelCloudChanged: defaultModel.cloudChanged,
+    defaultModelConflict: defaultModel.conflict,
+    memory,
+    browser,
+    baselineConverged: machineConverged || defaultModel.converged || memory.converged || browser.converged
+  };
+}
+function threeWayField(supported, authored, cloudRaw, lock, key2) {
+  const result2 = {
+    localChanged: false,
+    cloudChanged: false,
+    conflict: false,
+    converged: false
+  };
+  if (!supported)
+    return result2;
+  const cloudValue = cloudRaw ?? null;
+  const lockSupported = hasOwn(lock, key2);
+  const lockValue = lock?.[key2] ?? null;
+  if (authored === undefined) {
+    if (lockSupported)
+      result2.cloudChanged = cloudValue !== lockValue;
+    return result2;
+  }
+  const localValue = authored ?? null;
+  if (!lockSupported) {
+    result2.localChanged = localValue !== cloudValue;
+    result2.converged = localValue === cloudValue;
+    return result2;
+  }
+  const localMoved = localValue !== lockValue;
+  const cloudMoved = cloudValue !== lockValue;
+  result2.conflict = localMoved && cloudMoved && localValue !== cloudValue;
+  result2.localChanged = localMoved && localValue !== cloudValue;
+  result2.cloudChanged = cloudMoved && localValue !== cloudValue;
+  result2.converged = localMoved && cloudMoved && localValue === cloudValue;
+  return result2;
+}
+
+// src/core/mcp-merge.ts
+var RUNTIME_META_PREFIX = "runtime_";
+function runtimeMetaFromComponent(component) {
+  const meta = component.meta ?? {};
+  const carried = {};
+  for (const [key2, value] of Object.entries(meta)) {
+    if (key2.startsWith(RUNTIME_META_PREFIX) && value !== undefined) {
+      carried[key2] = value;
+    }
+  }
+  return Object.keys(carried).length > 0 ? carried : undefined;
+}
+function mcpEntriesFromCloudComponents(components) {
+  return components.filter((c2) => c2.type === "mcp").map((c2) => {
+    const payload = (c2.meta ?? {}).mcp ?? {};
+    const entry = { name: c2.slug };
+    if (typeof payload.url === "string")
+      entry.url = payload.url;
+    if (typeof payload.command === "string")
+      entry.command = payload.command;
+    if (Array.isArray(payload.args))
+      entry.args = payload.args.map(String);
+    if (payload.env && typeof payload.env === "object")
+      entry.env = payload.env;
+    if (payload.headers && typeof payload.headers === "object")
+      entry.headers = payload.headers;
+    if (typeof payload.is_enabled === "boolean")
+      entry.is_enabled = payload.is_enabled;
+    const runtimeMeta = runtimeMetaFromComponent(c2);
+    if (runtimeMeta)
+      entry.runtime_meta = runtimeMeta;
+    return entry;
+  });
+}
+
+// src/cli/sync.ts
+import path78 from "node:path";
+import fs70 from "node:fs";
+import os12 from "node:os";
+import crypto4 from "node:crypto";
 var import_picocolors24 = __toESM(require_picocolors(), 1);
 
 // src/core/memory-mcp.ts
@@ -63866,6 +64349,21 @@ async function runSync(cwd2, args) {
     declaredSlugs: declaredMcpSlugs,
     scope
   });
+  const localManifest = readManifest(cwd2);
+  for (const component of manifest.components) {
+    if (component.type !== "mcp")
+      continue;
+    const prior = prevState?.components.find((c2) => c2.type === "mcp" && c2.slug === component.slug);
+    const entry = localManifest?.mcp.find((c2) => c2.name === component.slug);
+    if (!prior || prior.hash !== component.hash || isDeepStrictEqual(component.meta?.runtime_mcp_auth, entry?.runtime_meta?.runtime_mcp_auth))
+      continue;
+    const harness = args.harness ?? link2.harness ?? link2.tracking?.harness;
+    const locallyReplaced = harness && readHarnessMcpEntry(harness, cwd2, scope, component.slug) !== undefined && !lockEntryOwnsMcpInStore(prior, { harness, cwd: cwd2, scope });
+    if (entry && hashMcpEntry(entry) !== prior.hash || locallyReplaced)
+      diff2.localModified.push(component);
+    else
+      diff2.upstreamUpdated.push(component);
+  }
   if (diff2.added.length === 0 && diff2.upstreamUpdated.length === 0 && diff2.localModified.length === 0 && diff2.deletedUpstream.length === 0 && builtinInstall.length === 0 && builtinRemoveSlugs.length === 0) {
     f2.info(`${sym.same} You're up to date.`);
     writeSyncState(cwd2, {
@@ -63962,10 +64460,10 @@ async function runSync(cwd2, args) {
       type: c2.type,
       slug: c2.slug,
       scope,
-      rootDir: path77.join(stageRoot, c2.type, c2.slug),
+      rootDir: path78.join(stageRoot, c2.type, c2.slug),
       description: c2.description,
       meta: c2.meta,
-      payload: proxifyMcpPayload(c2.meta?.mcp),
+      payload: proxifyMcpPayload(c2.meta?.mcp, undefined, c2.meta?.runtime_mcp_auth),
       checksum: c2.hash
     }));
     toInstall.push(...builtinInstall);
@@ -64032,11 +64530,11 @@ async function runSync(cwd2, args) {
           if (!exists(filePath))
             continue;
           try {
-            const stat = fs69.statSync(filePath);
+            const stat = fs70.statSync(filePath);
             if (stat.isDirectory())
-              fs69.rmSync(filePath, { recursive: true, force: true });
+              fs70.rmSync(filePath, { recursive: true, force: true });
             else
-              fs69.rmSync(filePath);
+              fs70.rmSync(filePath);
           } catch (err) {
             f2.warn(`Failed to remove ${filePath}: ${err.message}`);
           }
@@ -64077,10 +64575,23 @@ async function runSync(cwd2, args) {
       agentMeta: prevState?.agentMeta
     };
     writeSyncState(cwd2, newState);
+    if (localManifest) {
+      for (const component of manifest.components) {
+        if (component.type !== "mcp" || !justInstalledPaths.has(`mcp/${component.slug}`))
+          continue;
+        const index = localManifest.mcp.findIndex((entry2) => entry2.name === component.slug);
+        const entry = mcpEntriesFromCloudComponents([component])[0];
+        if (index >= 0)
+          localManifest.mcp[index] = entry;
+        else
+          localManifest.mcp.push(entry);
+      }
+      writeManifest(cwd2, localManifest);
+    }
     $e(`Synced ${link2.name} to revision ${manifest.revision}.`);
   } finally {
     try {
-      fs69.rmSync(stageRoot, { recursive: true, force: true });
+      fs70.rmSync(stageRoot, { recursive: true, force: true });
     } catch {}
   }
 }
@@ -64123,19 +64634,19 @@ function computeDiff(upstream, prev) {
 function computeLocalHash(paths) {
   if (paths.length === 0)
     return null;
-  const h2 = crypto3.createHash("sha256");
+  const h2 = crypto4.createHash("sha256");
   for (const filePath of paths) {
     if (!exists(filePath))
       return null;
     try {
-      const stat = fs69.statSync(filePath);
+      const stat = fs70.statSync(filePath);
       if (stat.isFile()) {
         h2.update("F " + filePath + " ");
-        h2.update(fs69.readFileSync(filePath));
+        h2.update(fs70.readFileSync(filePath));
         h2.update(`
 `);
       } else if (stat.isDirectory()) {
-        for (const name of fs69.readdirSync(filePath).sort()) {
+        for (const name of fs70.readdirSync(filePath).sort()) {
           h2.update("E " + name + `
 `);
         }
@@ -64147,14 +64658,14 @@ function computeLocalHash(paths) {
   return h2.digest("hex");
 }
 function stageManifest(components) {
-  const root = fs69.mkdtempSync(path77.join(os12.tmpdir(), "brainbase-sync-"));
+  const root = fs70.mkdtempSync(path78.join(os12.tmpdir(), "brainbase-sync-"));
   for (const c2 of components) {
-    const compDir = path77.join(root, c2.type, c2.slug);
+    const compDir = path78.join(root, c2.type, c2.slug);
     ensureDir(compDir);
     for (const f4 of c2.files) {
-      const target = path77.join(compDir, f4.path);
-      ensureDir(path77.dirname(target));
-      fs69.writeFileSync(target, f4.content);
+      const target = path78.join(compDir, f4.path);
+      ensureDir(path78.dirname(target));
+      fs70.writeFileSync(target, f4.content);
     }
   }
   return root;
@@ -64171,6 +64682,7 @@ function runHarnessInstall(harnessId, components, opts, agentName) {
 var import_picocolors39 = __toESM(require_picocolors(), 1);
 
 // src/cli/agent-pull.ts
+import { isDeepStrictEqual as isDeepStrictEqual2 } from "node:util";
 import { spawn as spawn2 } from "node:child_process";
 import path81 from "node:path";
 import fs74 from "node:fs";
@@ -64178,7 +64690,7 @@ import os14 from "node:os";
 var import_picocolors26 = __toESM(require_picocolors(), 1);
 
 // src/core/manifest-unsynced.ts
-import fs70 from "node:fs";
+import fs71 from "node:fs";
 var import_yaml3 = __toESM(require_dist(), 1);
 function findUnsyncedBlocks(manifest) {
   const found = [];
@@ -64256,7 +64768,7 @@ function readLocalOnlyContent(cwd2) {
   let raw = null;
   if (file) {
     try {
-      raw = import_yaml3.default.parse(fs70.readFileSync(file, "utf8"));
+      raw = import_yaml3.default.parse(fs71.readFileSync(file, "utf8"));
     } catch {
       raw = null;
     }
@@ -64278,7 +64790,7 @@ function readManifestAgentId(cwd2) {
   if (!file)
     return;
   try {
-    const raw = import_yaml3.default.parse(fs70.readFileSync(file, "utf8"));
+    const raw = import_yaml3.default.parse(fs71.readFileSync(file, "utf8"));
     if (!raw || typeof raw !== "object")
       return;
     return clean(raw.id);
@@ -64296,420 +64808,6 @@ function readLocalOnlyContentReporting(cwd2) {
   return content;
 }
 
-// src/core/agent-diff.ts
-import path78 from "node:path";
-import fs71 from "node:fs";
-import crypto4 from "node:crypto";
-function compKey(type, slug) {
-  return `${type}/${slug}`;
-}
-function hashString(s3) {
-  return crypto4.createHash("sha256").update(s3).digest("hex");
-}
-function jsonStringAsciiSafe(s3) {
-  return JSON.stringify(s3).replace(/[\u007f-\uffff]/g, (c2) => "\\u" + c2.charCodeAt(0).toString(16).padStart(4, "0"));
-}
-function canonicalJson2(value) {
-  if (value === null)
-    return "null";
-  if (typeof value === "boolean")
-    return value ? "true" : "false";
-  if (typeof value === "number") {
-    if (!Number.isFinite(value))
-      throw new Error("Non-finite numbers are not JSON");
-    return String(value);
-  }
-  if (typeof value === "string")
-    return jsonStringAsciiSafe(value);
-  if (Array.isArray(value)) {
-    return "[" + value.map(canonicalJson2).join(",") + "]";
-  }
-  if (typeof value === "object") {
-    const obj = value;
-    const keys2 = Object.keys(obj).sort();
-    return "{" + keys2.map((k3) => `${jsonStringAsciiSafe(k3)}:${canonicalJson2(obj[k3])}`).join(",") + "}";
-  }
-  throw new Error(`Unsupported value in canonicalJson: ${typeof value}`);
-}
-function hashMcpEntry(entry) {
-  const payload = {
-    args: entry.args ?? [],
-    env: entry.env ?? {},
-    headers: entry.headers ?? {}
-  };
-  if (entry.url !== undefined)
-    payload.url = entry.url;
-  if (entry.command !== undefined)
-    payload.command = entry.command;
-  payload.is_enabled = entry.is_enabled ?? true;
-  return crypto4.createHash("sha256").update(canonicalJson2(payload)).digest("hex");
-}
-function evalWirePayload(entry) {
-  return {
-    criteria: entry.criteria,
-    enabled: entry.enabled,
-    icon: entry.icon || null,
-    judge_agent: entry.judge_agent ?? null,
-    judge_model: entry.judge_model,
-    judge_type: entry.judge_type,
-    output_shape: entry.output_shape,
-    classification_values: entry.classification_values && entry.classification_values.length > 0 ? entry.classification_values : null
-  };
-}
-function hashEvalEntry(entry) {
-  return crypto4.createHash("sha256").update(canonicalJson2(evalWirePayload(entry))).digest("hex");
-}
-function fileHash(p2) {
-  if (!exists(p2))
-    return null;
-  try {
-    const buf = fs71.readFileSync(p2);
-    return crypto4.createHash("sha256").update(buf).digest("hex");
-  } catch {
-    return null;
-  }
-}
-function componentHashFromFileHashes(fileHashes) {
-  const h2 = crypto4.createHash("sha256");
-  for (const fh of [...fileHashes].sort()) {
-    h2.update(fh);
-    h2.update(`
-`);
-  }
-  return h2.digest("hex");
-}
-function hashDirectoryAsComponent(dir) {
-  if (!exists(dir))
-    return null;
-  const fileHashes = [];
-  const walk = (sub) => {
-    let entries;
-    try {
-      entries = fs71.readdirSync(sub, { withFileTypes: true });
-    } catch {
-      return;
-    }
-    for (const e2 of entries) {
-      const full = path78.join(sub, e2.name);
-      if (e2.isFile()) {
-        const fh = fileHash(full);
-        if (fh)
-          fileHashes.push(fh);
-      } else if (e2.isDirectory()) {
-        walk(full);
-      }
-    }
-  };
-  walk(dir);
-  return componentHashFromFileHashes(fileHashes);
-}
-function readLocalComponents(cwd2, manifest) {
-  const out = [];
-  const instr = readInstructions(cwd2, manifest);
-  if (instr !== null && instr.trim().length > 0) {
-    out.push({
-      type: "instruction",
-      slug: "agent-instructions",
-      hash: componentHashFromFileHashes([hashString(normalizeInstructionBody(instr))])
-    });
-  }
-  for (const entry of manifest.skills) {
-    let parsed;
-    try {
-      parsed = parseSkillSource2(entry.source);
-    } catch {
-      try {
-        const core = parseSkillSource(entry.source);
-        if (core.type !== "inline" && core.type !== "local") {
-          out.push({
-            type: "skill",
-            slug: defaultSkillSlug(core),
-            hash: null,
-            declaredSource: entry.source
-          });
-        }
-      } catch {}
-      continue;
-    }
-    if (parsed.kind === "registry") {
-      out.push({
-        type: "skill",
-        slug: registrySkillComponentSlug(parsed),
-        hash: null,
-        declaredSource: entry.source
-      });
-    } else {
-      const abs = path78.resolve(cwd2, parsed.path);
-      const slug = path78.basename(abs);
-      out.push({
-        type: "skill",
-        slug,
-        hash: hashDirectoryAsComponent(abs),
-        declaredSource: entry.source,
-        localPath: abs
-      });
-    }
-  }
-  for (const entry of manifest.mcp ?? []) {
-    out.push({
-      type: "mcp",
-      slug: entry.name,
-      hash: hashMcpEntry(entry)
-    });
-  }
-  const pbEntries = manifest.playbooks ?? [];
-  const pbSlugs = assignPlaybookSlugs(pbEntries.map((e2) => e2.title));
-  for (let i = 0;i < pbEntries.length; i++) {
-    const entry = pbEntries[i];
-    const slug = pbSlugs[i];
-    const body = resolvePlaybookContent(cwd2, entry);
-    if (body === null) {
-      out.push({ type: "playbook", slug, hash: null });
-      continue;
-    }
-    const wireBody = assemblePlaybookWireBody(entry, body);
-    out.push({
-      type: "playbook",
-      slug,
-      hash: componentHashFromFileHashes([hashString(wireBody)])
-    });
-  }
-  for (const entry of manifest.evals ?? []) {
-    out.push({
-      type: "eval",
-      slug: entry.slug,
-      hash: hashEvalEntry(entry)
-    });
-  }
-  return out;
-}
-function threeWayDiff(input) {
-  const lockMap = new Map;
-  for (const c2 of input.lock)
-    lockMap.set(compKey(c2.type, c2.slug), c2);
-  const cloudMap = new Map;
-  for (const c2 of input.cloud)
-    cloudMap.set(compKey(c2.type, c2.slug), c2);
-  const localMap = new Map;
-  for (const c2 of input.local)
-    localMap.set(compKey(c2.type, c2.slug), c2);
-  const keys2 = new Set;
-  for (const k3 of lockMap.keys())
-    keys2.add(k3);
-  for (const k3 of cloudMap.keys())
-    keys2.add(k3);
-  for (const k3 of localMap.keys())
-    keys2.add(k3);
-  const rows = [];
-  for (const key2 of [...keys2].sort()) {
-    const lock = lockMap.get(key2);
-    const cloud = cloudMap.get(key2);
-    const local = localMap.get(key2);
-    const [type, slug] = key2.split("/", 2);
-    let localHash = local?.hash ?? null;
-    if (local && local.hash === null && local.declaredSource && lock?.source === local.declaredSource && cloud) {
-      localHash = cloud.hash;
-    }
-    const cloudHash = cloud?.hash;
-    const lockHash = lock?.hash;
-    const declaredSource = local?.declaredSource;
-    const present = {
-      local: !!local,
-      lock: !!lock,
-      cloud: !!cloud
-    };
-    let status;
-    if (present.local && present.cloud && !present.lock) {
-      status = "added-local";
-    } else if (!present.local && present.cloud && !present.lock) {
-      status = "added-cloud";
-    } else if (present.local && !present.cloud && !present.lock) {
-      status = "added-only-local";
-    } else if (!present.local && present.lock) {
-      status = "removed-local";
-    } else if (present.local && !present.cloud && present.lock) {
-      status = "removed-cloud";
-    } else {
-      const sourceChanged = !!local && local.hash === null && !!local.declaredSource && lock?.source !== undefined && lock.source !== local.declaredSource;
-      const localChanged = sourceChanged || localHash !== null && lockHash !== undefined && localHash !== lockHash;
-      const cloudChanged = cloudHash !== undefined && lockHash !== undefined && cloudHash !== lockHash;
-      const converged = !sourceChanged && localHash !== null && cloudHash !== undefined && localHash === cloudHash;
-      if (converged)
-        status = "in-sync";
-      else if (localChanged && cloudChanged)
-        status = "modified-both";
-      else if (localChanged)
-        status = "modified-local";
-      else if (cloudChanged)
-        status = "modified-cloud";
-      else
-        status = "in-sync";
-    }
-    rows.push({
-      key: key2,
-      type,
-      slug,
-      status,
-      localHash: localHash ?? undefined,
-      lockHash,
-      cloudHash,
-      declaredSource
-    });
-  }
-  return rows;
-}
-function partitionPushRows(rows, force) {
-  const toSend = [];
-  const conflicts = [];
-  const upstreamOnly = [];
-  for (const r2 of rows) {
-    switch (r2.status) {
-      case "modified-local":
-      case "added-only-local":
-      case "added-local":
-      case "removed-local":
-        toSend.push(r2);
-        break;
-      case "modified-both":
-        if (force)
-          toSend.push(r2);
-        else
-          conflicts.push(r2);
-        break;
-      case "modified-cloud":
-      case "added-cloud":
-      case "removed-cloud":
-        upstreamOnly.push(r2);
-        break;
-      case "in-sync":
-        break;
-      default: {
-        const _exhaustive = r2.status;
-      }
-    }
-  }
-  return { toSend, conflicts, upstreamOnly };
-}
-function diffAgentMeta(manifestMeta, lockMeta, cloudMeta) {
-  const eq = (a3, b4) => {
-    if (!a3 && !b4)
-      return true;
-    if (!a3 || !b4)
-      return false;
-    return a3.name === b4.name && (a3.tagline ?? "") === (b4.tagline ?? "");
-  };
-  return {
-    localChanged: !!manifestMeta && !!lockMeta && !eq(manifestMeta, lockMeta),
-    cloudChanged: !!cloudMeta && !!lockMeta && !eq(cloudMeta, lockMeta)
-  };
-}
-var WRITABLE_CAPABILITIES = ["memory", "browser"];
-var MIRRORED_CAPABILITIES = ["slack", "meeting", "github", "linear"];
-function manifestConfigState(manifest) {
-  return {
-    ...manifest.machine_kind !== undefined ? { machine_kind: manifest.machine_kind } : {},
-    ...hasOwn(manifest, "default_model") ? { default_model: manifest.default_model ?? null } : {},
-    ...manifest.capabilities?.memory !== undefined ? { memory: manifest.capabilities.memory } : {},
-    ...manifest.capabilities?.browser !== undefined ? { browser: manifest.capabilities.browser } : {}
-  };
-}
-function cloudConfigState(agent) {
-  return {
-    ...agent.machine_kind !== undefined ? { machine_kind: agent.machine_kind } : {},
-    ...hasOwn(agent, "default_model") ? { default_model: agent.default_model ?? null } : {},
-    ...agent.memory_enabled !== undefined ? { memory: agent.memory_enabled } : {},
-    ...agent.browser_enabled !== undefined ? { browser: agent.browser_enabled } : {}
-  };
-}
-function hasOwn(value, key2) {
-  return !!value && Object.prototype.hasOwnProperty.call(value, key2);
-}
-function staleConnectionMirrors(manifest, cloud) {
-  const actualByName = {
-    slack: cloud.slack_connected,
-    meeting: cloud.meeting_connected,
-    github: cloud.github_connected,
-    linear: cloud.linear_connected
-  };
-  const stale = [];
-  for (const name of MIRRORED_CAPABILITIES) {
-    const authored = manifest.capabilities?.[name];
-    const actual = actualByName[name];
-    if (authored === undefined || actual === undefined)
-      continue;
-    if (authored !== actual)
-      stale.push({ name, authored, actual });
-  }
-  return stale;
-}
-function diffAgentConfig(manifest, lock, cloud) {
-  const unsupported = [];
-  const machineSupported = cloud.machine_kind !== undefined;
-  const defaultModelSupported = hasOwn(cloud, "default_model");
-  if (manifest.machine_kind !== undefined && !machineSupported) {
-    unsupported.push("machine_kind");
-  }
-  if (manifest.default_model !== undefined && !defaultModelSupported) {
-    unsupported.push("default_model");
-  }
-  const machineMismatch = manifest.machine_kind !== undefined && machineSupported && manifest.machine_kind !== cloud.machine_kind;
-  const machineLocalChanged = manifest.machine_kind !== undefined && machineSupported && (lock?.machine_kind !== undefined ? manifest.machine_kind !== lock.machine_kind && manifest.machine_kind !== cloud.machine_kind : manifest.machine_kind !== cloud.machine_kind);
-  const machineCloudChanged = lock?.machine_kind !== undefined && machineSupported && lock.machine_kind !== cloud.machine_kind && manifest.machine_kind !== cloud.machine_kind;
-  const machineConverged = manifest.machine_kind !== undefined && machineSupported && manifest.machine_kind === cloud.machine_kind && (lock?.machine_kind === undefined || lock.machine_kind !== cloud.machine_kind);
-  const defaultModel = threeWayField(defaultModelSupported, manifest.default_model, cloud.default_model, lock, "default_model");
-  const memory = threeWayField(hasOwn(cloud, "memory"), manifest.memory, cloud.memory, lock, "memory");
-  const browser = threeWayField(hasOwn(cloud, "browser"), manifest.browser, cloud.browser, lock, "browser");
-  if (manifest.memory !== undefined && !hasOwn(cloud, "memory")) {
-    unsupported.push("memory");
-  }
-  if (manifest.browser !== undefined && !hasOwn(cloud, "browser")) {
-    unsupported.push("browser");
-  }
-  return {
-    unsupported,
-    machineMismatch,
-    machineLocalChanged,
-    machineCloudChanged,
-    defaultModelLocalChanged: defaultModel.localChanged,
-    defaultModelCloudChanged: defaultModel.cloudChanged,
-    defaultModelConflict: defaultModel.conflict,
-    memory,
-    browser,
-    baselineConverged: machineConverged || defaultModel.converged || memory.converged || browser.converged
-  };
-}
-function threeWayField(supported, authored, cloudRaw, lock, key2) {
-  const result2 = {
-    localChanged: false,
-    cloudChanged: false,
-    conflict: false,
-    converged: false
-  };
-  if (!supported)
-    return result2;
-  const cloudValue = cloudRaw ?? null;
-  const lockSupported = hasOwn(lock, key2);
-  const lockValue = lock?.[key2] ?? null;
-  if (authored === undefined) {
-    if (lockSupported)
-      result2.cloudChanged = cloudValue !== lockValue;
-    return result2;
-  }
-  const localValue = authored ?? null;
-  if (!lockSupported) {
-    result2.localChanged = localValue !== cloudValue;
-    result2.converged = localValue === cloudValue;
-    return result2;
-  }
-  const localMoved = localValue !== lockValue;
-  const cloudMoved = cloudValue !== lockValue;
-  result2.conflict = localMoved && cloudMoved && localValue !== cloudValue;
-  result2.localChanged = localMoved && localValue !== cloudValue;
-  result2.cloudChanged = cloudMoved && localValue !== cloudValue;
-  result2.converged = localMoved && cloudMoved && localValue === cloudValue;
-  return result2;
-}
-
 // src/core/eval-merge.ts
 function evalsFromCloudComponents(components) {
   return components.filter((c2) => c2.type === "eval").map((c2) => {
@@ -64792,41 +64890,6 @@ function capabilityBaselineAfterPush(cloudAgent, previous, diff2) {
   return out;
 }
 
-// src/core/mcp-merge.ts
-var RUNTIME_META_PREFIX = "runtime_";
-function runtimeMetaFromComponent(component) {
-  const meta = component.meta ?? {};
-  const carried = {};
-  for (const [key2, value] of Object.entries(meta)) {
-    if (key2.startsWith(RUNTIME_META_PREFIX) && value !== undefined) {
-      carried[key2] = value;
-    }
-  }
-  return Object.keys(carried).length > 0 ? carried : undefined;
-}
-function mcpEntriesFromCloudComponents(components) {
-  return components.filter((c2) => c2.type === "mcp").map((c2) => {
-    const payload = (c2.meta ?? {}).mcp ?? {};
-    const entry = { name: c2.slug };
-    if (typeof payload.url === "string")
-      entry.url = payload.url;
-    if (typeof payload.command === "string")
-      entry.command = payload.command;
-    if (Array.isArray(payload.args))
-      entry.args = payload.args.map(String);
-    if (payload.env && typeof payload.env === "object")
-      entry.env = payload.env;
-    if (payload.headers && typeof payload.headers === "object")
-      entry.headers = payload.headers;
-    if (typeof payload.is_enabled === "boolean")
-      entry.is_enabled = payload.is_enabled;
-    const runtimeMeta = runtimeMetaFromComponent(c2);
-    if (runtimeMeta)
-      entry.runtime_meta = runtimeMeta;
-    return entry;
-  });
-}
-
 // src/core/secrets-env.ts
 import path79 from "node:path";
 import fs72 from "node:fs";
@@ -65035,7 +65098,8 @@ async function runAgentUnpack(cwd2, args) {
         slug: entry.name,
         scope,
         rootDir: compDir,
-        payload: proxifyMcpPayload(payload),
+        payload: proxifyMcpPayload(payload, undefined, entry.runtime_meta?.runtime_mcp_auth),
+        meta: entry.runtime_meta,
         checksum: ""
       });
     }
@@ -65426,13 +65490,28 @@ async function runAgentPull(cwd2, args) {
         break;
     }
   }
+  for (const r2 of rows) {
+    if (r2.type !== "mcp" || !["in-sync", "added-local"].includes(r2.status))
+      continue;
+    const remote = cloud.components.find((c2) => c2.type === "mcp" && c2.slug === r2.slug);
+    const local = existingManifest?.mcp.find((entry) => entry.name === r2.slug);
+    if (!remote || isDeepStrictEqual2(remote.meta?.runtime_mcp_auth, local?.runtime_meta?.runtime_mcp_auth))
+      continue;
+    const prior = lock?.components.find((c2) => c2.type === "mcp" && c2.slug === r2.slug);
+    const target = { harness, cwd: cwd2, scope: args.scope ?? "project" };
+    const locallyReplaced = prior && readHarnessMcpEntry(harness, cwd2, target.scope, r2.slug) !== undefined && !lockEntryOwnsMcpInStore(prior, target);
+    if (locallyReplaced && !override)
+      conflicts.push(r2);
+    else
+      toInstallKeys.add(r2.key);
+  }
   const keepLocalKeys = new Set;
   if (conflicts.length > 0) {
     requireInteractive(`${conflicts.length} file(s) changed both locally and in the cloud — resolve them in an interactive terminal, or pass --force to take the cloud copy.`);
   }
   for (const r2 of conflicts) {
     const choice = await ie({
-      message: r2.status === "modified-both" ? `${fmtType(r2.type)} ${import_picocolors26.default.bold(r2.slug)} — both you and the cloud edited it` : `${fmtType(r2.type)} ${import_picocolors26.default.bold(r2.slug)} — you have local edits not yet pushed`,
+      message: r2.status === "in-sync" || r2.status === "added-local" ? `${fmtType(r2.type)} ${import_picocolors26.default.bold(r2.slug)} — your installed server was replaced and its cloud authentication changed` : r2.status === "modified-both" ? `${fmtType(r2.type)} ${import_picocolors26.default.bold(r2.slug)} — both you and the cloud edited it` : `${fmtType(r2.type)} ${import_picocolors26.default.bold(r2.slug)} — you have local edits not yet pushed`,
       options: [
         { value: "cloud", label: "Use the cloud's version (discard local edits)" },
         { value: "keep", label: "Keep your local edits (skip this one)" }
@@ -65512,6 +65591,7 @@ async function runAgentPull(cwd2, args) {
   const installComponents = cloud.components.filter((c2) => toInstallKeys.has(`${c2.type}/${c2.slug}`));
   const stageRoot = stageManifestComponents(installComponents);
   const justInstalledPaths = new Map;
+  const skippedMcpSlugs = new Set;
   const justInstalledFingerprints = new Map;
   try {
     const availableSecrets = await pullSecrets(cwd2, agentId);
@@ -65525,7 +65605,7 @@ async function runAgentPull(cwd2, args) {
         rootDir: path81.join(stageRoot, c2.type, c2.slug),
         description: c2.description,
         meta: c2.meta,
-        payload: proxifyMcpPayload(structuredClone(c2.meta?.mcp)),
+        payload: proxifyMcpPayload(structuredClone(c2.meta?.mcp), undefined, c2.meta?.runtime_mcp_auth),
         checksum: c2.hash,
         source: skillSourceFromMeta(c2)
       }));
@@ -65550,6 +65630,8 @@ async function runAgentPull(cwd2, args) {
         }
       }
       for (const s3 of result2.skipped) {
+        if (s3.type === "mcp")
+          skippedMcpSlugs.add(s3.slug);
         if (s3.reason !== KEPT_UNOWNED_MCP_SKIP)
           continue;
         f2.warn(`Kept local MCP server ${import_picocolors26.default.bold(s3.slug)}: not installed by this agent; the cloud has it disabled. Remove it from your harness config to let the cloud's setting apply.`);
@@ -65597,6 +65679,24 @@ async function runAgentPull(cwd2, args) {
     materializeEntrypoint(cwd2, cloudAgent.entrypoint ?? "", existingManifest);
     materializePlaybooks(cwd2, cloud, toInstallKeys, keepLocalKeys, existingManifest);
     const yaml = mergeManifest(cwd2, existingManifest, cloud, cloudAgent, harness, override ? {} : readLocalOnlyContentReporting(cwd2), new Map((lock?.components ?? []).filter((c2) => c2.type === "eval").map((c2) => [c2.slug, c2.hash])), new Set([...keepLocalKeys].filter((key2) => key2.startsWith("eval/")).map((key2) => key2.slice("eval/".length))));
+    for (const entry of existingManifest?.mcp ?? []) {
+      if (!keepLocalKeys.has(`mcp/${entry.name}`))
+        continue;
+      const index = yaml.mcp.findIndex((c2) => c2.name === entry.name);
+      if (index >= 0)
+        yaml.mcp[index] = entry;
+    }
+    for (const entry of yaml.mcp) {
+      if (!skippedMcpSlugs.has(entry.name))
+        continue;
+      const priorAuth = existingManifest?.mcp.find((c2) => c2.name === entry.name)?.runtime_meta?.runtime_mcp_auth;
+      const runtimeMeta = { ...entry.runtime_meta };
+      if (priorAuth === undefined)
+        delete runtimeMeta.runtime_mcp_auth;
+      else
+        runtimeMeta.runtime_mcp_auth = priorAuth;
+      entry.runtime_meta = Object.keys(runtimeMeta).length > 0 ? runtimeMeta : undefined;
+    }
     writeManifest(cwd2, yaml);
     writeLink(cwd2, buildLinkFromAgent(cloudAgent, harness, readLink(cwd2)));
     const lockComponents = buildLockComponents({
@@ -69285,7 +69385,7 @@ async function installAgentFresh(input) {
         rootDir: path87.join(stageRoot, c2.type, c2.slug),
         description: c2.description,
         meta: c2.meta,
-        payload: proxifyMcpPayload(structuredClone(c2.meta?.mcp)),
+        payload: proxifyMcpPayload(structuredClone(c2.meta?.mcp), undefined, c2.meta?.runtime_mcp_auth),
         checksum: c2.hash
       }));
       toInstall.push(...builtinInstall);
@@ -71867,14 +71967,21 @@ import fs81 from "node:fs";
 function collectServers(cwd2, env3 = process.env) {
   const out = [];
   const seen = new Set;
+  let manifestEntries = [];
+  try {
+    manifestEntries = readManifest(cwd2)?.mcp ?? [];
+  } catch {}
+  const identities = new Map(manifestEntries.map((entry) => [entry.name, entry]));
   for (const source of [readClaudeCode, readCodex, readKafka, readResolvedMcps]) {
     for (const [name, entry] of source(cwd2)) {
-      pushResolved(out, seen, name, entry, env3);
+      const authored = identities.get(name);
+      const identity2 = typeof entry.url === "string" && typeof authored?.url === "string" && mcpUpstreamUrl(entry.url, env3) === mcpUpstreamUrl(authored.url, env3) ? authored.runtime_meta?.runtime_mcp_auth : undefined;
+      pushResolved(out, seen, name, entry, env3, identity2);
     }
   }
   return out;
 }
-function pushResolved(out, seen, name, entry, env3) {
+function pushResolved(out, seen, name, entry, env3, identity2) {
   if (seen.has(name))
     return;
   if (entry.is_enabled === false) {
@@ -71897,7 +72004,7 @@ function pushResolved(out, seen, name, entry, env3) {
     };
   }
   delete normalized.http_headers;
-  const proxied = proxifyMcpPayload(normalized, env3) ?? normalized;
+  const proxied = proxifyMcpPayload(normalized, env3, identity2) ?? normalized;
   const resolved = resolveMcpEnvTemplates(proxied, env3) ?? proxied;
   const finalUrl = resolved.url;
   if (typeof finalUrl !== "string" || finalUrl.length === 0)

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@brainbase-labs/cli",
-  "version": "0.32.0",
+  "version": "0.33.0",
   "description": "Pack, share, and install agent templates across harnesses (Claude Code, Codex, ...).",
   "type": "module",
   "bin": {