amalgm 0.1.79 → 0.1.80

package/runtime/scripts/amalgm-mcp/agents/store.js

@@ -32,6 +32,9 @@ const {
   readUserPreferences,
 } = require('../lib/prefs');
 const credentialAdapter = require('../../credential-adapter');
+const {
+  normalizeLoadout,
+} = require('../agent-config/loadout');
 
 const DEFAULT_AGENT_STATUS = 'unknown';
 const CUSTOM_AGENT_STATUS = 'ready';
@@ -89,9 +92,8 @@ const BUILTIN_AGENTS = BUILTIN_AGENT_BLUEPRINTS.map((agent) => ({
   files: [],
   skills: [],
   mcpAppIds: [],
-  nativeMcps: [],
-  tools: { mode: 'all', selectedToolIds: [] },
-  mcp: { inheritAll: true, customServers: [], appIds: [], nativeMcps: [] },
+  loadout: { toolIds: [] },
+  mcp: { inheritAll: false, customServers: [], appIds: [] },
   builtin: false,
   deletable: true,
   editable: true,
@@ -230,30 +232,23 @@ function defaultCapabilities(agent) {
     streaming: true,
     resume: true,
     cancel: true,
-    tools: agent?.tools?.mode === 'selected' ? 'selected' : 'all',
+    tools: 'selected',
   };
 }
 
-function normalizeMcpTransportConfig(toolConfig, mcpAppIds, nativeMcps) {
+function normalizeMcpTransportConfig(loadout, mcpAppIds) {
   return {
-    inheritAll: toolConfig.mode !== 'selected',
+    inheritAll: false,
     customServers: [],
     appIds: normalizeStringList(mcpAppIds),
-    nativeMcps: normalizeStringList(nativeMcps),
   };
 }
 
-function normalizeToolConfig(tools) {
-  const raw = isObject(tools) ? tools : null;
-  const selectedToolIds = normalizeStringList(
-    raw?.selectedToolIds
-    ?? raw?.selected
-    ?? [],
+function normalizeAgentLoadout(input, existing) {
+  return normalizeLoadout(
+    input?.loadout ?? input?.toolset ?? input?.tools,
+    existing?.loadout ?? existing?.tools,
   );
-  return {
-    mode: raw?.mode === 'selected' ? 'selected' : 'all',
-    selectedToolIds,
-  };
 }
 
 function normalizeAgent(input, existing) {
@@ -262,8 +257,8 @@ function normalizeAgent(input, existing) {
   const builtin = input.builtin === true;
   const baseHarnessId = nonEmptyString(input.baseHarnessId || input.base_harness_id) || id;
   const adapter = nonEmptyString(input.adapter) || baseHarnessId;
-  const toolConfig = normalizeToolConfig(input.tools);
-  const mcpConfig = normalizeMcpTransportConfig(toolConfig, input.mcpAppIds, input.nativeMcps);
+  const loadout = normalizeAgentLoadout(input, existing);
+  const mcpConfig = normalizeMcpTransportConfig(loadout, input.mcpAppIds);
   const ownerComputerId = nonEmptyString(input.ownerComputerId || input.owner_computer_id)
     || nonEmptyString(existing?.ownerComputerId)
     || computerId();
@@ -286,11 +281,9 @@ function normalizeAgent(input, existing) {
     files: normalizeStringList(input.files),
     skills: normalizeStringList(input.skills),
     mcpAppIds: normalizeStringList(mcpConfig.appIds),
-    nativeMcps: normalizeStringList(mcpConfig.nativeMcps),
-    tools: toolConfig,
+    loadout,
     mcp: {
       ...mcpConfig,
-      inheritAll: toolConfig.mode !== 'selected',
     },
     authMethod: input.authMethod || existing?.authMethod || persistedAuthMethod(baseHarnessId),
     location,
@@ -300,8 +293,8 @@ function normalizeAgent(input, existing) {
     installStatus: input.installStatus || existing?.installStatus || (builtin ? 'unknown' : 'external'),
     authStatus: input.authStatus || existing?.authStatus || 'unknown',
     capabilities: isObject(input.capabilities)
-      ? { ...defaultCapabilities({ tools: toolConfig }), ...input.capabilities }
-      : defaultCapabilities({ tools: toolConfig }),
+      ? { ...defaultCapabilities({ loadout }), ...input.capabilities }
+      : defaultCapabilities({ loadout }),
     builtin,
     deletable: input.deletable === false ? false : true,
     editable: input.editable === false ? false : true,
@@ -469,13 +462,11 @@ function seedBuiltinAgents(options = {}) {
         files: existing?.files || [],
         skills: existing?.skills || [],
         mcpAppIds: existing?.mcpAppIds || [],
-        nativeMcps: [],
-        tools: existing?.tools || { mode: 'all', selectedToolIds: [] },
+        loadout: existing?.loadout || existing?.tools || { toolIds: [] },
         mcp: {
-          inheritAll: existing?.tools?.mode !== 'selected',
+          inheritAll: false,
           customServers: [],
           appIds: existing?.mcpAppIds || [],
-          nativeMcps: [],
         },
         builtin: false,
         deletable: true,

package/runtime/scripts/amalgm-mcp/agents/talk.js

@@ -38,8 +38,9 @@ const {
   getChatInputText,
   normalizeChatInput,
 } = require('../../../lib/chatInput');
-const { getAgentConfig, legacyFieldsFromConfig } = require('../agent-config/store');
+const { agentFieldsFromConfig, getAgentConfig } = require('../agent-config/store');
 const { renderAgentInstructions } = require('../agent-config/renderers/instructions');
+const { loadoutToolIds } = require('../agent-config/loadout');
 const credentialAdapter = require('../../credential-adapter');
 const { buildLocalMcpServerConfigs } = require('../lib/mcp-resolver');
 const {
@@ -599,19 +600,17 @@ async function handleTalkToAgent(args, context = {}) {
     agent.authMethod || preferredAuthMethod,
   );
   const agentConfig = getAgentConfig(agent);
-  const configLegacy = legacyFieldsFromConfig(agentConfig);
+  const agentFields = agentFieldsFromConfig(agentConfig);
   const agentFiles = normalizeStringList(agent.files);
-  const agentSkills = normalizeStringList(configLegacy.skills);
-  const agentTools = configLegacy.tools || agent.tools || { mode: 'all', selectedToolIds: [] };
-  const agentMcpAppIds = toolboxService.externalMcpToolIdsForMode(
-    agentTools.mode,
-    agentTools.selectedToolIds,
-  );
+  const agentSkills = normalizeStringList(agentFields.skills);
+  const agentLoadout = agentConfig.loadout || agent.loadout || agent.tools || { toolIds: [] };
+  const agentLoadoutToolIds = loadoutToolIds(agentLoadout);
+  const agentMcpAppIds = toolboxService.externalMcpToolIdsForLoadout(agentLoadoutToolIds);
   const baseAgentSystemPrompt = [
     renderAgentInstructions(agentConfig, { includeAgentToAgentPrompt: true }),
     buildAgentFilesBlock(agentFiles),
   ].filter(Boolean).join('\n\n') || buildAgentInstructions(
-    configLegacy.systemPrompt || agent.systemPrompt,
+    agentFields.systemPrompt || agent.systemPrompt,
     agentFiles,
     agentSkills,
   );
@@ -641,8 +640,7 @@ async function handleTalkToAgent(args, context = {}) {
     },
     tools: {
       ...((isObject(chatInput) && isObject(chatInput.tools)) ? chatInput.tools : {}),
-      mode: agentTools.mode,
-      toolIds: normalizeStringList(agentTools.selectedToolIds),
+      toolIds: agentLoadoutToolIds,
       mcpAppIds: agentMcpAppIds,
     },
     execution: {
@@ -783,7 +781,7 @@ async function handleTalkToAgent(args, context = {}) {
             files: agentFiles,
             skills: agentSkills,
             mcpAppIds: agentMcpAppIds,
-            tools: agentTools,
+            loadout: agentConfig.loadout,
             agentConfig,
             ...(parentOrigin || {}),
           },

package/runtime/scripts/amalgm-mcp/agents/tools.js

@@ -64,7 +64,7 @@ module.exports = [
           getSelectedModel(agent.baseHarnessId) ||
           DEFAULT_SELECTED_MODELS[agent.baseHarnessId],
         systemPrompt: agent.systemPrompt ? '(configured)' : '(none)',
-        tools: agent.tools || { mode: 'all', selectedToolIds: [] },
+        loadout: agent.loadout || { toolIds: [] },
         location: agent.location || null,
         locationName: agent.locationName || null,
         ownerComputerId: agent.ownerComputerId || null,

package/runtime/scripts/amalgm-mcp/automations/runner.js

@@ -311,12 +311,7 @@ async function runToolCell(cell, args, allowlist) {
   }
 
   const result = await callToolboxMcpTool(toolboxMcpToolName(resolved.action), args, {
-    sessionMetadata: {
-      tools: {
-        mode: 'selected',
-        selectedToolIds: [resolved.tool.id, resolved.action.id],
-      },
-    },
+    loadout: { toolIds: [resolved.tool.id, resolved.action.id] },
   });
   return mcpResultToOutput(result, actionKey);
 }

package/runtime/scripts/amalgm-mcp/email/inbound.js

@@ -25,6 +25,9 @@ const {
   resolveModelSelection,
   DEFAULT_SELECTED_MODELS,
 } = require('../lib/prefs');
+const { getAgentConfig } = require('../agent-config/store');
+const { loadoutToolIds } = require('../agent-config/loadout');
+const { defaultToolboxService: toolboxService } = require('../toolbox/service');
 const { buildLocalMcpServerConfigs } = require('../lib/mcp-resolver');
 const {
   chatInputToLegacyFields,
@@ -50,12 +53,14 @@ function normalizeStringList(values) {
 }
 
 function sessionToolConfig(metadata) {
-  const tools = metadata?.tools && typeof metadata.tools === 'object' && !Array.isArray(metadata.tools)
-    ? metadata.tools
-    : {};
+  const agentId = asString(metadata?.agentConfigId) || asString(metadata?.agentId);
+  const loadout = agentId
+    ? getAgentConfig(agentId).loadout
+    : metadata?.loadout || metadata?.tools || {};
+  const toolIds = loadoutToolIds(loadout);
   return {
-    mode: tools.mode === 'selected' ? 'selected' : 'all',
-    toolIds: normalizeStringList(tools.selectedToolIds),
+    toolIds,
+    mcpAppIds: toolboxService.externalMcpToolIdsForLoadout(toolIds),
   };
 }
 
@@ -154,8 +159,7 @@ async function handleEmailInbound(body, sendJson) {
       systemPrompt: asString(metadata.systemPrompt),
     },
     tools: {
-      mcpAppIds: Array.isArray(metadata.mcpAppIds) ? metadata.mcpAppIds : [],
-      mode: toolConfig.mode,
+      mcpAppIds: toolConfig.mcpAppIds,
       toolIds: toolConfig.toolIds,
     },
     execution: {
@@ -170,7 +174,7 @@ async function handleEmailInbound(body, sendJson) {
     cwd,
     computerId,
     systemPrompt: asString(metadata.systemPrompt),
-    mcpAppIds: Array.isArray(metadata.mcpAppIds) ? metadata.mcpAppIds : [],
+    mcpAppIds: toolConfig.mcpAppIds,
   });
 
   const legacyChatFields = chatInputToLegacyFields(normalizedChatInput, {

package/runtime/scripts/amalgm-mcp/mcp-connections/rest.js

@@ -4,7 +4,6 @@
  */
 
 const fs = require('fs');
-const os = require('os');
 const path = require('path');
 const { AMALGM_DIR } = require('../config');
 const { appendStateEvent } = require('../state/events');
@@ -13,7 +12,6 @@ const {
 } = require('../toolbox/service');
 
 const CONNECTIONS_FILE = path.join(AMALGM_DIR, 'mcp-connections.json');
-const CLAUDE_FILE = path.join(os.homedir(), '.claude.json');
 let mcpRegistry = null;
 let mcpRegistryLoadAttempted = false;
 let warnedRegistryLoadFailure = false;
@@ -96,21 +94,10 @@ function sanitizeConnections(connections) {
   return sanitized;
 }
 
-function readNativeMcps() {
-  try {
-    const raw = fs.readFileSync(CLAUDE_FILE, 'utf8');
-    const parsed = JSON.parse(raw);
-    return Array.isArray(parsed?.claudeAiMcpEverConnected) ? parsed.claudeAiMcpEverConnected : [];
-  } catch {
-    return [];
-  }
-}
-
 function buildConnectionsSnapshot() {
   const file = readConnectionsFile();
   return {
     connections: sanitizeConnections(file.connections),
-    nativeMcps: readNativeMcps(),
   };
 }
 

package/runtime/scripts/amalgm-mcp/server/mcp-request-context.js

@@ -21,6 +21,11 @@ async function buildMcpRequestContext(extra) {
     const parent = Array.isArray(rows) ? rows[0] : null;
     if (parent) {
       ctx.sessionMetadata = parent.metadata || {};
+      ctx.agentConfigId =
+        parent.metadata?.agentConfigId
+        || parent.metadata?.agentId
+        || parent.metadata?.customAgentId
+        || undefined;
       ctx.originName = parent.title || undefined;
       ctx.originHarnessId = parent.harness || undefined;
       ctx.originBaseHarnessId = parent.metadata?.baseHarnessId || undefined;

package/runtime/scripts/amalgm-mcp/slack/inbound.js

@@ -23,6 +23,9 @@ const {
   resolveModelSelection,
   DEFAULT_SELECTED_MODELS,
 } = require('../lib/prefs');
+const { getAgentConfig } = require('../agent-config/store');
+const { loadoutToolIds } = require('../agent-config/loadout');
+const { defaultToolboxService: toolboxService } = require('../toolbox/service');
 const { buildLocalMcpServerConfigs } = require('../lib/mcp-resolver');
 const {
   chatInputToLegacyFields,
@@ -48,12 +51,14 @@ function normalizeStringList(values) {
 }
 
 function sessionToolConfig(metadata) {
-  const tools = metadata?.tools && typeof metadata.tools === 'object' && !Array.isArray(metadata.tools)
-    ? metadata.tools
-    : {};
+  const agentId = asString(metadata?.agentConfigId) || asString(metadata?.agentId);
+  const loadout = agentId
+    ? getAgentConfig(agentId).loadout
+    : metadata?.loadout || metadata?.tools || {};
+  const toolIds = loadoutToolIds(loadout);
   return {
-    mode: tools.mode === 'selected' ? 'selected' : 'all',
-    toolIds: normalizeStringList(tools.selectedToolIds),
+    toolIds,
+    mcpAppIds: toolboxService.externalMcpToolIdsForLoadout(toolIds),
   };
 }
 
@@ -147,8 +152,7 @@ async function handleSlackInbound(body, sendJson) {
       systemPrompt: slackSystemPrompt || null,
     },
     tools: {
-      mcpAppIds: Array.isArray(metadata.mcpAppIds) ? metadata.mcpAppIds : [],
-      mode: toolConfig.mode,
+      mcpAppIds: toolConfig.mcpAppIds,
       toolIds: toolConfig.toolIds,
     },
     execution: {
@@ -163,7 +167,7 @@ async function handleSlackInbound(body, sendJson) {
     cwd,
     computerId,
     systemPrompt: slackSystemPrompt || undefined,
-    mcpAppIds: Array.isArray(metadata.mcpAppIds) ? metadata.mcpAppIds : [],
+    mcpAppIds: toolConfig.mcpAppIds,
   });
 
   const legacyChatFields = chatInputToLegacyFields(normalizedChatInput, {

package/runtime/scripts/amalgm-mcp/tests/agent-config.test.js

@@ -65,7 +65,7 @@ test('codex native import ports command hooks without inheriting MCP or auth con
     assert.equal(config.hooks[0].timeout, 90);
     assert.equal(config.hooks[0].statusMessage, 'Searching memories...');
     assert.equal(config.hooks[0].source.provider, 'codex');
-    assert.equal(config.tools.mode, 'all');
+    assert.deepEqual(config.loadout.toolIds, []);
 
     const serialized = JSON.stringify(config);
     assert.equal(serialized.includes('mcp_servers'), false);

package/runtime/scripts/amalgm-mcp/tests/agents-source-of-truth.test.js

@@ -70,13 +70,11 @@ test('custom agent auth and model settings survive normalization', () => {
     baseModelId: 'openai/gpt-5.5',
     authMethod: 'provider_auth',
     modelSettings: { effort: 'medium', fastMode: true },
-    tools: { mode: 'selected', selectedToolIds: ['tool.search'] },
+    loadout: { toolIds: ['tool.search'] },
   });
 
   assert.equal(agent.authMethod, 'provider_auth');
   assert.deepEqual(agent.modelSettings, { effort: 'medium', fastMode: true });
-  assert.deepEqual(agent.tools, {
-    mode: 'selected',
-    selectedToolIds: ['tool.search'],
-  });
+  assert.deepEqual(agent.loadout, { toolIds: ['tool.search'] });
+  assert.equal(Object.prototype.hasOwnProperty.call(agent, 'tools'), false);
 });

package/runtime/scripts/amalgm-mcp/tests/chat-payloads.test.js

@@ -34,7 +34,7 @@ test('chat payloads persist in local SQLite and snapshot by id', () => {
     customAgentId: null,
     systemPrompt: null,
     mcpAppIds: ['github'],
-    tools: { mode: 'selected', selectedToolIds: ['tool.search'] },
+    loadout: { toolIds: ['tool.search'] },
     pendingWorktree: false,
   };
 

package/runtime/scripts/amalgm-mcp/tests/mcp-surface.test.js

@@ -131,12 +131,7 @@ test('MCP surface filters static tools in selected-tool mode', async () => {
     },
   });
   const context = {
-    sessionMetadata: {
-      tools: {
-        mode: 'selected',
-        selectedToolIds: ['amalgm.test'],
-      },
-    },
+    loadout: { toolIds: ['amalgm.test'] },
   };
 
   const listed = await surface.listTools(context);
@@ -167,12 +162,7 @@ test('MCP surface accepts legacy selected ids for first-party tools', async () =
   });
 
   const listed = await surface.listTools({
-    sessionMetadata: {
-      tools: {
-        mode: 'selected',
-        selectedToolIds: ['amalgm.browser'],
-      },
-    },
+    loadout: { toolIds: ['amalgm.browser'] },
   });
 
   assert.deepEqual(listed.map((tool) => tool.name), ['toolbox__browser_browser_navigate']);

package/runtime/scripts/amalgm-mcp/tests/toolbox-service.test.js

@@ -186,7 +186,7 @@ test('toolbox service resolves only runnable CLI/API actions', () => {
   assert.equal(service.resolveRunnableAction('amalgm', 'notify_user'), null);
 
   const selected = service.listRunnableActions({
-    sessionMetadata: { tools: { mode: 'selected', selectedToolIds: ['api.weather.lookup'] } },
+    loadout: { toolIds: ['api.weather.lookup'] },
   });
   assert.deepEqual(selected.map(({ action }) => action.id), ['api.weather.lookup']);
 });
@@ -194,9 +194,8 @@ test('toolbox service resolves only runnable CLI/API actions', () => {
 test('toolbox service derives only external MCP ids from selected tools', () => {
   const service = createToolboxService(createRepository());
 
-  assert.deepEqual(service.externalMcpToolIdsForMode('all'), ['remote.mcp']);
   assert.deepEqual(
-    service.externalMcpToolIdsForSelection([
+    service.externalMcpToolIdsForLoadout([
       'remote.mcp',
       'browser',
       'api.weather',
@@ -209,7 +208,7 @@ test('toolbox service derives only external MCP ids from selected tools', () =>
 test('toolbox service exposes portable MCP descriptors', () => {
   const service = createToolboxService(createRepository());
   const descriptors = service.listMcpTools({
-    sessionMetadata: { tools: { mode: 'selected', selectedToolIds: ['api.weather.lookup'] } },
+    loadout: { toolIds: ['api.weather.lookup'] },
   });
 
   assert.equal(descriptors.length, 1);

package/runtime/scripts/amalgm-mcp/toolbox/loadout-context.js

@@ -0,0 +1,57 @@
+'use strict';
+
+const { loadoutToolIds } = require('../agent-config/loadout');
+
+const FIRST_PARTY_TOOL_IDS = new Set([
+  'automations',
+  'notifications',
+  'agents',
+  'apps',
+  'browser',
+]);
+
+function agentConfigIdFromContext(context) {
+  const metadata = context?.sessionMetadata || {};
+  return (
+    context?.agentConfigId
+    || metadata.agentConfigId
+    || metadata.agentId
+    || metadata.customAgentId
+    || null
+  );
+}
+
+function loadoutSetFromContext(context) {
+  const direct = context?.loadout || context?.toolset || null;
+  if (direct) return new Set(loadoutToolIds(direct));
+
+  const agentConfigId = agentConfigIdFromContext(context);
+  if (!agentConfigId) return null;
+
+  const { getAgentConfig } = require('../agent-config/store');
+  return new Set(loadoutToolIds(getAgentConfig(agentConfigId)));
+}
+
+function loadoutHas(loadoutToolIds, id) {
+  if (!loadoutToolIds || !id) return false;
+  const value = String(id || '').trim();
+  if (loadoutToolIds.has(value)) return true;
+  const toolId = value.split('.')[0];
+  if (loadoutToolIds.has(toolId)) return true;
+  if (FIRST_PARTY_TOOL_IDS.has(toolId) && loadoutToolIds.has(`amalgm.${value}`)) return true;
+  if (FIRST_PARTY_TOOL_IDS.has(value) && loadoutToolIds.has(`amalgm.${value}`)) return true;
+  if (value === 'notifications.notify_user' && loadoutToolIds.has('amalgm.notify_user')) return true;
+  if (value === 'agents.talk_to_agent' && loadoutToolIds.has('amalgm.talk_to_agent')) return true;
+  return false;
+}
+
+function loadoutContainsToolOrAction(loadoutToolIds, toolId, actionId) {
+  if (!loadoutToolIds) return true;
+  return loadoutHas(loadoutToolIds, toolId) || loadoutHas(loadoutToolIds, actionId);
+}
+
+module.exports = {
+  agentConfigIdFromContext,
+  loadoutContainsToolOrAction,
+  loadoutSetFromContext,
+};

package/runtime/scripts/amalgm-mcp/toolbox/mcp-surface.js

@@ -13,9 +13,9 @@ const { CORE_TOOLS } = require('../server/core-tools');
 const { toolboxMcpToolName } = require('./names');
 const { callToolboxMcpTool } = require('./runner');
 const {
-  selectedContainsToolOrAction,
-  selectedToolIdsForContext,
-} = require('./selection');
+  loadoutContainsToolOrAction,
+  loadoutSetFromContext,
+} = require('./loadout-context');
 const {
   defaultToolboxService: toolboxService,
 } = require('./service');
@@ -43,9 +43,9 @@ function defaultListDynamicTools(context) {
   return toolboxService.listMcpTools(context);
 }
 
-function isStaticToolSelected(tool, selectedToolIds) {
-  return selectedContainsToolOrAction(
-    selectedToolIds,
+function isStaticToolInLoadout(tool, loadoutToolIds) {
+  return loadoutContainsToolOrAction(
+    loadoutToolIds,
     tool.toolboxToolId,
     tool.toolboxActionId,
   );
@@ -59,8 +59,8 @@ function createToolboxMcpSurface(options = {}) {
   const callDynamicTool = options.callDynamicTool || callToolboxMcpTool;
 
   function staticToolsForContext(context) {
-    const selectedToolIds = selectedToolIdsForContext(context);
-    return staticTools.filter((tool) => isStaticToolSelected(tool, selectedToolIds));
+    const loadoutToolIds = loadoutSetFromContext(context);
+    return staticTools.filter((tool) => isStaticToolInLoadout(tool, loadoutToolIds));
   }
 
   function findStaticTool(toolName, context) {

package/runtime/scripts/amalgm-mcp/toolbox/service.js

@@ -10,9 +10,9 @@
 const store = require('./store');
 const { portableInputSchema, toolboxMcpToolName } = require('./names');
 const {
-  selectedContainsToolOrAction,
-  selectedToolIdsForContext,
-} = require('./selection');
+  loadoutContainsToolOrAction,
+  loadoutSetFromContext,
+} = require('./loadout-context');
 const { mergeSystemToolboxCatalog } = require('./system-catalog');
 
 function actionRef(toolId, actionName) {
@@ -132,7 +132,15 @@ function createToolboxService(repository = store) {
     };
   }
 
-  function externalMcpToolIdsForMode(mode = 'all', toolIds = []) {
+  function libraryToolIds() {
+    const toolbox = readCatalog();
+    return Object.values(toolbox.tools || {})
+      .filter((tool) => tool?.status === 'enabled')
+      .map((tool) => tool.id)
+      .filter(Boolean);
+  }
+
+  function externalMcpToolIdsForLoadout(toolIds = []) {
     const selected = new Set(
       (Array.isArray(toolIds) ? toolIds : [])
         .map((value) => String(value || '').trim())
@@ -140,23 +148,19 @@ function createToolboxService(repository = store) {
     );
     const toolbox = readCatalog();
     return Object.values(toolbox.tools || {})
-      .filter((tool) => mode !== 'selected' || selected.has(tool.id))
+      .filter((tool) => selected.has(tool.id))
       .filter(isExternalMcpTool)
       .map((tool) => tool.id);
   }
 
-  function externalMcpToolIdsForSelection(toolIds = []) {
-    return externalMcpToolIdsForMode('selected', toolIds);
-  }
-
   function listRunnableActions(context) {
     const toolbox = readToolbox();
-    const selectedToolIds = selectedToolIdsForContext(context);
+    const loadoutToolIds = loadoutSetFromContext(context);
     return Object.values(toolbox.toolActions || {})
       .map((action) => ({ action, tool: toolbox.tools?.[action.toolId] }))
       .filter(({ action, tool }) => {
         if (!isRunnableToolboxTool(tool) || action.status !== 'enabled') return false;
-        return selectedContainsToolOrAction(selectedToolIds, tool.id, action.id);
+        return loadoutContainsToolOrAction(loadoutToolIds, tool.id, action.id);
       });
   }
 
@@ -196,11 +200,11 @@ function createToolboxService(repository = store) {
   return {
     deleteAction: repository.deleteToolAction,
     deleteTool: repository.deleteTool,
-    externalMcpToolIdsForMode,
-    externalMcpToolIdsForSelection,
+    externalMcpToolIdsForLoadout,
     getAction,
     getTool,
     listMcpTools,
+    libraryToolIds,
     listRunnableActions,
     listTools,
     readCatalog,

package/runtime/scripts/amalgm-mcp/workflows/runner.js

@@ -317,12 +317,7 @@ async function runToolCell(cell, args, allowlist) {
   }
 
   const result = await callToolboxMcpTool(toolboxMcpToolName(resolved.action), args, {
-    sessionMetadata: {
-      tools: {
-        mode: 'selected',
-        selectedToolIds: [resolved.tool.id, resolved.action.id],
-      },
-    },
+    loadout: { toolIds: [resolved.tool.id, resolved.action.id] },
   });
   return mcpResultToOutput(result, actionKey);
 }