@bastani/atomic 0.9.23 → 0.9.24

package/CHANGELOG.md

@@ -2,6 +2,48 @@
 
 ## [Unreleased]
 
+## [0.9.24] - 2026-09-29
+
+### Added
+
+- Added inherited Claude Sonnet 5.5 support for Anthropic with adaptive thinking, mid-conversation effort, and a 1M context window.
+- llama.cpp models are now also listed as classifier models with the same ID, so a local model can make `model: "auto"` routing decisions the way TypeSafe Jev does. Because an explicit `routerModel` resolves a classifier before a chat model, `routerModel: "llama.cpp/<id>"` now routes with the classifier instead of the chat model ([#10119](https://github.com/earendil-works/pi/pull/10119)).
+- Packages can contribute MCP servers with `"atomic": { "mcpServers": "./mcp.json" }` or an inline `mcpServers` object, and extensions can add runtime-computed servers with `pi.registerMcpServer(name, config)` from the factory or `session_start`. Contributed servers are the lowest-precedence MCP layer, so a same-named server in any user or project MCP config replaces them. Package filters accept `mcpServers` name patterns, project packages contribute servers only in trusted projects, and workflow stages see the same servers ([#3355](https://github.com/bastani-inc/atomic/issues/3355)).
+
+### Changed
+
+- Recorded Claude Sonnet 5.5 results in the evals snapshot used by automatic model routing: Artificial Analysis Intelligence Index rows for max, xhigh, high, medium and low effort, Cognition FrontierCode 1.1, and Anthropic's published OSWorld, AutomationBench, BenchCAD, Humanity's Last Exam (with tools) and Terminal-Bench-Science scores.
+
+### Fixed
+
+- OpenCode Go now defaults to Kimi K3 (`kimi-k3`). models.dev deprecated Kimi K2.6 for OpenCode Go, which removed it from the built-in catalog, so the previous default no longer resolved.
+- Together now defaults to Kimi K3 (`moonshotai/Kimi-K3`). models.dev removed Kimi K2.6 from Together, which removed it from the built-in catalog, so the previous default no longer resolved.
+- Fixed extension tool schemas leaking TypeBox `~kind`/`~optional` metadata into provider requests, which made Fireworks reject every request with `JSON Schema not supported` ([#3330](https://github.com/bastani-inc/atomic/issues/3330)).
+- Resuming a session no longer appends a spurious system-prompt `tools` update when only the order of the active tools changed, so the resumed session keeps its prompt cache and the model is no longer told that unchanged tools were removed ([#3346](https://github.com/bastani-inc/atomic/issues/3346)).
+- Switching sessions with `/resume` or closing a session before sending a message no longer leaves a header-only session file behind ([#3347](https://github.com/bastani-inc/atomic/issues/3347)).
+- Fixed pasting files copied in Finder with `Ctrl+V` inserting the file icon as an image instead of the file paths. Copied files now paste as their paths, shell-quoted in bash mode, and clipboard read errors are reported instead of pasting the icon ([#10136](https://github.com/earendil-works/pi/pull/10136)).
+
+## [0.9.24-alpha.1] - 2026-09-28
+
+### Added
+
+- Added inherited Claude Sonnet 5.5 support for Anthropic with adaptive thinking, mid-conversation effort, and a 1M context window.
+- llama.cpp models are now also listed as classifier models with the same ID, so a local model can make `model: "auto"` routing decisions the way TypeSafe Jev does. Because an explicit `routerModel` resolves a classifier before a chat model, `routerModel: "llama.cpp/<id>"` now routes with the classifier instead of the chat model ([#10119](https://github.com/earendil-works/pi/pull/10119)).
+- Packages can contribute MCP servers with `"atomic": { "mcpServers": "./mcp.json" }` or an inline `mcpServers` object, and extensions can add runtime-computed servers with `pi.registerMcpServer(name, config)` from the factory or `session_start`. Contributed servers are the lowest-precedence MCP layer, so a same-named server in any user or project MCP config replaces them. Package filters accept `mcpServers` name patterns, project packages contribute servers only in trusted projects, and workflow stages see the same servers ([#3355](https://github.com/bastani-inc/atomic/issues/3355)).
+
+### Changed
+
+- Recorded Claude Sonnet 5.5 results in the evals snapshot used by automatic model routing: Artificial Analysis Intelligence Index rows for max, xhigh, high, medium and low effort, Cognition FrontierCode 1.1, and Anthropic's published OSWorld, AutomationBench, BenchCAD, Humanity's Last Exam (with tools) and Terminal-Bench-Science scores.
+
+### Fixed
+
+- OpenCode Go now defaults to Kimi K3 (`kimi-k3`). models.dev deprecated Kimi K2.6 for OpenCode Go, which removed it from the built-in catalog, so the previous default no longer resolved.
+- Together now defaults to Kimi K3 (`moonshotai/Kimi-K3`). models.dev removed Kimi K2.6 from Together, which removed it from the built-in catalog, so the previous default no longer resolved.
+- Fixed extension tool schemas leaking TypeBox `~kind`/`~optional` metadata into provider requests, which made Fireworks reject every request with `JSON Schema not supported` ([#3330](https://github.com/bastani-inc/atomic/issues/3330)).
+- Resuming a session no longer appends a spurious system-prompt `tools` update when only the order of the active tools changed, so the resumed session keeps its prompt cache and the model is no longer told that unchanged tools were removed ([#3346](https://github.com/bastani-inc/atomic/issues/3346)).
+- Switching sessions with `/resume` or closing a session before sending a message no longer leaves a header-only session file behind ([#3347](https://github.com/bastani-inc/atomic/issues/3347)).
+- Fixed pasting files copied in Finder with `Ctrl+V` inserting the file icon as an image instead of the file paths. Copied files now paste as their paths, shell-quoted in bash mode, and clipboard read errors are reported instead of pasting the icon ([#10136](https://github.com/earendil-works/pi/pull/10136)).
+
 ## [0.9.23] - 2026-09-27
 
 ### Fixed

package/dist/builtin/intercom/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/intercom",
-  "version": "0.9.23",
+  "version": "0.9.24",
   "private": true,
   "description": "Atomic extension providing a private coordination channel between parent and child agent sessions. Fork of: https://github.com/nicobailon/pi-intercom",
   "contributors": [

package/dist/builtin/mcp/CHANGELOG.md

@@ -7,6 +7,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [0.9.24] - 2026-09-29
+
+### Added
+
+- MCP servers contributed by packages and by `pi.registerMcpServer()` load as the lowest-precedence config layer, including registrations made after MCP has started. A same-named server in any MCP config file replaces a contributed one, and `"disabled": true` on a server entry, alone or with other fields, removes it. `/mcp` and connection errors show which package or extension contributed each server ([#3355](https://github.com/bastani-inc/atomic/issues/3355)).
+
+## [0.9.24-alpha.1] - 2026-09-28
+
+### Added
+
+- MCP servers contributed by packages and by `pi.registerMcpServer()` load as the lowest-precedence config layer, including registrations made after MCP has started. A same-named server in any MCP config file replaces a contributed one, and `"disabled": true` on a server entry, alone or with other fields, removes it. `/mcp` and connection errors show which package or extension contributed each server ([#3355](https://github.com/bastani-inc/atomic/issues/3355)).
+
 ## [0.9.20] - 2026-09-24
 
 ### Fixed

package/dist/builtin/mcp/README.md

@@ -141,6 +141,7 @@ Pi-specific files are the write targets for imported or shared global servers wh
 | `directTools` | `true`, `string[]`, or `false` — register tools individually instead of through proxy |
 | `excludeTools` | `string[]` of tool names to hide (matches original names like `get_screenshot` and prefixed names like `figma_get_screenshot`) |
 | `debug` | Show server stderr (default: false) |
+| `disabled` | `true` removes the server from the effective config; `{ "disabled": true }` alone turns off a server contributed by a package or extension |
 
 `timeoutMs` is an **inactivity timeout**, not a total wall-clock limit. Each MCP progress notification resets the timer, so a tool that continues reporting progress can run indefinitely. The value must be a finite number greater than zero; invalid values produce a configuration error when the MCP config loads.
 

package/dist/builtin/mcp/index.bundle.mjs

@@ -6517,15 +6517,51 @@ function getMcpDiscoverySummary(overridePath, cwd = process.cwd()) {
     repoPrompt: detectRepoPrompt(summaryWithoutRepoPrompt, cwd)
   };
 }
-function loadMcpConfig(overridePath, cwd = process.cwd()) {
-  let config = { mcpServers: {} };
+function loadMcpConfig(overridePath, cwd = process.cwd(), contributions = []) {
+  let config = { mcpServers: validateContributedServers(contributions) };
   for (const source of getConfigSources(overridePath, cwd)) {
     const loaded = readValidatedConfig(source.readPath, `MCP config from ${source.readPath}`);
     if (!loaded)
       continue;
     config = mergeConfigs(config, expandImports(loaded, cwd));
   }
-  return config;
+  return withoutDisabledServers(config);
+}
+function describeMcpContributionSource(contribution) {
+  const { origin, sourceInfo } = contribution;
+  if (origin === "package")
+    return `package ${sourceInfo.source}`;
+  return sourceInfo.origin === "package" ? `extension from package ${sourceInfo.source}` : `extension ${sourceInfo.path}`;
+}
+function getContributedServerSources(overridePath, cwd, contributions) {
+  const sources = new Map;
+  if (contributions.length === 0)
+    return sources;
+  for (const [name, provenance] of getServerProvenance(overridePath, cwd, contributions)) {
+    if (provenance.kind === "contributed" && provenance.source)
+      sources.set(name, provenance.source);
+  }
+  return sources;
+}
+function validateContributedServers(contributions) {
+  const servers = {};
+  for (const contribution of contributions) {
+    try {
+      Object.assign(servers, validateMcpServerTimeouts({ [contribution.name]: contribution.config }));
+    } catch (error) {
+      const reason = error instanceof Error ? error.message : String(error);
+      const message = `Ignoring MCP server "${contribution.name}" from ${describeMcpContributionSource(contribution)}: ${reason}`;
+      if (!reportOwnedMcpLog("warn"))
+        console.warn(message);
+    }
+  }
+  return servers;
+}
+function withoutDisabledServers(config) {
+  const enabled = Object.entries(config.mcpServers).filter(([, entry]) => entry.disabled !== true);
+  if (enabled.length === Object.keys(config.mcpServers).length)
+    return config;
+  return { ...config, mcpServers: Object.fromEntries(enabled) };
 }
 function getConfigSources(overridePath, cwd = process.cwd()) {
   const userPath = getPiGlobalConfigPath(overridePath);
@@ -6806,9 +6842,16 @@ function writeSharedServerEntry(filePath, serverName, entry) {
   writeRawConfigObject(filePath, raw);
   return filePath;
 }
-function getServerProvenance(overridePath, cwd = process.cwd()) {
+function getServerProvenance(overridePath, cwd = process.cwd(), contributions = []) {
   const provenance = new Map;
   const userPath = getPiGlobalConfigPath(overridePath);
+  for (const contribution of contributions) {
+    provenance.set(contribution.name, {
+      path: userPath,
+      kind: "contributed",
+      source: describeMcpContributionSource(contribution)
+    });
+  }
   for (const source of getConfigSources(overridePath, cwd)) {
     const loaded = readValidatedConfig(source.readPath, `MCP config from ${source.readPath}`);
     if (!loaded)
@@ -6822,7 +6865,7 @@ function getServerProvenance(overridePath, cwd = process.cwd()) {
           const imported = JSON.parse(readFileSync2(importPath, "utf-8"));
           const servers = extractServers(imported, importKind);
           for (const name of Object.keys(servers)) {
-            if (!provenance.has(name)) {
+            if (!provenance.has(name) || provenance.get(name)?.kind === "contributed") {
               provenance.set(name, { path: userPath, kind: "import", importKind });
             }
           }
@@ -6854,7 +6897,7 @@ function writeDirectToolsConfig(changes, provenance, fullConfig) {
     const raw = readRawConfigObject(filePath);
     const servers = getServersObject(raw);
     for (const { name, value, prov } of entries) {
-      if (prov.kind === "import") {
+      if (prov.kind === "import" || prov.kind === "contributed") {
         const fullDef = fullConfig.mcpServers[name];
         if (fullDef) {
           servers[name] = { ...fullDef, directTools: value };
@@ -7193,6 +7236,11 @@ class McpLifecycleManager {
       this.serverSettings.set(name, settings);
     }
   }
+  unregisterServer(name) {
+    this.allServers.delete(name);
+    this.keepAliveServers.delete(name);
+    this.serverSettings.delete(name);
+  }
   setGlobalIdleTimeout(minutes) {
     this.globalIdleTimeout = minutes * 60 * 1000;
   }
@@ -7200,6 +7248,8 @@ class McpLifecycleManager {
     this.onIdleShutdown = callback;
   }
   startHealthChecks(intervalMs = 30000) {
+    if (this.healthCheckInterval)
+      return;
     this.healthCheckInterval = setInterval(() => {
       this.checkConnections();
     }, intervalMs);
@@ -7238,6 +7288,7 @@ class McpLifecycleManager {
   async gracefulShutdown() {
     if (this.healthCheckInterval) {
       clearInterval(this.healthCheckInterval);
+      this.healthCheckInterval = undefined;
     }
     await this.manager.closeAll();
   }
@@ -22249,7 +22300,9 @@ var init_ui_resource_handler = __esm(() => {
 // dist/builtin/mcp/init.ts
 var exports_init = {};
 __export(exports_init, {
+  applyMcpConfigChanges: () => applyMcpConfigChanges,
   flushMetadataCache: () => flushMetadataCache,
+  formatMcpServerName: () => formatMcpServerName,
   getFailureAgeSeconds: () => getFailureAgeSeconds,
   initializeMcp: () => initializeMcp,
   lazyConnect: () => lazyConnect,
@@ -22260,7 +22313,8 @@ __export(exports_init, {
 import { existsSync as existsSync6 } from "node:fs";
 async function initializeMcp(pi, ctx) {
   const configPath = pi.getFlag("mcp-config");
-  const config = loadMcpConfig(configPath, ctx.cwd);
+  const contributions = pi.getMcpServerContributions?.() ?? [];
+  const config = loadMcpConfig(configPath, ctx.cwd, contributions);
   const manager = new McpServerManager;
   const lifecycle = new McpLifecycleManager(manager);
   try {
@@ -22284,6 +22338,7 @@ async function initializeMcp(pi, ctx) {
       lifecycle,
       toolMetadata,
       config,
+      contributedSources: getContributedServerSources(configPath, ctx.cwd, contributions),
       failureTracker,
       uiResourceHandler,
       consentManager,
@@ -22310,16 +22365,7 @@ async function initializeMcp(pi, ctx) {
     }
     const prefix = config.settings?.toolPrefix ?? "server";
     for (const [name, definition] of serverEntries) {
-      const lifecycleMode = definition.lifecycle ?? "lazy";
-      const idleOverride = definition.idleTimeout ?? (lifecycleMode === "eager" ? 0 : undefined);
-      lifecycle.registerServer(name, definition, idleOverride !== undefined ? { idleTimeout: idleOverride } : undefined);
-      if (lifecycleMode === "keep-alive") {
-        lifecycle.markKeepAlive(name, definition);
-      }
-      if (cache?.servers?.[name] && isServerCacheValid(cache.servers[name], definition)) {
-        const metadata = reconstructToolMetadata(name, cache.servers[name], prefix, definition);
-        toolMetadata.set(name, metadata);
-      }
+      registerServer(state, name, definition, cache, prefix);
     }
     const startupServers = serverEntries.filter(([, definition]) => {
       const mode = definition.lifecycle ?? "lazy";
@@ -22343,7 +22389,7 @@ async function initializeMcp(pi, ctx) {
     for (const { name, definition, connection, error } of results) {
       if (error || !connection) {
         if (ctx.hasUI) {
-          ctx.ui.notify(`MCP: Failed to connect to ${name}: ${error}`, "error");
+          ctx.ui.notify(`MCP: Failed to connect to ${formatMcpServerName(state, name)}: ${error}`, "error");
         }
         reportMcpDiagnostic(pi, "MCP startup connection failed");
         continue;
@@ -22362,18 +22408,7 @@ async function initializeMcp(pi, ctx) {
       const msg = failedCount > 0 ? `MCP: ${connectedCount}/${startupServers.length} servers connected (${totalTools} tools)` : `MCP: ${connectedCount} servers connected (${totalTools} tools)`;
       ctx.ui.notify(msg, "info");
     }
-    lifecycle.setReconnectCallback((serverName) => {
-      updateServerMetadata(state, serverName);
-      updateMetadataCache(state, serverName);
-      state.failureTracker.delete(serverName);
-      updateStatusBar(state);
-    });
-    lifecycle.setIdleShutdownCallback((serverName) => {
-      const idleMinutes = getEffectiveIdleTimeoutMinutes(state, serverName);
-      logger.debug(`${serverName} shut down (idle ${idleMinutes}m)`);
-      updateStatusBar(state);
-    });
-    lifecycle.startHealthChecks();
+    startLifecycle(state);
     return state;
   } catch (error) {
     try {
@@ -22385,6 +22420,61 @@ async function initializeMcp(pi, ctx) {
     throw error;
   }
 }
+function formatMcpServerName(state, name) {
+  const source = state.contributedSources?.get(name);
+  return source ? `${name} (${source})` : name;
+}
+function registerServer(state, name, definition, cache, prefix) {
+  const lifecycleMode = definition.lifecycle ?? "lazy";
+  const idleOverride = definition.idleTimeout ?? (lifecycleMode === "eager" ? 0 : undefined);
+  state.lifecycle.registerServer(name, definition, idleOverride !== undefined ? { idleTimeout: idleOverride } : undefined);
+  if (lifecycleMode === "keep-alive") {
+    state.lifecycle.markKeepAlive(name, definition);
+  }
+  if (cache?.servers?.[name] && isServerCacheValid(cache.servers[name], definition)) {
+    const metadata = reconstructToolMetadata(name, cache.servers[name], prefix, definition);
+    state.toolMetadata.set(name, metadata);
+  }
+}
+function startLifecycle(state) {
+  state.lifecycle.setReconnectCallback((serverName) => {
+    updateServerMetadata(state, serverName);
+    updateMetadataCache(state, serverName);
+    state.failureTracker.delete(serverName);
+    updateStatusBar(state);
+  });
+  state.lifecycle.setIdleShutdownCallback((serverName) => {
+    const idleMinutes = getEffectiveIdleTimeoutMinutes(state, serverName);
+    logger.debug(`${serverName} shut down (idle ${idleMinutes}m)`);
+    updateStatusBar(state);
+  });
+  state.lifecycle.startHealthChecks();
+}
+async function applyMcpConfigChanges(state, configPath, cwd, contributions) {
+  const previous = state.config.mcpServers;
+  const next = loadMcpConfig(configPath, cwd, contributions).mcpServers;
+  const changed = [...new Set([...Object.keys(previous), ...Object.keys(next)])].filter((name) => JSON.stringify(previous[name]) !== JSON.stringify(next[name]));
+  state.config = { ...state.config, mcpServers: next };
+  state.contributedSources = getContributedServerSources(configPath, cwd, contributions);
+  if (changed.length === 0)
+    return changed;
+  const cache = loadMetadataCache();
+  const settings = state.config.settings;
+  const prefix = settings?.toolPrefix ?? "server";
+  state.lifecycle.setGlobalIdleTimeout(typeof settings?.idleTimeout === "number" ? settings.idleTimeout : 10);
+  for (const name of changed) {
+    await state.manager.close(name);
+    state.lifecycle.unregisterServer(name);
+    state.toolMetadata.delete(name);
+    state.failureTracker.delete(name);
+    const definition = next[name];
+    if (definition)
+      registerServer(state, name, definition, cache, prefix);
+  }
+  startLifecycle(state);
+  updateStatusBar(state);
+  return changed;
+}
 function updateServerMetadata(state, serverName) {
   const connection = state.manager.getConnection(serverName);
   if (!connection || connection.status !== "connected")
@@ -23148,6 +23238,7 @@ function buildServerStates(config, cache, provenance, callbacks, authOnly, prefi
       expanded: false,
       source: prov?.kind ?? "user",
       importKind: prov?.importKind,
+      contributedBy: prov?.source,
       excludeTools: definition.excludeTools,
       exposeResources: definition.exposeResources !== false,
       connectionStatus: callbacks.getConnectionStatus(serverName),
@@ -23323,7 +23414,8 @@ function renderServerRow(context, server, isCursor) {
   const expandIcon = server.expanded ? "▾" : "▸";
   const prefix = isCursor ? fg2(t.selected, expandIcon) : fg2(t.border, server.expanded ? expandIcon : "·");
   const nameStr = isCursor ? bold(fg2(t.selected, server.name)) : server.name;
-  const importLabel = server.source === "import" ? fg2(t.description, ` (${server.importKind ?? "import"})`) : "";
+  const originLabel = server.source === "import" ? ` (${server.importKind ?? "import"})` : server.source === "contributed" ? ` (${server.contributedBy ?? "contributed"})` : "";
+  const importLabel = originLabel ? fg2(t.description, originLabel) : "";
   const statusLabel = renderConnectionStatus(context, server);
   if (!server.hasCachedData && !context.authOnly) {
     return `${prefix}   ${nameStr}${importLabel}  ${fg2(t.description, "(not cached)")}${statusLabel}`;
@@ -23692,9 +23784,8 @@ class McpPanel {
     if (item.toolIndex !== undefined) {
       const tool = server.tools[item.toolIndex];
       tool.isDirect = !tool.isDirect;
-      if (tool.isDirect && server.source === "import") {
-        this.importNotice = `Imported from ${server.importKind ?? "external"} — will copy to user config on save`;
-      }
+      if (tool.isDirect)
+        this.noteCopyToUserConfig(server);
       this.updateDirty();
     }
   }
@@ -23748,23 +23839,28 @@ class McpPanel {
       this.tui.requestRender();
     });
   }
+  noteCopyToUserConfig(server) {
+    if (server.source === "import") {
+      this.importNotice = `Imported from ${server.importKind ?? "external"} — will copy to user config on save`;
+    } else if (server.source === "contributed") {
+      this.importNotice = `Contributed by ${server.contributedBy ?? "a package"} — will copy to user config on save`;
+    }
+  }
   toggleItem(item) {
     if (this.authOnly)
       return;
     const server = this.servers[item.serverIndex];
     if (item.type === "server") {
       const newState = !server.tools.every((tool) => tool.isDirect);
-      if (server.source === "import" && newState) {
-        this.importNotice = `Imported from ${server.importKind ?? "external"} — will copy to user config on save`;
-      }
+      if (newState)
+        this.noteCopyToUserConfig(server);
       for (const tool of server.tools)
         tool.isDirect = newState;
     } else if (item.toolIndex !== undefined) {
       const tool = server.tools[item.toolIndex];
       tool.isDirect = !tool.isDirect;
-      if (tool.isDirect && server.source === "import") {
-        this.importNotice = `Imported from ${server.importKind ?? "external"} — will copy to user config on save`;
-      }
+      if (tool.isDirect)
+        this.noteCopyToUserConfig(server);
     }
     this.updateDirty();
   }
@@ -23865,7 +23961,7 @@ async function showStatus(state, ctx) {
       status = "cached";
     }
     const toolSuffix = failed ? "" : ` (${toolCount} tools${status === "cached" ? ", cached" : ""})`;
-    lines.push(`${statusIcon} ${name}: ${status}${toolSuffix}`);
+    lines.push(`${statusIcon} ${formatMcpServerName(state, name)}: ${status}${toolSuffix}`);
   }
   if (Object.keys(state.config.mcpServers).length === 0) {
     lines.push("No MCP servers configured");
@@ -23925,7 +24021,7 @@ async function reconnectServers(state, ctx, targetServer) {
       const message = error instanceof Error ? error.message : String(error);
       state.failureTracker.set(name, Date.now());
       if (ctx.hasUI) {
-        ctx.ui.notify(`MCP: Failed to reconnect to ${name}: ${message}`, "error");
+        ctx.ui.notify(`MCP: Failed to reconnect to ${formatMcpServerName(state, name)}: ${message}`, "error");
       }
     }
   }
@@ -24091,7 +24187,7 @@ async function openMcpPanel(state, pi, ctx, configOverridePath) {
   const config = state.config;
   const cache = loadMetadataCache();
   const configPath = pi.getFlag("mcp-config") ?? configOverridePath;
-  const provenanceMap = getServerProvenance(configPath, ctx.cwd);
+  const provenanceMap = getServerProvenance(configPath, ctx.cwd, pi.getMcpServerContributions?.() ?? []);
   const { lines: noticeLines, fingerprint } = buildSharedConfigNoticeLines(configPath, ctx.cwd);
   const callbacks = buildMcpPanelCallbacks(state, config, ctx);
   await Promise.resolve().then(() => init_mcp_panel());
@@ -24125,7 +24221,7 @@ async function openMcpAuthPanel(state, pi, ctx, configOverridePath) {
   }
   const cache = loadMetadataCache();
   const configPath = pi.getFlag("mcp-config") ?? configOverridePath;
-  const provenanceMap = getServerProvenance(configPath, ctx.cwd);
+  const provenanceMap = getServerProvenance(configPath, ctx.cwd, pi.getMcpServerContributions?.() ?? []);
   const callbacks = buildMcpPanelCallbacks(state, config, ctx);
   await Promise.resolve().then(() => init_mcp_panel());
   await new Promise((resolve) => {
@@ -27076,13 +27172,29 @@ function mcpAdapter(pi) {
   let renderConfig;
   let initPromise = null;
   let lifecycleGeneration = 0;
-  let registeredDirectToolNames = new Set;
+  let registeredDirectTools = new Map;
+  const retiredDirectToolNames = new Set;
   let registeredProxyTool = false;
   let startupWarmupCancel = null;
   let activeSession = null;
   let stateOwner = null;
   const cleanupBarrier = new McpSessionCleanupBarrier;
   const unpublishedCleanupFailures = [];
+  let contributionRevision = 0;
+  let contributionRefresh = Promise.resolve();
+  const getContributions = () => pi.getMcpServerContributions?.() ?? [];
+  const getConfigPath = () => pi.getFlag("mcp-config") ?? earlyConfigPath;
+  function forgetDirectToolRegistrations() {
+    registeredDirectTools = new Map([...registeredDirectTools.keys()].map((name) => [name, ""]));
+  }
+  function startsWithSession(server) {
+    return server?.lifecycle === "eager" || server?.lifecycle === "keep-alive";
+  }
+  function registerProxyToolIfNeeded(config, directToolState) {
+    if (config.settings?.disableProxyTool !== true || directToolState.directToolCount === 0 || directToolState.missingConfiguredDirectToolServers.length > 0) {
+      registerProxyTool();
+    }
+  }
   async function registerDirectToolsFromConfig(config, cache, subagentPolicy) {
     const [{ resolveDirectTools, createDirectToolExecutor, getMissingConfiguredDirectToolServers }, { truncateAtWord }] = await Promise.all([
       Promise.resolve().then(() => (init_direct_tools(), exports_direct_tools)),
@@ -27091,10 +27203,22 @@ function mcpAdapter(pi) {
     const prefix = config.settings?.toolPrefix ?? "server";
     const directTools = subagentPolicy?.mcpDirectTools;
     const directSpecs = resolveDirectTools(config, cache, prefix, directTools === undefined ? undefined : [...directTools]);
+    const resolvedNames = new Set(directSpecs.map((spec) => spec.prefixedName));
+    const obsoleteNames = [...registeredDirectTools.keys()].filter((name) => !resolvedNames.has(name));
+    const revivedNames = directSpecs.map((spec) => spec.prefixedName).filter((name) => retiredDirectToolNames.has(name));
+    const activeNames = new Set(obsoleteNames.length > 0 ? pi.getActiveTools() : []);
+    for (const name of obsoleteNames) {
+      registeredDirectTools.delete(name);
+      if (activeNames.has(name))
+        retiredDirectToolNames.add(name);
+    }
+    for (const name of revivedNames)
+      retiredDirectToolNames.delete(name);
     for (const spec of directSpecs) {
-      if (registeredDirectToolNames.has(spec.prefixedName))
+      const signature = JSON.stringify([spec.serverName, spec.originalName, spec.description, spec.inputSchema]);
+      if (registeredDirectTools.get(spec.prefixedName) === signature)
         continue;
-      registeredDirectToolNames.add(spec.prefixedName);
+      registeredDirectTools.set(spec.prefixedName, signature);
       pi.registerTool({
         name: spec.prefixedName,
         label: `MCP: ${spec.originalName}`,
@@ -27108,6 +27232,10 @@ function mcpAdapter(pi) {
     }
     const refreshTools = pi.refreshTools;
     refreshTools?.();
+    if (obsoleteNames.length > 0 || revivedNames.length > 0) {
+      const obsolete = new Set(obsoleteNames);
+      pi.setActiveTools([...pi.getActiveTools().filter((name) => !obsolete.has(name)), ...revivedNames]);
+    }
     return {
       directToolCount: directSpecs.length,
       missingConfiguredDirectToolServers: getMissingConfiguredDirectToolServers(config, cache, directTools)
@@ -27188,6 +27316,7 @@ function mcpAdapter(pi) {
       throw new Error(`${STALE_INITIALIZATION_PREFIX} before startup`);
     }
     let candidate = null;
+    const revision = contributionRevision;
     try {
       candidate = await initializeMcp(pi, session.ctx);
       const initializedState = candidate;
@@ -27198,9 +27327,7 @@ function mcpAdapter(pi) {
       if (!isCurrentSession(session) || initPromise !== expectedPromise.current) {
         throw new Error(`${STALE_INITIALIZATION_PREFIX} after tool registration`);
       }
-      if (initializedState.config.settings?.disableProxyTool !== true || directToolState.directToolCount === 0 || directToolState.missingConfiguredDirectToolServers.length > 0) {
-        registerProxyTool();
-      }
+      registerProxyToolIfNeeded(initializedState.config, directToolState);
       updateStatusBar(initializedState);
       let cancelWarmup = null;
       const warmup = scheduleMcpStartupWarmup(initializedState, {
@@ -27222,6 +27349,8 @@ function mcpAdapter(pi) {
       startupWarmupCancel = cancelWarmup;
       stateOwner = session;
       state = initializedState;
+      if (revision !== contributionRevision)
+        scheduleContributionRefresh(session);
       return initializedState;
     } catch (error) {
       if (candidate && state !== candidate) {
@@ -27268,6 +27397,56 @@ function mcpAdapter(pi) {
     });
     return attempt;
   }
+  function scheduleContributionRefresh(session) {
+    contributionRefresh = contributionRefresh.then(() => refreshContributedServers(session)).catch((error) => {
+      if (!isCurrentSession(session) || isStaleExtensionContextError(error))
+        return;
+      if (!reportOwnedMcpLog("error"))
+        console.error("MCP: failed to apply contributed MCP server changes", error);
+    });
+  }
+  async function refreshContributedServers(session) {
+    if (!isCurrentSession(session))
+      return;
+    const configPath = getConfigPath();
+    const contributions = getContributions();
+    const current = state;
+    if (current && isOwnedState(current, session)) {
+      await Promise.resolve().then(() => init_init());
+      const changed = await applyMcpConfigChanges(current, configPath, session.ctx.cwd, contributions);
+      renderConfig = current.config;
+      if (!isOwnedState(current, session))
+        return;
+      registerProxyToolIfNeeded(current.config, await registerDirectTools(current, session.ctx.subagentPolicy));
+      for (const name of changed) {
+        if (!startsWithSession(current.config.mcpServers[name]))
+          continue;
+        lazyConnect(current, name).then(async (connected) => {
+          if (!isOwnedState(current, session)) {
+            await current.manager.close(name);
+          } else if (connected) {
+            registerProxyToolIfNeeded(current.config, await registerDirectTools(current, session.ctx.subagentPolicy));
+          } else if (current.failureTracker.has(name)) {
+            current.ui?.notify(`MCP: Failed to connect to ${formatMcpServerName(current, name)}`, "error");
+          }
+        }).catch(() => {
+          return;
+        });
+      }
+      return;
+    }
+    const config = loadMcpConfig(configPath, session.ctx.cwd, contributions);
+    renderConfig = config;
+    await Promise.resolve().then(() => init_metadata_cache());
+    if (!isCurrentSession(session))
+      return;
+    registerProxyToolIfNeeded(config, await registerDirectToolsFromConfig(config, loadMetadataCache()));
+    if (isCurrentSession(session) && !state && !initPromise && Object.values(config.mcpServers).some(startsWithSession)) {
+      ensureMcpInitialized().catch(() => {
+        return;
+      });
+    }
+  }
   pi.on("session_start", async (_event, ctx) => {
     const generation = ++lifecycleGeneration;
     const previousState = state;
@@ -27276,7 +27455,7 @@ function mcpAdapter(pi) {
     renderConfig = undefined;
     stateOwner = null;
     initPromise = null;
-    registeredDirectToolNames = new Set;
+    forgetDirectToolRegistrations();
     cancelStartupWarmup();
     const previousStateCleanup = cleanupSessionResources(previousState, "session_restart", "MCP: failed to shut down previous session state");
     const cleanup = cleanupBarrier.retain([retiredInitialization, previousStateCleanup]);
@@ -27284,8 +27463,9 @@ function mcpAdapter(pi) {
     await cleanup;
     if (!isStartCurrent())
       return;
+    const revision = contributionRevision;
     try {
-      const config = loadMcpConfig(earlyConfigPath, ctx.cwd);
+      const config = loadMcpConfig(earlyConfigPath, ctx.cwd, getContributions());
       await Promise.resolve().then(() => init_metadata_cache());
       if (!isStartCurrent())
         return;
@@ -27293,9 +27473,7 @@ function mcpAdapter(pi) {
       const directToolState = await registerDirectToolsFromConfig(config, loadMetadataCache());
       if (!isStartCurrent())
         return;
-      if (config.settings?.disableProxyTool !== true || directToolState.directToolCount === 0 || directToolState.missingConfiguredDirectToolServers.length > 0) {
-        registerProxyTool();
-      }
+      registerProxyToolIfNeeded(config, directToolState);
     } catch (error) {
       if (!isStartCurrent() || isStaleExtensionContextError(error))
         return;
@@ -27305,12 +27483,20 @@ function mcpAdapter(pi) {
     }
     if (!isStartCurrent())
       return;
-    activeSession = { generation, ctx, cleanup };
-    if (ctx.hasUI || Object.values(renderConfig?.mcpServers ?? {}).some((server) => server.lifecycle === "eager" || server.lifecycle === "keep-alive")) {
+    const session = { generation, ctx, cleanup };
+    activeSession = session;
+    if (ctx.hasUI || Object.values(renderConfig?.mcpServers ?? {}).some(startsWithSession)) {
       ensureMcpInitialized().catch(() => {
         return;
       });
     }
+    if (revision !== contributionRevision)
+      scheduleContributionRefresh(session);
+  });
+  pi.onMcpServerContributionsChanged?.(() => {
+    contributionRevision++;
+    if (activeSession)
+      scheduleContributionRefresh(activeSession);
   });
   pi.on("session_shutdown", async () => {
     ++lifecycleGeneration;
@@ -27321,7 +27507,7 @@ function mcpAdapter(pi) {
     renderConfig = undefined;
     stateOwner = null;
     initPromise = null;
-    registeredDirectToolNames = new Set;
+    forgetDirectToolRegistrations();
     cancelStartupWarmup();
     const stateCleanup = cleanupSessionResources(currentState, "session_shutdown", "MCP: session shutdown cleanup failed");
     const failures = [];

package/dist/builtin/mcp/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/mcp",
-  "version": "0.9.23",
+  "version": "0.9.24",
   "private": true,
   "description": "Atomic extension that adapts MCP (Model Context Protocol) servers into the coding agent. Fork of: https://github.com/nicobailon/pi-mcp-adapter",
   "contributors": [