@bastani/atomic 0.9.25-alpha.3 → 0.9.25-alpha.5

package/dist/builtin/mcp/native-client-licenses/LICENSES/modelcontextprotocol-typescript-sdk.txt

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Anthropic, PBC
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/dist/builtin/mcp/native-client-licenses/NOTICE

@@ -0,0 +1,30 @@
+This directory vendors packages/mcp/src from earendil-works/pi at commit
+8ce69e9d2b171d173fe4b6b2b6256f1f4411e69d:
+https://github.com/earendil-works/pi/tree/8ce69e9d2b171d173fe4b6b2b6256f1f4411e69d/packages/mcp
+
+Relative TypeScript imports use .js extensions for Atomic's compiled package.
+Atomic patches OAuth discovery to refresh changed authorization-server metadata.
+Upstream's license is reproduced below. The additional MCP TypeScript SDK
+notice is retained in LICENSES/modelcontextprotocol-typescript-sdk.txt.
+
+MIT License
+
+Copyright (c) 2025 Mario Zechner
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/dist/builtin/mcp/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@bastani/mcp",
-  "version": "0.9.25-alpha.3",
+  "version": "0.9.25-alpha.5",
   "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",
+  "description": "Atomic's pi-compatible MCP integration for server connections, OAuth, tools, resources, and terminal management.",
   "contributors": [
     "Norin Lavaee",
     "Alex Lavaee"
@@ -18,8 +18,7 @@
     ".": "./index.ts"
   },
   "files": [
-    "*.ts",
-    "app-bridge.bundle.js",
+    "index.ts",
     "README.md",
     "OAUTH.md",
     "CHANGELOG.md",
@@ -31,31 +30,11 @@
     ]
   },
   "peerDependencies": {
-    "@bastani/atomic": "*",
-    "@bastani/pi-ai": "*",
-    "@earendil-works/pi-tui": "^0.99.2",
-    "zod": "^3.25.0 || ^4.0.0",
-    "typebox": "*"
+    "@bastani/atomic": "*"
   },
   "peerDependenciesMeta": {
     "@bastani/atomic": {
       "optional": true
-    },
-    "@bastani/pi-ai": {
-      "optional": true
-    },
-    "@earendil-works/pi-tui": {
-      "optional": true
     }
-  },
-  "dependencies": {
-    "@modelcontextprotocol/ext-apps": "^1.7.5",
-    "@modelcontextprotocol/sdk": "^1.30.0",
-    "open": "^11.0.1",
-    "proper-lockfile": "4.1.2",
-    "zod": "^3.25.0 || ^4.0.0"
-  },
-  "devDependencies": {
-    "@types/proper-lockfile": "4.1.4"
   }
 }

package/dist/builtin/subagents/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/subagents",
-  "version": "0.9.25-alpha.3",
+  "version": "0.9.25-alpha.5",
   "private": true,
   "description": "Atomic extension for delegating tasks to subagents with parallel execution. Fork of: https://github.com/nicobailon/pi-subagents",
   "contributors": [

package/dist/builtin/web-access/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/web-access",
-  "version": "0.9.25-alpha.3",
+  "version": "0.9.25-alpha.5",
   "private": true,
   "description": "Atomic extension for web search, URL fetching, GitHub repo cloning, PDF/video extraction. Fork of: https://github.com/nicobailon/pi-web-access",
   "contributors": [

package/dist/builtin/workflows/CHANGELOG.md

@@ -6,6 +6,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 
 ## [Unreleased]
 
+## [0.9.25-alpha.5] - 2026-09-30
+
+### Fixed
+
+- Pausing a run whose only active stage is waiting for human input now marks the run paused instead of rejecting with `no_active_stages`. An already-open question stays open, questions not yet shown wait until resume, and hosts can hold answers until they resume the run ([#3391](https://github.com/bastani-inc/atomic/issues/3391)).
+
 ## [0.9.25-alpha.3] - 2026-09-30
 
 ### Added

package/dist/builtin/workflows/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@bastani/workflows",
-  "version": "0.9.25-alpha.3",
+  "version": "0.9.25-alpha.5",
   "private": true,
   "description": "Atomic extension for multi-stage workflow authoring and execution.",
   "contributors": [

package/dist/builtin/workflows/src/extension/index.bundle.mjs

@@ -92555,7 +92555,8 @@ async function pauseRunWithAction(runId, opts, action = "pause") {
     const toolControls = opts?.toolControlRegistry ?? toolControlRegistry;
     const runtimeControls = ownedRuntimeControls(activeStore, toolControls, runId);
     const activeRunIds = new Set([...controlRunIds, ...runtimeControls.map(({ controlRunId }) => controlRunId)]);
-    if (runtimeControls.some(({ controlRunId }) => controlRunId === runId) && [...activeRunIds].every((id) => toolControls.active(id).length === 0 && registry.run(id).stages().length === 0)) {
+    const stageHandles = [...activeRunIds].flatMap((id) => registry.run(id).stages());
+    if (runtimeControls.some(({ controlRunId }) => controlRunId === runId) && [...activeRunIds].every((id) => toolControls.active(id).length === 0) && stageHandles.every((handle) => handle.status === "awaiting_input") && (stageHandles.length === 0 || !isRunFullyPaused(activeStore, runId, controlRunIds))) {
       await Promise.all(runtimeControls.map(({ handle }) => handle.pause()));
       activeStore.recordRunPaused(runId);
       return {
@@ -92565,6 +92566,14 @@ async function pauseRunWithAction(runId, opts, action = "pause") {
         message: `Run ${runId} paused (${run.controlPersistence ?? "observed"}). ${run.controlPersistence === "durable" ? "Database persistence confirmed." : "Pause observed locally, not confirmed persisted."} Resume with /workflow resume on this live process; untracked initialization or workflow code may still finish, but further workflow steps and completion wait for resume. Cross-process resume requires durable checkpoint or pending prompt progress.`
       };
     }
+    const controlRuns = activeStore.runs().filter((candidate) => controlRunIds.includes(candidate.id));
+    const waitingRuns = controlRuns.filter((candidate) => candidate.stages.some((stage) => stage.status === "awaiting_input"));
+    if (runtimeControls.length === 0 && waitingRuns.length > 0 && !isRunFullyPaused(activeStore, runId, controlRunIds) && controlRuns.every((candidate) => candidate.stages.every((stage) => stage.status !== "running" && stage.status !== "pending")) && [...activeRunIds].every((id) => toolControls.active(id).length === 0)) {
+      for (const waitingRun of waitingRuns)
+        activeStore.recordRunPaused(waitingRun.id);
+      activeStore.recordRunPaused(runId);
+      return { ok: true, runId, paused: [] };
+    }
     return {
       ok: false,
       runId,
@@ -116513,7 +116522,7 @@ function bindWorkflowHumanInput(store, ctx, stageUiBroker = currentStageUiBroker
       return;
     const pending = new Set;
     for (const run of store.runs()) {
-      if (run.status !== "running")
+      if (run.status !== "running" && run.status !== "paused")
         continue;
       for (const stage of run.stages) {
         if (stage.status !== "awaiting_input")
@@ -116533,13 +116542,19 @@ function bindWorkflowHumanInput(store, ctx, stageUiBroker = currentStageUiBroker
         const ownBinding = childInput?.usesOwnBinding() === true;
         const input = ownBinding ? workflowInputBridge(childInput.ui) : ownerInput;
         const available = ownBinding ? input?.available() : ctx.hasUI === false && ctx.hasHumanInput === true;
-        if (requests.has(key) || !available)
+        if (requests.has(key) || run.status === "paused" || !available)
           continue;
         const controller = new AbortController;
         requests.set(key, { controller, ownBinding });
         Promise.resolve().then(async () => {
           if (controller.signal.aborted)
             return;
+          if (store.runs().find((candidate) => candidate.id === run.id)?.status !== "running") {
+            if (requests.get(key)?.controller === controller)
+              requests.delete(key);
+            controller.abort();
+            return;
+          }
           try {
             const scoped = input?.scope(run.id, stage.id, questionnaire?.sessionId);
             if (questionnaire) {

package/dist/cli/args.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"args.d.ts","sourceRoot":"","sources":["../../src/cli/args.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,+BAA+B,CAAC;AAYnE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,6BAA6B,CAAC;AAEjE,MAAM,MAAM,IAAI,GAAG,MAAM,GAAG,MAAM,GAAG,KAAK,CAAC;AAE3C,MAAM,WAAW,IAAI;IACpB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,kBAAkB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC9B,QAAQ,CAAC,EAAE,aAAa,CAAC;IACzB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,IAAI,CAAC,EAAE,OAAO,CAAC;IACf,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,IAAI,CAAC,EAAE,IAAI,CAAC;IACZ,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,EAAE,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,EAAE,CAAC;IACxB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,UAAU,CAAC,EAAE,MAAM,EAAE,CAAC;IACtB,YAAY,CAAC,EAAE,OAAO,CAAC;IACvB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,eAAe,CAAC,EAAE,MAAM,EAAE,CAAC;IAC3B,iBAAiB,CAAC,EAAE,OAAO,CAAC;IAC5B,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,cAAc,CAAC,EAAE,OAAO,CAAC;IACzB,UAAU,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,OAAO,CAAC,EAAE,OAAO,CAAC;IAClB,oBAAoB,CAAC,EAAE,OAAO,CAAC;IAC/B,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,QAAQ,EAAE,MAAM,EAAE,CAAC;IACnB,8EAA8E;IAC9E,YAAY,EAAE,GAAG,CAAC,MAAM,EAAE,OAAO,GAAG,MAAM,CAAC,CAAC;IAC5C,WAAW,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,SAAS,GAAG,OAAO,CAAC;QAAC,OAAO,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CACnE;AAID,wBAAgB,oBAAoB,CAAC,KAAK,EAAE,MAAM,GAAG,KAAK,IAAI,aAAa,CAE1E;AAED;;;;;;GAMG;AACH,wBAAgB,mCAAmC,CAAC,IAAI,EAAE,MAAM,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,EAAE,CAI9F;AAED,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG,IAAI,CA0K9C;AAED,wBAAgB,SAAS,CAAC,cAAc,CAAC,EAAE,aAAa,EAAE,GAAG,IAAI,CAwMhE"}

package/dist/cli/args.js

@@ -257,7 +257,8 @@ ${chalk.bold("Commands:")}
   ${APP_NAME} list                      List installed extensions from settings
   ${APP_NAME} config [-l]               Open resource TUI (Tab switches global/project scope)
   ${APP_NAME} auth <command>            Print credentials or check provider readiness
-  ${APP_NAME} <command> --help          Show help for install/remove/uninstall/update/list/config/auth
+  ${APP_NAME} mcp <command>             Configure MCP servers, check connections, and sign in
+  ${APP_NAME} <command> --help          Show help for install/remove/uninstall/update/list/config/auth/mcp
 
 ${chalk.bold("Options:")}
   --provider <name>              Provider name (default: google)

package/dist/cli/args.js.map

@@ -1 +1 @@
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[];\n\t\t\tresult.skills.push(args[++i]);\n\t\t} else if (arg === \"--prompt-template\" && i + 1 < args.length) {\n\t\t\tresult.promptTemplates = result.promptTemplates ?? [];\n\t\t\tresult.promptTemplates.push(args[++i]);\n\t\t} else if (arg === \"--theme\" && i + 1 < args.length) {\n\t\t\tresult.themes = result.themes ?? [];\n\t\t\tresult.themes.push(args[++i]);\n\t\t} else if (arg === \"--use-theme\") {\n\t\t\tconst themeName = args[i + 1];\n\t\t\tif (themeName === undefined || themeName.startsWith(\"-\")) {\n\t\t\t\tresult.diagnostics.push({ type: \"error\", message: \"--use-theme requires a theme name\" });\n\t\t\t} else {\n\t\t\t\tresult.useTheme = themeName;\n\t\t\t\ti++;\n\t\t\t}\n\t\t} else if (arg === \"--no-skills\" || arg === \"-ns\") {\n\t\t\tresult.noSkills = true;\n\t\t} else if (arg === \"--no-prompt-templates\" || arg === \"-np\") {\n\t\t\tresult.noPromptTemplates = true;\n\t\t} else if (arg === \"--no-themes\") {\n\t\t\tresult.noThemes = true;\n\t\t} else if (arg === \"--no-context-files\" || arg === \"-nc\") {\n\t\t\tresult.noContextFiles = true;\n\t\t} else if (arg === \"--list-models\") {\n\t\t\t// Check if next arg is a search pattern (not a flag or file arg)\n\t\t\tif (i + 1 < args.length && !args[i + 1].startsWith(\"-\") && !args[i + 1].startsWith(\"@\")) {\n\t\t\t\tresult.listModels = args[++i];\n\t\t\t} else {\n\t\t\t\tresult.listModels = true;\n\t\t\t}\n\t\t} else if (arg === \"--verbose\") {\n\t\t\tresult.verbose = true;\n\t\t} else if (arg === \"--approve\" || arg === \"-a\") {\n\t\t\tresult.projectTrustOverride = true;\n\t\t} else if (arg === \"--no-approve\" || arg === \"-na\") {\n\t\t\tresult.projectTrustOverride = false;\n\t\t} else if (arg === \"--offline\") {\n\t\t\tresult.offline = true;\n\t\t} else if (arg.startsWith(\"@\")) {\n\t\t\tresult.fileArgs.push(arg.slice(1)); // Remove @ prefix\n\t\t} else if (arg.startsWith(\"--\")) {\n\t\t\tconst eqIndex = arg.indexOf(\"=\");\n\t\t\tif (eqIndex !== -1) {\n\t\t\t\tresult.unknownFlags.set(arg.slice(2, eqIndex), arg.slice(eqIndex + 1));\n\t\t\t} else {\n\t\t\t\tconst flagName = arg.slice(2);\n\t\t\t\tconst next = args[i + 1];\n\t\t\t\tif (next !== undefined && !next.startsWith(\"-\") && !next.startsWith(\"@\")) {\n\t\t\t\t\tresult.unknownFlags.set(flagName, next);\n\t\t\t\t\ti++;\n\t\t\t\t} else {\n\t\t\t\t\tresult.unknownFlags.set(flagName, true);\n\t\t\t\t}\n\t\t\t}\n\t\t} else if (arg.startsWith(\"-\") && !arg.startsWith(\"--\")) {\n\t\t\tresult.diagnostics.push({ type: \"error\", message: `Unknown option: ${arg}` });\n\t\t} else if (!arg.startsWith(\"-\")) {\n\t\t\tresult.messages.push(arg);\n\t\t}\n\t}\n\n\treturn result;\n}\n\nexport function printHelp(extensionFlags?: ExtensionFlag[]): void {\n\tconst extensionFlagsText =\n\t\textensionFlags && extensionFlags.length > 0\n\t\t\t? `\\n${chalk.bold(\"Extension CLI Flags:\")}\\n${extensionFlags\n\t\t\t\t\t.map((flag) => {\n\t\t\t\t\t\tconst value = flag.type === \"string\" ? \" <value>\" : \"\";\n\t\t\t\t\t\tconst description = flag.description ?? `Registered by ${flag.extensionPath}`;\n\t\t\t\t\t\treturn `  --${flag.name}${value}`.padEnd(30) + description;\n\t\t\t\t\t})\n\t\t\t\t\t.join(\"\\n\")}\\n`\n\t\t\t: \"\";\n\tconsole.log(`${chalk.bold(APP_NAME)} - AI coding assistant with read, bash, edit, write, find, search, ask_user_question, todo tools\n\n${chalk.bold(\"Usage:\")}\n  ${APP_NAME} [options] [--] [@files...] [messages...]\n\n${chalk.bold(\"Commands:\")}\n  ${APP_NAME} install <source> [-l]     Install extension source and add to settings\n  ${APP_NAME} remove <source> [-l]      Remove extension source from settings\n  ${APP_NAME} uninstall <source> [-l]   Alias for remove\n  ${APP_NAME} update [source|self|${APP_NAME}] [--all]   Update ${APP_NAME} (use --all for ${APP_NAME} and extensions)\n  ${APP_NAME} list                      List installed extensions from settings\n  ${APP_NAME} config [-l]               Open resource TUI (Tab switches global/project scope)\n  ${APP_NAME} auth <command>            Print credentials or check provider readiness\n  ${APP_NAME} <command> --help          Show help for install/remove/uninstall/update/list/config/auth\n\n${chalk.bold(\"Options:\")}\n  --provider <name>              Provider name (default: google)\n  --model <pattern>              Model pattern or ID (supports \"provider/id\" and optional \":<thinking>\")\n  --api-key <key>                API key (defaults to env vars)\n  --system-prompt <text>         System prompt (default: coding assistant prompt)\n  --append-system-prompt <text>  Append text or file contents to the system prompt (can be used multiple times)\n  --mode <mode>                  Output mode: text (default), json, or rpc\n  --print, -p                    Non-interactive mode: process prompt and exit\n  --continue, -c                 Continue previous session\n  --resume, -r                   Select a session to resume\n  --session <path|id>            Use file, exact ID, or unique 8-hex UUID prefix\n  --session-id <id>              Use exact project session ID, creating it if missing\n  --fork <path|id>               Fork file, exact ID, or unique 8-hex UUID prefix into a new session\n  --session-dir <dir>            Directory for session storage and lookup\n  --no-session                   Don't save session (ephemeral)\n  --name, -n <name>              Set session display name\n  --models <patterns>            Comma-separated model patterns for ctrl+p cycling\n                                 Supports globs (anthropic/*, *sonnet*) and fuzzy matching\n  --no-tools, -nt                Disable every tool except mandatory ordinary intercom\n  --no-builtin-tools, -nbt       Disable built-in tools by default but keep extension/custom tools enabled\n  --tools, -t <tools>            Comma-separated allowlist of non-mandatory tool names\n                                 Mandatory ordinary intercom remains available\n  --exclude-tools, -xt <tools>   Comma-separated denylist of non-mandatory tool names\n                                 Mandatory ordinary intercom cannot be excluded\n  --thinking <level>             Set thinking level: off, minimal, low, medium, high, xhigh, max\n  --extension, -e <path>         Load an extension file (can be used multiple times)\n  --no-extensions, -ne           Disable optional extension discovery; mandatory bundled Intercom remains loaded\n  --skill <path>                 Load a skill file or directory (can be used multiple times)\n  --no-skills, -ns               Disable skills discovery and loading\n  --prompt-template <path>       Load a prompt template file or directory (can be used multiple times)\n  --no-prompt-templates, -np     Disable prompt template discovery and loading\n  --theme <path>                 Load a theme file or directory (can be used multiple times)\n  --use-theme <name[/name]>      Set the interactive theme for this run without saving it\n  --no-themes                    Disable theme discovery and loading\n  --no-context-files, -nc        Disable context-file discovery and loading\n  --export <file>                Export session file to HTML and exit\n  --list-models [search]         List available models (with optional fuzzy search)\n  --verbose                      Force verbose startup (overrides quietStartup setting)\n  --approve, -a                  Trust project-local files for this run\n  --no-approve, -na              Ignore project-local files for this run\n  --offline                      Disable startup network operations (same as ${ENV_OFFLINE}=1)\n  --                             End option parsing; treat remaining arguments as messages/files\n  --help, -h                     Show this help\n  --version, -v                  Show version number\n\nExtensions can register additional flags (e.g., --plan from plan-mode extension).${extensionFlagsText}\n\n${chalk.bold(\"Examples:\")}\n  # Print a provider API key for an external client\n  ${APP_NAME} auth print-api-key --model gpt-5.5 --provider openai\n\n  # Check configured provider readiness before starting a session\n  ${APP_NAME} auth check --provider openai\n\n  # Print an OAuth bearer token, refreshing it when under the minimum expiry\n  ${APP_NAME} auth print-bearer-token --model gpt-5.5 --provider openai-codex --min-expiry 30m\n\n  # Interactive mode\n  ${APP_NAME}\n\n  # Interactive mode with initial prompt\n  ${APP_NAME} \"List all .ts files in src/\"\n\n  # Include files in initial message\n  ${APP_NAME} @prompt.md @image.png \"What color is the sky?\"\n\n  # Non-interactive mode (process and exit)\n  ${APP_NAME} -p \"List all .ts files in src/\"\n\n  # Prompt beginning with a dash\n  ${APP_NAME} -p -- \"- Summarize these points\"\n\n  # Multiple messages (interactive)\n  ${APP_NAME} \"Read package.json\" \"What dependencies do we have?\"\n\n  # Continue previous session\n  ${APP_NAME} --continue \"What did we discuss?\"\n\n  # Start a named session\n  ${APP_NAME} --name \"Refactor auth module\"\n\n  # Use different model\n  ${APP_NAME} --provider openai --model gpt-4o-mini \"Help me refactor this code\"\n\n  # Use model with provider prefix (no --provider needed)\n  ${APP_NAME} --model openai/gpt-4o \"Help me refactor this code\"\n\n  # Use model with thinking level shorthand\n  ${APP_NAME} --model sonnet:high \"Solve this complex problem\"\n\n  # Limit model cycling to specific models\n  ${APP_NAME} --models claude-sonnet,claude-haiku,gpt-4o\n\n  # Limit to a specific provider with glob pattern\n  ${APP_NAME} --models \"github-copilot/*\"\n\n  # Cycle models with fixed thinking levels\n  ${APP_NAME} --models sonnet:high,haiku:low\n\n  # Start with a specific thinking level\n  ${APP_NAME} --thinking high \"Solve this complex problem\"\n\n  # Read-only mode (no file modifications possible)\n  ${APP_NAME} --tools read,search,find,ls -p \"Review the code in src/\"\n\n  # Disable one tool while keeping the rest available\n  ${APP_NAME} --exclude-tools ask_user_question\n\n  # Export a session file to HTML\n  ${APP_NAME} --export ~/${CONFIG_DIR_NAME}/agent/sessions/--path--/session.jsonl\n  ${APP_NAME} --export session.jsonl output.html\n\n${chalk.bold(\"Environment Variables:\")}\n  ANTHROPIC_AUTH_TOKEN             - Anthropic bearer auth token\n  ANTHROPIC_API_KEY                - Anthropic Claude API key\n  ANTHROPIC_OAUTH_TOKEN            - Anthropic OAuth token (alternative to API key)\n  OPENAI_API_KEY                   - OpenAI GPT API key\n  AZURE_OPENAI_API_KEY             - Azure OpenAI API key\n  AZURE_OPENAI_BASE_URL            - Azure OpenAI/Cognitive Services base URL (e.g. https://{resource}.openai.azure.com)\n  AZURE_OPENAI_RESOURCE_NAME       - Azure OpenAI resource name (alternative to base URL)\n  AZURE_OPENAI_API_VERSION         - Azure OpenAI API version (default: v1)\n  AZURE_OPENAI_DEPLOYMENT_NAME_MAP - Azure OpenAI model=deployment map (comma-separated)\n  DEEPSEEK_API_KEY                 - DeepSeek API key\n  GEMINI_API_KEY                   - Google Gemini API key\n  GROQ_API_KEY                     - Groq API key\n  CEREBRAS_API_KEY                 - Cerebras API key\n  XAI_API_KEY                      - xAI Grok API key\n  FIREWORKS_API_KEY                - Fireworks API key\n  TOGETHER_API_KEY                 - Together AI API key\n  BASETEN_API_KEY                  - Baseten API key\n  OPENROUTER_API_KEY               - OpenRouter API key\n  AI_GATEWAY_API_KEY               - Vercel AI Gateway API key\n  ZAI_API_KEY                      - ZAI API key\n  MISTRAL_API_KEY                  - Mistral API key\n  MINIMAX_API_KEY                  - MiniMax API key\n  MOONSHOT_API_KEY                 - Moonshot AI API key\n  OPENCODE_API_KEY                 - OpenCode Zen/OpenCode Go API key\n  KIMI_API_KEY                     - Kimi For Coding API key\n  META_API_KEY                     - Meta Model API key\n  CLOUDFLARE_API_KEY               - Cloudflare API token (Workers AI and AI Gateway)\n  CLOUDFLARE_ACCOUNT_ID            - Cloudflare account id (required for both)\n  CLOUDFLARE_GATEWAY_ID            - Cloudflare AI Gateway slug (required for AI Gateway)\n  QWEN_TOKEN_PLAN_API_KEY          - Qwen Token Plan API key (international region)\n  QWEN_TOKEN_PLAN_CN_API_KEY       - Qwen Token Plan API key (China region)\n  XIAOMI_API_KEY                   - Xiaomi MiMo API key (api.xiaomimimo.com billing)\n  XIAOMI_TOKEN_PLAN_CN_API_KEY     - Xiaomi MiMo Token Plan API key (China region)\n  XIAOMI_TOKEN_PLAN_AMS_API_KEY    - Xiaomi MiMo Token Plan API key (Amsterdam region)\n  XIAOMI_TOKEN_PLAN_SGP_API_KEY    - Xiaomi MiMo Token Plan API key (Singapore region)\n  AWS_PROFILE                      - AWS profile for Amazon Bedrock\n  AWS_ACCESS_KEY_ID                - AWS access key for Amazon Bedrock\n  AWS_SECRET_ACCESS_KEY            - AWS secret key for Amazon Bedrock\n  AWS_BEARER_TOKEN_BEDROCK         - Bedrock API key (bearer token)\n  AWS_REGION                       - AWS region for Amazon Bedrock (e.g., us-east-1)\n  ${ENV_AGENT_DIR.padEnd(32)} - Config directory (default: ~/${CONFIG_DIR_NAME}/agent)\n  ${ENV_SESSION_DIR.padEnd(32)} - Session storage directory (overridden by --session-dir)\n  ${ENV_PACKAGE_DIR.padEnd(32)} - Override package directory (for Nix/Guix store paths)\n  ${ENV_OFFLINE.padEnd(32)} - Disable startup network operations when set to 1/true/yes\n  ${ENV_TELEMETRY.padEnd(32)} - Override install telemetry when set to 1/true/yes or 0/false/no\n  ${ENV_SHARE_VIEWER_URL.padEnd(32)} - Base URL for /share command (default: https://pi.dev/session/)\n  PI_* aliases are also supported for app-specific variables above.\n\n${chalk.bold(\"Built-in Tool Names:\")}\n  read              - Read path selectors (files, dirs, archives, URLs)\n  bash              - Execute shell commands\n  powershell        - Execute PowerShell commands on Windows\n  edit              - Apply hashline-anchored source edits\n  write             - Create or overwrite writable path selectors\n  find              - Find filesystem paths by glob pattern (default)\n  search            - Search file contents with regex (default)\n  ask_user_question - Ask structured questions in the TUI (default)\n  todo              - Manage file-based todos (default)\n  ls                - Legacy directory listing helper (read-only, off by default)\n`);\n}\n"]}
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[];\n\t\t\tresult.skills.push(args[++i]);\n\t\t} else if (arg === \"--prompt-template\" && i + 1 < args.length) {\n\t\t\tresult.promptTemplates = result.promptTemplates ?? [];\n\t\t\tresult.promptTemplates.push(args[++i]);\n\t\t} else if (arg === \"--theme\" && i + 1 < args.length) {\n\t\t\tresult.themes = result.themes ?? [];\n\t\t\tresult.themes.push(args[++i]);\n\t\t} else if (arg === \"--use-theme\") {\n\t\t\tconst themeName = args[i + 1];\n\t\t\tif (themeName === undefined || themeName.startsWith(\"-\")) {\n\t\t\t\tresult.diagnostics.push({ type: \"error\", message: \"--use-theme requires a theme name\" });\n\t\t\t} else {\n\t\t\t\tresult.useTheme = themeName;\n\t\t\t\ti++;\n\t\t\t}\n\t\t} else if (arg === \"--no-skills\" || arg === \"-ns\") {\n\t\t\tresult.noSkills = true;\n\t\t} else if (arg === \"--no-prompt-templates\" || arg === \"-np\") {\n\t\t\tresult.noPromptTemplates = true;\n\t\t} else if (arg === \"--no-themes\") {\n\t\t\tresult.noThemes = true;\n\t\t} else if (arg === \"--no-context-files\" || arg === \"-nc\") {\n\t\t\tresult.noContextFiles = true;\n\t\t} else if (arg === \"--list-models\") {\n\t\t\t// Check if next arg is a search pattern (not a flag or file arg)\n\t\t\tif (i + 1 < args.length && !args[i + 1].startsWith(\"-\") && !args[i + 1].startsWith(\"@\")) {\n\t\t\t\tresult.listModels = args[++i];\n\t\t\t} else {\n\t\t\t\tresult.listModels = true;\n\t\t\t}\n\t\t} else if (arg === \"--verbose\") {\n\t\t\tresult.verbose = true;\n\t\t} else if (arg === \"--approve\" || arg === \"-a\") {\n\t\t\tresult.projectTrustOverride = true;\n\t\t} else if (arg === \"--no-approve\" || arg === \"-na\") {\n\t\t\tresult.projectTrustOverride = false;\n\t\t} else if (arg === \"--offline\") {\n\t\t\tresult.offline = true;\n\t\t} else if (arg.startsWith(\"@\")) {\n\t\t\tresult.fileArgs.push(arg.slice(1)); // Remove @ prefix\n\t\t} else if (arg.startsWith(\"--\")) {\n\t\t\tconst eqIndex = arg.indexOf(\"=\");\n\t\t\tif (eqIndex !== -1) {\n\t\t\t\tresult.unknownFlags.set(arg.slice(2, eqIndex), arg.slice(eqIndex + 1));\n\t\t\t} else {\n\t\t\t\tconst flagName = arg.slice(2);\n\t\t\t\tconst next = args[i + 1];\n\t\t\t\tif (next !== undefined && !next.startsWith(\"-\") && !next.startsWith(\"@\")) {\n\t\t\t\t\tresult.unknownFlags.set(flagName, next);\n\t\t\t\t\ti++;\n\t\t\t\t} else {\n\t\t\t\t\tresult.unknownFlags.set(flagName, true);\n\t\t\t\t}\n\t\t\t}\n\t\t} else if (arg.startsWith(\"-\") && !arg.startsWith(\"--\")) {\n\t\t\tresult.diagnostics.push({ type: \"error\", message: `Unknown option: ${arg}` });\n\t\t} else if (!arg.startsWith(\"-\")) {\n\t\t\tresult.messages.push(arg);\n\t\t}\n\t}\n\n\treturn result;\n}\n\nexport function printHelp(extensionFlags?: ExtensionFlag[]): void {\n\tconst extensionFlagsText =\n\t\textensionFlags && extensionFlags.length > 0\n\t\t\t? `\\n${chalk.bold(\"Extension CLI Flags:\")}\\n${extensionFlags\n\t\t\t\t\t.map((flag) => {\n\t\t\t\t\t\tconst value = flag.type === \"string\" ? \" <value>\" : \"\";\n\t\t\t\t\t\tconst description = flag.description ?? `Registered by ${flag.extensionPath}`;\n\t\t\t\t\t\treturn `  --${flag.name}${value}`.padEnd(30) + description;\n\t\t\t\t\t})\n\t\t\t\t\t.join(\"\\n\")}\\n`\n\t\t\t: \"\";\n\tconsole.log(`${chalk.bold(APP_NAME)} - AI coding assistant with read, bash, edit, write, find, search, ask_user_question, todo tools\n\n${chalk.bold(\"Usage:\")}\n  ${APP_NAME} [options] [--] [@files...] [messages...]\n\n${chalk.bold(\"Commands:\")}\n  ${APP_NAME} install <source> [-l]     Install extension source and add to settings\n  ${APP_NAME} remove <source> [-l]      Remove extension source from settings\n  ${APP_NAME} uninstall <source> [-l]   Alias for remove\n  ${APP_NAME} update [source|self|${APP_NAME}] [--all]   Update ${APP_NAME} (use --all for ${APP_NAME} and extensions)\n  ${APP_NAME} list                      List installed extensions from settings\n  ${APP_NAME} config [-l]               Open resource TUI (Tab switches global/project scope)\n  ${APP_NAME} auth <command>            Print credentials or check provider readiness\n  ${APP_NAME} mcp <command>             Configure MCP servers, check connections, and sign in\n  ${APP_NAME} <command> --help          Show help for install/remove/uninstall/update/list/config/auth/mcp\n\n${chalk.bold(\"Options:\")}\n  --provider <name>              Provider name (default: google)\n  --model <pattern>              Model pattern or ID (supports \"provider/id\" and optional \":<thinking>\")\n  --api-key <key>                API key (defaults to env vars)\n  --system-prompt <text>         System prompt (default: coding assistant prompt)\n  --append-system-prompt <text>  Append text or file contents to the system prompt (can be used multiple times)\n  --mode <mode>                  Output mode: text (default), json, or rpc\n  --print, -p                    Non-interactive mode: process prompt and exit\n  --continue, -c                 Continue previous session\n  --resume, -r                   Select a session to resume\n  --session <path|id>            Use file, exact ID, or unique 8-hex UUID prefix\n  --session-id <id>              Use exact project session ID, creating it if missing\n  --fork <path|id>               Fork file, exact ID, or unique 8-hex UUID prefix into a new session\n  --session-dir <dir>            Directory for session storage and lookup\n  --no-session                   Don't save session (ephemeral)\n  --name, -n <name>              Set session display name\n  --models <patterns>            Comma-separated model patterns for ctrl+p cycling\n                                 Supports globs (anthropic/*, *sonnet*) and fuzzy matching\n  --no-tools, -nt                Disable every tool except mandatory ordinary intercom\n  --no-builtin-tools, -nbt       Disable built-in tools by default but keep extension/custom tools enabled\n  --tools, -t <tools>            Comma-separated allowlist of non-mandatory tool names\n                                 Mandatory ordinary intercom remains available\n  --exclude-tools, -xt <tools>   Comma-separated denylist of non-mandatory tool names\n                                 Mandatory ordinary intercom cannot be excluded\n  --thinking <level>             Set thinking level: off, minimal, low, medium, high, xhigh, max\n  --extension, -e <path>         Load an extension file (can be used multiple times)\n  --no-extensions, -ne           Disable optional extension discovery; mandatory bundled Intercom remains loaded\n  --skill <path>                 Load a skill file or directory (can be used multiple times)\n  --no-skills, -ns               Disable skills discovery and loading\n  --prompt-template <path>       Load a prompt template file or directory (can be used multiple times)\n  --no-prompt-templates, -np     Disable prompt template discovery and loading\n  --theme <path>                 Load a theme file or directory (can be used multiple times)\n  --use-theme <name[/name]>      Set the interactive theme for this run without saving it\n  --no-themes                    Disable theme discovery and loading\n  --no-context-files, -nc        Disable context-file discovery and loading\n  --export <file>                Export session file to HTML and exit\n  --list-models [search]         List available models (with optional fuzzy search)\n  --verbose                      Force verbose startup (overrides quietStartup setting)\n  --approve, -a                  Trust project-local files for this run\n  --no-approve, -na              Ignore project-local files for this run\n  --offline                      Disable startup network operations (same as ${ENV_OFFLINE}=1)\n  --                             End option parsing; treat remaining arguments as messages/files\n  --help, -h                     Show this help\n  --version, -v                  Show version number\n\nExtensions can register additional flags (e.g., --plan from plan-mode extension).${extensionFlagsText}\n\n${chalk.bold(\"Examples:\")}\n  # Print a provider API key for an external client\n  ${APP_NAME} auth print-api-key --model gpt-5.5 --provider openai\n\n  # Check configured provider readiness before starting a session\n  ${APP_NAME} auth check --provider openai\n\n  # Print an OAuth bearer token, refreshing it when under the minimum expiry\n  ${APP_NAME} auth print-bearer-token --model gpt-5.5 --provider openai-codex --min-expiry 30m\n\n  # Interactive mode\n  ${APP_NAME}\n\n  # Interactive mode with initial prompt\n  ${APP_NAME} \"List all .ts files in src/\"\n\n  # Include files in initial message\n  ${APP_NAME} @prompt.md @image.png \"What color is the sky?\"\n\n  # Non-interactive mode (process and exit)\n  ${APP_NAME} -p \"List all .ts files in src/\"\n\n  # Prompt beginning with a dash\n  ${APP_NAME} -p -- \"- Summarize these points\"\n\n  # Multiple messages (interactive)\n  ${APP_NAME} \"Read package.json\" \"What dependencies do we have?\"\n\n  # Continue previous session\n  ${APP_NAME} --continue \"What did we discuss?\"\n\n  # Start a named session\n  ${APP_NAME} --name \"Refactor auth module\"\n\n  # Use different model\n  ${APP_NAME} --provider openai --model gpt-4o-mini \"Help me refactor this code\"\n\n  # Use model with provider prefix (no --provider needed)\n  ${APP_NAME} --model openai/gpt-4o \"Help me refactor this code\"\n\n  # Use model with thinking level shorthand\n  ${APP_NAME} --model sonnet:high \"Solve this complex problem\"\n\n  # Limit model cycling to specific models\n  ${APP_NAME} --models claude-sonnet,claude-haiku,gpt-4o\n\n  # Limit to a specific provider with glob pattern\n  ${APP_NAME} --models \"github-copilot/*\"\n\n  # Cycle models with fixed thinking levels\n  ${APP_NAME} --models sonnet:high,haiku:low\n\n  # Start with a specific thinking level\n  ${APP_NAME} --thinking high \"Solve this complex problem\"\n\n  # Read-only mode (no file modifications possible)\n  ${APP_NAME} --tools read,search,find,ls -p \"Review the code in src/\"\n\n  # Disable one tool while keeping the rest available\n  ${APP_NAME} --exclude-tools ask_user_question\n\n  # Export a session file to HTML\n  ${APP_NAME} --export ~/${CONFIG_DIR_NAME}/agent/sessions/--path--/session.jsonl\n  ${APP_NAME} --export session.jsonl output.html\n\n${chalk.bold(\"Environment Variables:\")}\n  ANTHROPIC_AUTH_TOKEN             - Anthropic bearer auth token\n  ANTHROPIC_API_KEY                - Anthropic Claude API key\n  ANTHROPIC_OAUTH_TOKEN            - Anthropic OAuth token (alternative to API key)\n  OPENAI_API_KEY                   - OpenAI GPT API key\n  AZURE_OPENAI_API_KEY             - Azure OpenAI API key\n  AZURE_OPENAI_BASE_URL            - Azure OpenAI/Cognitive Services base URL (e.g. https://{resource}.openai.azure.com)\n  AZURE_OPENAI_RESOURCE_NAME       - Azure OpenAI resource name (alternative to base URL)\n  AZURE_OPENAI_API_VERSION         - Azure OpenAI API version (default: v1)\n  AZURE_OPENAI_DEPLOYMENT_NAME_MAP - Azure OpenAI model=deployment map (comma-separated)\n  DEEPSEEK_API_KEY                 - DeepSeek API key\n  GEMINI_API_KEY                   - Google Gemini API key\n  GROQ_API_KEY                     - Groq API key\n  CEREBRAS_API_KEY                 - Cerebras API key\n  XAI_API_KEY                      - xAI Grok API key\n  FIREWORKS_API_KEY                - Fireworks API key\n  TOGETHER_API_KEY                 - Together AI API key\n  BASETEN_API_KEY                  - Baseten API key\n  OPENROUTER_API_KEY               - OpenRouter API key\n  AI_GATEWAY_API_KEY               - Vercel AI Gateway API key\n  ZAI_API_KEY                      - ZAI API key\n  MISTRAL_API_KEY                  - Mistral API key\n  MINIMAX_API_KEY                  - MiniMax API key\n  MOONSHOT_API_KEY                 - Moonshot AI API key\n  OPENCODE_API_KEY                 - OpenCode Zen/OpenCode Go API key\n  KIMI_API_KEY                     - Kimi For Coding API key\n  META_API_KEY                     - Meta Model API key\n  CLOUDFLARE_API_KEY               - Cloudflare API token (Workers AI and AI Gateway)\n  CLOUDFLARE_ACCOUNT_ID            - Cloudflare account id (required for both)\n  CLOUDFLARE_GATEWAY_ID            - Cloudflare AI Gateway slug (required for AI Gateway)\n  QWEN_TOKEN_PLAN_API_KEY          - Qwen Token Plan API key (international region)\n  QWEN_TOKEN_PLAN_CN_API_KEY       - Qwen Token Plan API key (China region)\n  XIAOMI_API_KEY                   - Xiaomi MiMo API key (api.xiaomimimo.com billing)\n  XIAOMI_TOKEN_PLAN_CN_API_KEY     - Xiaomi MiMo Token Plan API key (China region)\n  XIAOMI_TOKEN_PLAN_AMS_API_KEY    - Xiaomi MiMo Token Plan API key (Amsterdam region)\n  XIAOMI_TOKEN_PLAN_SGP_API_KEY    - Xiaomi MiMo Token Plan API key (Singapore region)\n  AWS_PROFILE                      - AWS profile for Amazon Bedrock\n  AWS_ACCESS_KEY_ID                - AWS access key for Amazon Bedrock\n  AWS_SECRET_ACCESS_KEY            - AWS secret key for Amazon Bedrock\n  AWS_BEARER_TOKEN_BEDROCK         - Bedrock API key (bearer token)\n  AWS_REGION                       - AWS region for Amazon Bedrock (e.g., us-east-1)\n  ${ENV_AGENT_DIR.padEnd(32)} - Config directory (default: ~/${CONFIG_DIR_NAME}/agent)\n  ${ENV_SESSION_DIR.padEnd(32)} - Session storage directory (overridden by --session-dir)\n  ${ENV_PACKAGE_DIR.padEnd(32)} - Override package directory (for Nix/Guix store paths)\n  ${ENV_OFFLINE.padEnd(32)} - Disable startup network operations when set to 1/true/yes\n  ${ENV_TELEMETRY.padEnd(32)} - Override install telemetry when set to 1/true/yes or 0/false/no\n  ${ENV_SHARE_VIEWER_URL.padEnd(32)} - Base URL for /share command (default: https://pi.dev/session/)\n  PI_* aliases are also supported for app-specific variables above.\n\n${chalk.bold(\"Built-in Tool Names:\")}\n  read              - Read path selectors (files, dirs, archives, URLs)\n  bash              - Execute shell commands\n  powershell        - Execute PowerShell commands on Windows\n  edit              - Apply hashline-anchored source edits\n  write             - Create or overwrite writable path selectors\n  find              - Find filesystem paths by glob pattern (default)\n  search            - Search file contents with regex (default)\n  ask_user_question - Ask structured questions in the TUI (default)\n  todo              - Manage file-based todos (default)\n  ls                - Legacy directory listing helper (read-only, off by default)\n`);\n}\n"]}

package/dist/core/agent-session-extension-bindings.d.ts.map

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package/dist/core/agent-session-extension-bindings.js

@@ -8,10 +8,13 @@ import { ExtensionRunner } from "./extensions/index.js";
 import { factoryAcquisitions, factoryRollbackError, rollbackFactoryAcquisitions, } from "./extensions/loader-rollback.js";
 import { emitSessionShutdownEvent } from "./extensions/runner.js";
 import { bindExtensionContextPublication } from "./extensions/runner-context.js";
+import { isMandatoryRuntimeTool, isTrustedMandatoryRuntimeTool } from "./mandatory-runtime-tools.js";
+import { isSelectedNativeMcpTool } from "./mcp-child-policy.js";
 import { ModelRegistry } from "./model-registry.js";
 import { abortSessionWork, assertSessionOpen, drainSessionWork, hasSessionReload, renewSessionWork, retireSessionReloadGeneration, sessionGenerationClosing, trackSessionReload, trackSessionWork, } from "./session-lifecycle-work.js";
 import { completeStartup, rollbackStartup } from "./session-startup-rollback.js";
 import { getSkillCatalog } from "./skill-catalog.js";
+import { createSyntheticSourceInfo } from "./source-info.js";
 import { getDefaultToolNames } from "./tools/index.js";
 class ExtensionPublicationGate {
     resourceLoader;
@@ -241,6 +244,55 @@ export function _bindExtensionCore(runner, publication) {
     runner.bindWorkOwner(this);
     bindExtensionContextPublication(runner.createContext(), publication && ((effect) => publication.stageStart(effect)));
     runner.bindTaskHost(() => this.getAgentTaskHost());
+    // A transactional successor starts before it is published. Its callbacks must inspect and
+    // activate its own definitions, never the retiring session's registry. Keep this view local;
+    // only accepted candidates release the deferred activation into the live session.
+    const candidateDefinitions = () => {
+        const definitions = new Map();
+        const permitted = (name) => (!this._allowedToolNames || this._allowedToolNames.has(name)) && !this._excludedToolNames?.has(name);
+        for (const [name, definition] of this._baseToolDefinitions) {
+            if (permitted(name))
+                definitions.set(name, {
+                    definition,
+                    sourceInfo: createSyntheticSourceInfo(`<builtin:${name}>`, { source: "builtin" }),
+                });
+        }
+        const registered = runner
+            .getAllRegisteredTools()
+            .filter((tool) => !isMandatoryRuntimeTool(tool.definition.name) || isTrustedMandatoryRuntimeTool(tool));
+        for (const tool of registered) {
+            const name = tool.definition.name;
+            if (permitted(name) ||
+                (!this._excludedToolNames?.has(name) && isSelectedNativeMcpTool(tool, this._subagentPolicy)))
+                definitions.set(name, tool);
+        }
+        for (const definition of this._customTools) {
+            if (!isMandatoryRuntimeTool(definition.name) && permitted(definition.name))
+                definitions.set(definition.name, {
+                    definition,
+                    sourceInfo: createSyntheticSourceInfo(`<sdk:${definition.name}>`, { source: "sdk" }),
+                });
+        }
+        return definitions;
+    };
+    let candidateActiveTools = this.getActiveToolNames();
+    const candidateRegistryNames = new Set(this._baseToolDefinitions.keys());
+    const refreshCandidateTools = () => {
+        const definitions = candidateDefinitions();
+        for (const [name, { definition }] of definitions) {
+            const exposure = definition.exposure ?? "direct";
+            if (!candidateRegistryNames.has(name) &&
+                definition.defaultActive !== false &&
+                (exposure === "direct" || exposure === "model-only"))
+                candidateActiveTools.push(name);
+            candidateRegistryNames.add(name);
+        }
+        candidateActiveTools = [...new Set(candidateActiveTools)].filter((name) => {
+            const tool = definitions.get(name);
+            return tool && tool.definition.exposure !== "hidden";
+        });
+        return definitions;
+    };
     const getCommands = () => {
         const extensionCommands = runner.getRegisteredCommands().map((command) => ({
             name: command.invocationName,
@@ -336,16 +388,46 @@ export function _bindExtensionCore(runner, publication) {
             else
                 this.sessionManager.appendLabelChange(entryId, label);
         },
-        getActiveTools: () => this.getActiveToolNames(),
-        getAllTools: () => this.getAllTools(),
+        getActiveTools: () => {
+            if (!publication)
+                return this.getActiveToolNames();
+            refreshCandidateTools();
+            return [...candidateActiveTools];
+        },
+        getAllTools: () => {
+            if (!publication)
+                return this.getAllTools();
+            return [...refreshCandidateTools().values()].map(({ definition, sourceInfo }) => ({
+                name: definition.name,
+                description: definition.description,
+                parameters: definition.parameters,
+                ...(Object.hasOwn(definition, "constrainedSampling")
+                    ? { constrainedSampling: definition.constrainedSampling }
+                    : {}),
+                promptGuidelines: definition.promptGuidelines,
+                exposure: definition.exposure ?? "direct",
+                namespace: definition.namespace,
+                annotations: definition.annotations,
+                sourceInfo,
+            }));
+        },
         setActiveTools: (toolNames) => {
-            if (publication)
-                publication.defer(() => this.setActiveToolsByName(toolNames));
+            if (publication) {
+                const definitions = refreshCandidateTools();
+                candidateActiveTools = [...new Set(toolNames)].filter((name) => {
+                    const tool = definitions.get(name);
+                    return tool && tool.definition.exposure !== "hidden";
+                });
+                const accepted = [...candidateActiveTools];
+                publication.defer(() => this.setActiveToolsByName(accepted));
+            }
             else
                 this.setActiveToolsByName(toolNames);
         },
         refreshTools: () => {
-            if (!publication)
+            if (publication)
+                refreshCandidateTools();
+            else
                 this._refreshToolRegistry();
         },
         getCommands,