wave-code 0.19.7 → 0.19.8

package/dist/components/ConfirmationSelector.js

@@ -14,7 +14,7 @@ const getHeaderColor = (header) => {
 };
 export const ConfirmationSelector = ({ toolName, toolInput, suggestedPrefix, hidePersistentOption, isExpanded = false, onDecision, onCancel, }) => {
     const [state, dispatch] = useReducer(confirmationReducer, {
-        selectedOption: toolName === EXIT_PLAN_MODE_TOOL_NAME ? "clear" : "allow",
+        selectedOption: "allow",
         alternativeText: "",
         alternativeCursorPosition: 0,
         hasUserInput: false,
@@ -104,8 +104,9 @@ export const ConfirmationSelector = ({ toolName, toolInput, suggestedPrefix, hid
                                                 ? "[x] "
                                                 : "[ ] "
                                             : "", option.label, option.description ? ` - ${option.description}` : "", isOther && isSelected && (_jsxs(Text, { children: [":", " ", questionState.otherText ? (_jsxs(_Fragment, { children: [questionState.otherText.slice(0, questionState.otherCursorPosition), _jsx(Text, { backgroundColor: "white", color: "black", children: questionState.otherText[questionState.otherCursorPosition] || " " }), questionState.otherText.slice(questionState.otherCursorPosition + 1)] })) : (_jsx(Text, { color: "gray", dimColor: true, children: "[Type your answer...]" }))] }))] }) }, index));
-                        }) }), _jsx(Box, { marginTop: 1, children: _jsxs(Text, { dimColor: true, children: ["Question ", questionState.currentQuestionIndex + 1, " of", " ", questions.length, " \u2022", currentQuestion.multiSelect ? " Space to toggle •" : "", " Use \u2191\u2193 or Tab to navigate \u2022 Enter to confirm"] }) })] })), toolName !== ASK_USER_QUESTION_TOOL_NAME && !isExpanded && (_jsxs(_Fragment, { children: [_jsx(Box, { marginTop: 1, children: _jsx(Text, { children: "Do you want to proceed?" }) }), _jsxs(Box, { marginTop: 1, flexDirection: "column", children: [toolName === EXIT_PLAN_MODE_TOOL_NAME && (_jsx(Box, { children: _jsxs(Text, { color: state.selectedOption === "clear" ? "black" : "white", backgroundColor: state.selectedOption === "clear" ? "yellow" : undefined, bold: state.selectedOption === "clear", children: [state.selectedOption === "clear" ? "> " : "  ", "Yes, clear context and auto-accept edits"] }) }, "clear-option")), _jsx(Box, { children: _jsxs(Text, { color: state.selectedOption === "allow" ? "black" : "white", backgroundColor: state.selectedOption === "allow" ? "yellow" : undefined, bold: state.selectedOption === "allow", children: [state.selectedOption === "allow" ? "> " : "  ", toolName === EXIT_PLAN_MODE_TOOL_NAME
+                        }) }), _jsx(Box, { marginTop: 1, children: _jsxs(Text, { dimColor: true, children: ["Question ", questionState.currentQuestionIndex + 1, " of", " ", questions.length, " \u2022", currentQuestion.multiSelect ? " Space to toggle •" : "", " Use \u2191\u2193 or Tab to navigate \u2022 Enter to confirm"] }) })] })), toolName !== ASK_USER_QUESTION_TOOL_NAME && !isExpanded && (_jsxs(_Fragment, { children: [_jsx(Box, { marginTop: 1, children: _jsx(Text, { children: "Do you want to proceed?" }) }), _jsxs(Box, { marginTop: 1, flexDirection: "column", children: [_jsx(Box, { children: _jsxs(Text, { color: state.selectedOption === "allow" ? "black" : "white", backgroundColor: state.selectedOption === "allow" ? "yellow" : undefined, bold: state.selectedOption === "allow", children: [state.selectedOption === "allow" ? "> " : "  ", toolName === EXIT_PLAN_MODE_TOOL_NAME
                                             ? "Yes, manually approve edits"
-                                            : "Yes, proceed"] }) }, "allow-option"), !hidePersistentOption && (_jsx(Box, { children: _jsxs(Text, { color: state.selectedOption === "auto" ? "black" : "white", backgroundColor: state.selectedOption === "auto" ? "yellow" : undefined, bold: state.selectedOption === "auto", children: [state.selectedOption === "auto" ? "> " : "  ", getAutoOptionText()] }) }, "auto-option")), _jsx(Box, { children: _jsxs(Text, { color: state.selectedOption === "alternative" ? "black" : "white", backgroundColor: state.selectedOption === "alternative" ? "yellow" : undefined, bold: state.selectedOption === "alternative", children: [state.selectedOption === "alternative" ? "> " : "  ", toolName === ENTER_PLAN_MODE_TOOL_NAME && showPlaceholder ? (_jsx(Text, { color: "gray", dimColor: true, children: "No, start implementing now" })) : showPlaceholder ? (_jsx(Text, { color: "gray", dimColor: true, children: placeholderText })) : (_jsx(Text, { children: state.alternativeText ? (_jsxs(_Fragment, { children: [state.alternativeText.slice(0, state.alternativeCursorPosition), _jsx(Text, { backgroundColor: "white", color: "black", children: state.alternativeText[state.alternativeCursorPosition] || " " }), state.alternativeText.slice(state.alternativeCursorPosition + 1)] })) : ("Type here to tell Wave what to change") }))] }) }, "alternative-option")] }), _jsx(Box, { marginTop: 1, children: _jsx(Text, { dimColor: true, children: "Use \u2191\u2193 or Tab to navigate \u2022 ESC to cancel" }) })] }))] }));
+                                            : "Yes, proceed"] }) }, "allow-option"), !hidePersistentOption && (_jsx(Box, { children: _jsxs(Text, { color: state.selectedOption === "auto" ? "black" : "white", backgroundColor: state.selectedOption === "auto" ? "yellow" : undefined, bold: state.selectedOption === "auto", children: [state.selectedOption === "auto" ? "> " : "  ", getAutoOptionText()] }) }, "auto-option")), (toolName === BASH_TOOL_NAME ||
+                                toolName === EXIT_PLAN_MODE_TOOL_NAME) && (_jsx(Box, { children: _jsxs(Text, { color: state.selectedOption === "bypass" ? "black" : "white", backgroundColor: state.selectedOption === "bypass" ? "yellow" : undefined, bold: state.selectedOption === "bypass", children: [state.selectedOption === "bypass" ? "> " : "  ", "Yes, and bypass permissions"] }) }, "bypass-option")), _jsx(Box, { children: _jsxs(Text, { color: state.selectedOption === "alternative" ? "black" : "white", backgroundColor: state.selectedOption === "alternative" ? "yellow" : undefined, bold: state.selectedOption === "alternative", children: [state.selectedOption === "alternative" ? "> " : "  ", toolName === ENTER_PLAN_MODE_TOOL_NAME && showPlaceholder ? (_jsx(Text, { color: "gray", dimColor: true, children: "No, start implementing now" })) : showPlaceholder ? (_jsx(Text, { color: "gray", dimColor: true, children: placeholderText })) : (_jsx(Text, { children: state.alternativeText ? (_jsxs(_Fragment, { children: [state.alternativeText.slice(0, state.alternativeCursorPosition), _jsx(Text, { backgroundColor: "white", color: "black", children: state.alternativeText[state.alternativeCursorPosition] || " " }), state.alternativeText.slice(state.alternativeCursorPosition + 1)] })) : ("Type here to tell Wave what to change") }))] }) }, "alternative-option")] }), _jsx(Box, { marginTop: 1, children: _jsx(Text, { dimColor: true, children: "Use \u2191\u2193 or Tab to navigate \u2022 ESC to cancel" }) })] }))] }));
 };
 ConfirmationSelector.displayName = "ConfirmationSelector";

package/dist/contexts/useChat.js

@@ -235,7 +235,7 @@ export const ChatProvider = ({ children, bypassPermissions, permissionMode: init
             agentRef.current = agent;
             // Inject worktree session into this agent's own DI container so system
             // prompts and permission checks reflect the CLI -w worktree. This state is
-            // per-session, not process-global (see specs/047-worktree.md FR-042).
+            // per-session, not process-global (see docs/specs/multi-agent/worktree.md FR-042).
             if (worktreeSession) {
                 const session = {
                     originalCwd: originalCwd ?? worktreeSession.repoRoot,

package/dist/index.js

@@ -1,7 +1,7 @@
 import yargs from "yargs";
 import { hideBin } from "yargs/helpers";
 import { startCli } from "./cli.js";
-import { generateRandomName } from "wave-agent-sdk";
+import { generateRandomName, loadMergedWaveConfig, } from "wave-agent-sdk";
 import { createWorktree } from "./utils/worktree.js";
 import path from "path";
 import { readFileSync } from "fs";
@@ -236,7 +236,8 @@ export async function main() {
             if (!name || name === "") {
                 name = generateRandomName();
             }
-            worktreeSession = createWorktree(name, originalCwd);
+            const baseRef = loadMergedWaveConfig(originalCwd)?.worktree?.baseRef;
+            worktreeSession = createWorktree(name, originalCwd, { baseRef });
             // Note: the full worktree session (originalCwd etc.) is injected into the
             // agent's DI container after the agent is created in useChat.tsx. This keeps
             // worktree state per-session instead of process-global.

package/dist/print-cli.js

@@ -104,8 +104,16 @@ export async function startPrintCli(options) {
             await agent.sendMessage(message);
             process.stdout.write("\n");
         }
-        // Wait for running background tasks and subagents to complete
-        while (agent.hasRunningBackgroundWork) {
+        // Wait for running background tasks/subagents to complete AND for the main
+        // agent to finish processing their completion notifications. The last
+        // background task flips status to "completed" before its notification is
+        // enqueued and before the main agent's follow-up turn runs, so
+        // hasRunningBackgroundWork alone becomes false while the main agent is
+        // still mid-turn — causing a TOCTOU race that aborts the final response.
+        // Including isLoading and queued notifications closes that gap.
+        while (agent.hasRunningBackgroundWork ||
+            agent.isLoading ||
+            agent.hasPendingMessages) {
             await new Promise((resolve) => setTimeout(resolve, 500));
         }
         // Display usage summary before exit

package/dist/reducers/confirmationReducer.d.ts

@@ -1,7 +1,7 @@
 import { Key } from "ink";
 import type { PermissionDecision } from "wave-agent-sdk";
 export interface ConfirmationState {
-    selectedOption: "clear" | "auto" | "allow" | "alternative";
+    selectedOption: "auto" | "bypass" | "allow" | "alternative";
     alternativeText: string;
     alternativeCursorPosition: number;
     hasUserInput: boolean;

package/dist/reducers/confirmationReducer.js

@@ -47,14 +47,7 @@ export function confirmationReducer(state, action) {
             const { input, key, toolName, toolInput, suggestedPrefix, hidePersistentOption, } = action;
             if (key.return) {
                 let decision = null;
-                if (state.selectedOption === "clear") {
-                    decision = {
-                        behavior: "allow",
-                        newPermissionMode: "acceptEdits",
-                        clearContext: true,
-                    };
-                }
-                else if (state.selectedOption === "allow") {
+                if (state.selectedOption === "allow") {
                     if (toolName === EXIT_PLAN_MODE_TOOL_NAME) {
                         decision = { behavior: "allow", newPermissionMode: "default" };
                     }
@@ -91,6 +84,12 @@ export function confirmationReducer(state, action) {
                         decision = { behavior: "allow", newPermissionMode: "acceptEdits" };
                     }
                 }
+                else if (state.selectedOption === "bypass") {
+                    decision = {
+                        behavior: "allow",
+                        newPermissionMode: "bypassPermissions",
+                    };
+                }
                 else if (state.alternativeText.trim()) {
                     decision = {
                         behavior: "deny",
@@ -123,11 +122,11 @@ export function confirmationReducer(state, action) {
                 }
             }
             const availableOptions = [];
-            if (toolName === EXIT_PLAN_MODE_TOOL_NAME)
-                availableOptions.push("clear");
             availableOptions.push("allow");
             if (!hidePersistentOption)
                 availableOptions.push("auto");
+            if (toolName === BASH_TOOL_NAME || toolName === EXIT_PLAN_MODE_TOOL_NAME)
+                availableOptions.push("bypass");
             availableOptions.push("alternative");
             if (key.upArrow) {
                 const currentIndex = availableOptions.indexOf(state.selectedOption);

package/dist/stdio/agentBridge.d.ts

@@ -45,6 +45,11 @@ export declare class AgentBridge {
     private deleteQueuedMessageById;
     private getMessages;
     private getFullMessageThread;
+    private compact;
+    private getBackgroundTaskOutput;
+    private stopBackgroundTask;
+    private getWorkflowRuns;
+    private stopWorkflowRun;
     private setPermissionMode;
     private getPermissionMode;
     private getMcpServers;

package/dist/stdio/agentBridge.js

@@ -112,6 +112,17 @@ export class AgentBridge {
                 return this.removeMarketplace(p.name, p.scope, p.workdir, sessionId);
             case "updateMarketplace":
                 return this.updateMarketplace(p.name, p.workdir, sessionId);
+            case "compact":
+                return this.compact(p.customInstructions, sessionId);
+            // ── Background tasks ──
+            case "getBackgroundTaskOutput":
+                return this.getBackgroundTaskOutput(p.taskId, sessionId);
+            case "stopBackgroundTask":
+                return this.stopBackgroundTask(p.taskId, sessionId);
+            case "getWorkflowRuns":
+                return this.getWorkflowRuns(sessionId);
+            case "stopWorkflowRun":
+                return this.stopWorkflowRun(p.runId, sessionId);
             default:
                 throw new RpcError(PROTOCOL_METHOD_NOT_FOUND, `Method not found: ${method}`);
         }
@@ -302,6 +313,37 @@ export class AgentBridge {
         const entry = this.requireSession(sessionId);
         return entry.agent.getFullMessageThread();
     }
+    async compact(customInstructions, sessionId) {
+        const entry = this.requireSession(sessionId);
+        await entry.agent.compact(customInstructions);
+        return null;
+    }
+    // ── Background tasks ──
+    getBackgroundTaskOutput(taskId, sessionId) {
+        const entry = this.requireSession(sessionId);
+        return { output: entry.agent.getBackgroundTaskOutput(taskId) };
+    }
+    stopBackgroundTask(taskId, sessionId) {
+        const entry = this.requireSession(sessionId);
+        const success = entry.agent.stopBackgroundTask(taskId);
+        return { success };
+    }
+    async getWorkflowRuns(sessionId) {
+        const entry = this.requireSession(sessionId);
+        const runs = await entry.agent.getWorkflowRuns();
+        return {
+            runs: runs.map((r) => {
+                const { completionPromise, ...rest } = r;
+                void completionPromise;
+                return rest;
+            }),
+        };
+    }
+    stopWorkflowRun(runId, sessionId) {
+        const entry = this.requireSession(sessionId);
+        entry.agent.stopWorkflowRun(runId);
+        return { success: true };
+    }
     // ── Permissions ───────────────────────────────────────────────
     async setPermissionMode(mode, sessionId) {
         const entry = this.requireSession(sessionId);
@@ -485,6 +527,21 @@ export class AgentBridge {
             onTasksChange: (tasks) => {
                 this.emit("tasksChange", { tasks }, ctx.registeredSessionId);
             },
+            onBackgroundTasksChange: (tasks) => {
+                const summaries = tasks.map((t) => ({
+                    id: t.id,
+                    type: t.type,
+                    status: t.status,
+                    startTime: t.startTime,
+                    endTime: t.endTime,
+                    command: t.command,
+                    description: t.description,
+                    exitCode: t.exitCode,
+                    runtime: t.runtime,
+                    outputPath: t.outputPath,
+                }));
+                this.emit("backgroundTasksChange", { tasks: summaries }, ctx.registeredSessionId);
+            },
             onSessionIdChange: (newSessionId) => {
                 const oldSessionId = ctx.registeredSessionId;
                 // Emit with the OLD sessionId so the client's router can deliver it
@@ -526,6 +583,9 @@ export class AgentBridge {
             onCompactBlockAdded: (content) => {
                 this.emit("compactBlockAdded", { content }, ctx.registeredSessionId);
             },
+            onCompactionStateChange: (isCompacting) => {
+                this.emit("compactionStateChange", { isCompacting }, ctx.registeredSessionId);
+            },
         };
     }
     findLastUserMessage(agent) {

package/dist/stdio/protocol.d.ts

@@ -34,8 +34,8 @@ export declare const INVALID_REQUEST = -32600;
 export declare const METHOD_NOT_FOUND = -32601;
 export declare const INVALID_PARAMS = -32602;
 export declare const INTERNAL_ERROR = -32603;
-export type RequestMethod = "initialize" | "destroy" | "restoreSession" | "listSessions" | "getSessionInfo" | "sendMessage" | "bang" | "abortMessage" | "clearMessages" | "rewindToMessage" | "deleteQueuedMessage" | "updateQueuedMessage" | "deleteQueuedMessageById" | "getMessages" | "getFullMessageThread" | "setPermissionMode" | "getPermissionMode" | "getMcpServers" | "connectMcpServer" | "disconnectMcpServer" | "getSlashCommands" | "searchFiles" | "getPromptHistory" | "searchPromptHistory" | "updateConfig" | "getAuthStatus" | "login" | "logout" | "listPlugins" | "installPlugin" | "uninstallPlugin" | "enablePlugin" | "disablePlugin" | "updatePlugin" | "listMarketplaces" | "addMarketplace" | "removeMarketplace" | "updateMarketplace";
+export type RequestMethod = "initialize" | "destroy" | "restoreSession" | "listSessions" | "getSessionInfo" | "sendMessage" | "bang" | "abortMessage" | "clearMessages" | "rewindToMessage" | "deleteQueuedMessage" | "updateQueuedMessage" | "deleteQueuedMessageById" | "getMessages" | "getFullMessageThread" | "setPermissionMode" | "getPermissionMode" | "getMcpServers" | "connectMcpServer" | "disconnectMcpServer" | "getSlashCommands" | "searchFiles" | "getPromptHistory" | "searchPromptHistory" | "updateConfig" | "getAuthStatus" | "login" | "logout" | "listPlugins" | "installPlugin" | "uninstallPlugin" | "enablePlugin" | "disablePlugin" | "updatePlugin" | "listMarketplaces" | "addMarketplace" | "removeMarketplace" | "updateMarketplace" | "compact" | "getBackgroundTaskOutput" | "stopBackgroundTask" | "getWorkflowRuns" | "stopWorkflowRun";
 export type ClientNotificationMethod = "permissionResponse";
-export type ServerNotificationMethod = "messagesChange" | "userMessageAdded" | "assistantMessageAdded" | "assistantContentUpdated" | "assistantReasoningUpdated" | "toolBlockUpdated" | "errorBlockAdded" | "loadingChange" | "commandRunningChange" | "queuedMessagesChange" | "tasksChange" | "sessionIdChange" | "permissionModeChange" | "mcpServersChange" | "workdirChange" | "bangMessageAdded" | "bangMessageUpdated" | "bangMessageCompleted" | "notificationMessageAdded" | "permissionRequest" | "authUrl" | "compactBlockAdded";
+export type ServerNotificationMethod = "messagesChange" | "userMessageAdded" | "assistantMessageAdded" | "assistantContentUpdated" | "assistantReasoningUpdated" | "toolBlockUpdated" | "errorBlockAdded" | "loadingChange" | "commandRunningChange" | "queuedMessagesChange" | "tasksChange" | "sessionIdChange" | "permissionModeChange" | "mcpServersChange" | "workdirChange" | "bangMessageAdded" | "bangMessageUpdated" | "bangMessageCompleted" | "notificationMessageAdded" | "permissionRequest" | "authUrl" | "compactBlockAdded" | "compactionStateChange" | "backgroundTasksChange";
 export declare function isRequest(msg: unknown): msg is JsonRpcRequest;
 export declare function isNotification(msg: unknown): msg is JsonRpcNotification;

package/dist/utils/worktree.d.ts

@@ -11,9 +11,13 @@ export interface WorktreeSession {
  * Create a new git worktree
  * @param name Worktree name
  * @param cwd Current working directory
+ * @param options Optional creation options
+ * @param options.baseRef "fresh" (default, origin/<default-branch>) | "head" (local HEAD)
  * @returns Worktree session details
  */
-export declare function createWorktree(name: string, cwd: string): WorktreeSession;
+export declare function createWorktree(name: string, cwd: string, options?: {
+    baseRef?: "fresh" | "head";
+}): WorktreeSession;
 /**
  * Remove a git worktree and its associated branch
  * @param session Worktree session details

package/dist/utils/worktree.js

@@ -6,13 +6,16 @@ import { getDefaultRemoteBranch, getGitMainRepoRoot } from "wave-agent-sdk";
  * Create a new git worktree
  * @param name Worktree name
  * @param cwd Current working directory
+ * @param options Optional creation options
+ * @param options.baseRef "fresh" (default, origin/<default-branch>) | "head" (local HEAD)
  * @returns Worktree session details
  */
-export function createWorktree(name, cwd) {
+export function createWorktree(name, cwd, options) {
     const repoRoot = getGitMainRepoRoot(cwd);
     const worktreePath = path.join(repoRoot, ".wave", "worktrees", name);
     const branchName = `worktree-${name}`;
-    const baseBranch = getDefaultRemoteBranch(cwd);
+    const useHead = options?.baseRef === "head";
+    const baseBranch = useHead ? "HEAD" : getDefaultRemoteBranch(cwd);
     // Ensure parent directory exists
     const parentDir = path.dirname(worktreePath);
     if (!fs.existsSync(parentDir)) {
@@ -70,8 +73,9 @@ export function createWorktree(name, cwd) {
                 throw new Error(`Failed to add existing worktree branch: ${innerError.message}`);
             }
         }
-        if (stderr.includes("not a valid object name") ||
-            stderr.includes("unknown revision")) {
+        if (!useHead &&
+            (stderr.includes("not a valid object name") ||
+                stderr.includes("unknown revision"))) {
             // Base branch not fetched yet — try fetching then retrying
             const branchNameOnly = baseBranch.split("/").pop();
             try {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "wave-code",
-  "version": "0.19.7",
+  "version": "0.19.8",
   "description": "CLI-based code assistant powered by AI, built with React and Ink",
   "repository": {
     "type": "git",
@@ -41,7 +41,7 @@
     "semver": "^7.7.4",
     "yargs": "^17.7.2",
     "zod": "^3.23.8",
-    "wave-agent-sdk": "0.19.7"
+    "wave-agent-sdk": "0.19.8"
   },
   "devDependencies": {
     "@types/react": "^19.1.8",

package/src/components/ConfirmationSelector.tsx

@@ -39,7 +39,7 @@ export const ConfirmationSelector: React.FC<ConfirmationSelectorProps> = ({
   onCancel,
 }) => {
   const [state, dispatch] = useReducer(confirmationReducer, {
-    selectedOption: toolName === EXIT_PLAN_MODE_TOOL_NAME ? "clear" : "allow",
+    selectedOption: "allow",
     alternativeText: "",
     alternativeCursorPosition: 0,
     hasUserInput: false,
@@ -212,20 +212,6 @@ export const ConfirmationSelector: React.FC<ConfirmationSelectorProps> = ({
             <Text>Do you want to proceed?</Text>
           </Box>
           <Box marginTop={1} flexDirection="column">
-            {toolName === EXIT_PLAN_MODE_TOOL_NAME && (
-              <Box key="clear-option">
-                <Text
-                  color={state.selectedOption === "clear" ? "black" : "white"}
-                  backgroundColor={
-                    state.selectedOption === "clear" ? "yellow" : undefined
-                  }
-                  bold={state.selectedOption === "clear"}
-                >
-                  {state.selectedOption === "clear" ? "> " : "  "}
-                  Yes, clear context and auto-accept edits
-                </Text>
-              </Box>
-            )}
             <Box key="allow-option">
               <Text
                 color={state.selectedOption === "allow" ? "black" : "white"}
@@ -254,6 +240,21 @@ export const ConfirmationSelector: React.FC<ConfirmationSelectorProps> = ({
                 </Text>
               </Box>
             )}
+            {(toolName === BASH_TOOL_NAME ||
+              toolName === EXIT_PLAN_MODE_TOOL_NAME) && (
+              <Box key="bypass-option">
+                <Text
+                  color={state.selectedOption === "bypass" ? "black" : "white"}
+                  backgroundColor={
+                    state.selectedOption === "bypass" ? "yellow" : undefined
+                  }
+                  bold={state.selectedOption === "bypass"}
+                >
+                  {state.selectedOption === "bypass" ? "> " : "  "}
+                  Yes, and bypass permissions
+                </Text>
+              </Box>
+            )}
             <Box key="alternative-option">
               <Text
                 color={

package/src/contexts/useChat.tsx

@@ -482,7 +482,7 @@ export const ChatProvider: React.FC<ChatProviderProps> = ({
 
         // Inject worktree session into this agent's own DI container so system
         // prompts and permission checks reflect the CLI -w worktree. This state is
-        // per-session, not process-global (see specs/047-worktree.md FR-042).
+        // per-session, not process-global (see docs/specs/multi-agent/worktree.md FR-042).
         if (worktreeSession) {
           const session: WorktreeSession = {
             originalCwd: originalCwd ?? worktreeSession.repoRoot,

package/src/index.ts

@@ -1,7 +1,12 @@
 import yargs from "yargs";
 import { hideBin } from "yargs/helpers";
 import { startCli } from "./cli.js";
-import { Scope, generateRandomName, type PermissionMode } from "wave-agent-sdk";
+import {
+  Scope,
+  generateRandomName,
+  loadMergedWaveConfig,
+  type PermissionMode,
+} from "wave-agent-sdk";
 import { createWorktree, type WorktreeSession } from "./utils/worktree.js";
 import path from "path";
 import { readFileSync } from "fs";
@@ -320,7 +325,8 @@ export async function main() {
       if (!name || name === "") {
         name = generateRandomName();
       }
-      worktreeSession = createWorktree(name, originalCwd);
+      const baseRef = loadMergedWaveConfig(originalCwd)?.worktree?.baseRef;
+      worktreeSession = createWorktree(name, originalCwd, { baseRef });
 
       // Note: the full worktree session (originalCwd etc.) is injected into the
       // agent's DI container after the agent is created in useChat.tsx. This keeps

package/src/print-cli.ts

@@ -154,8 +154,18 @@ export async function startPrintCli(options: PrintCliOptions): Promise<void> {
       process.stdout.write("\n");
     }
 
-    // Wait for running background tasks and subagents to complete
-    while (agent.hasRunningBackgroundWork) {
+    // Wait for running background tasks/subagents to complete AND for the main
+    // agent to finish processing their completion notifications. The last
+    // background task flips status to "completed" before its notification is
+    // enqueued and before the main agent's follow-up turn runs, so
+    // hasRunningBackgroundWork alone becomes false while the main agent is
+    // still mid-turn — causing a TOCTOU race that aborts the final response.
+    // Including isLoading and queued notifications closes that gap.
+    while (
+      agent.hasRunningBackgroundWork ||
+      agent.isLoading ||
+      agent.hasPendingMessages
+    ) {
       await new Promise((resolve) => setTimeout(resolve, 500));
     }
 

package/src/reducers/confirmationReducer.ts

@@ -7,7 +7,7 @@ import {
 } from "wave-agent-sdk";
 
 export interface ConfirmationState {
-  selectedOption: "clear" | "auto" | "allow" | "alternative";
+  selectedOption: "auto" | "bypass" | "allow" | "alternative";
   alternativeText: string;
   alternativeCursorPosition: number;
   hasUserInput: boolean;
@@ -99,13 +99,7 @@ export function confirmationReducer(
 
       if (key.return) {
         let decision: PermissionDecision | null = null;
-        if (state.selectedOption === "clear") {
-          decision = {
-            behavior: "allow",
-            newPermissionMode: "acceptEdits",
-            clearContext: true,
-          };
-        } else if (state.selectedOption === "allow") {
+        if (state.selectedOption === "allow") {
           if (toolName === EXIT_PLAN_MODE_TOOL_NAME) {
             decision = { behavior: "allow", newPermissionMode: "default" };
           } else if (toolName === ENTER_PLAN_MODE_TOOL_NAME) {
@@ -134,6 +128,11 @@ export function confirmationReducer(
           } else {
             decision = { behavior: "allow", newPermissionMode: "acceptEdits" };
           }
+        } else if (state.selectedOption === "bypass") {
+          decision = {
+            behavior: "allow",
+            newPermissionMode: "bypassPermissions",
+          };
         } else if (state.alternativeText.trim()) {
           decision = {
             behavior: "deny",
@@ -174,9 +173,10 @@ export function confirmationReducer(
       }
 
       const availableOptions: ConfirmationState["selectedOption"][] = [];
-      if (toolName === EXIT_PLAN_MODE_TOOL_NAME) availableOptions.push("clear");
       availableOptions.push("allow");
       if (!hidePersistentOption) availableOptions.push("auto");
+      if (toolName === BASH_TOOL_NAME || toolName === EXIT_PLAN_MODE_TOOL_NAME)
+        availableOptions.push("bypass");
       availableOptions.push("alternative");
 
       if (key.upArrow) {

package/src/stdio/agentBridge.ts

@@ -19,6 +19,9 @@ import {
   Agent,
   type AgentCallbacks,
   type AgentOptions,
+  type BackgroundTask,
+  type BackgroundTaskSummary,
+  type SerializableWorkflowRun,
   type Message,
   type PermissionDecision,
   type PermissionMode,
@@ -278,6 +281,22 @@ export class AgentBridge {
           p.workdir as string | undefined,
           sessionId,
         );
+      case "compact":
+        return this.compact(
+          p.customInstructions as string | undefined,
+          sessionId,
+        );
+
+      // ── Background tasks ──
+      case "getBackgroundTaskOutput":
+        return this.getBackgroundTaskOutput(p.taskId as string, sessionId);
+      case "stopBackgroundTask":
+        return this.stopBackgroundTask(p.taskId as string, sessionId);
+
+      case "getWorkflowRuns":
+        return this.getWorkflowRuns(sessionId);
+      case "stopWorkflowRun":
+        return this.stopWorkflowRun(p.runId as string, sessionId);
 
       default:
         throw new RpcError(
@@ -555,6 +574,57 @@ export class AgentBridge {
     return entry.agent.getFullMessageThread();
   }
 
+  private async compact(
+    customInstructions: string | undefined,
+    sessionId?: string,
+  ): Promise<null> {
+    const entry = this.requireSession(sessionId);
+    await entry.agent.compact(customInstructions);
+    return null;
+  }
+
+  // ── Background tasks ──
+
+  private getBackgroundTaskOutput(
+    taskId: string,
+    sessionId?: string,
+  ): { output: ReturnType<Agent["getBackgroundTaskOutput"]> } {
+    const entry = this.requireSession(sessionId);
+    return { output: entry.agent.getBackgroundTaskOutput(taskId) };
+  }
+
+  private stopBackgroundTask(
+    taskId: string,
+    sessionId?: string,
+  ): { success: boolean } {
+    const entry = this.requireSession(sessionId);
+    const success = entry.agent.stopBackgroundTask(taskId);
+    return { success };
+  }
+
+  private async getWorkflowRuns(
+    sessionId?: string,
+  ): Promise<{ runs: SerializableWorkflowRun[] }> {
+    const entry = this.requireSession(sessionId);
+    const runs = await entry.agent.getWorkflowRuns();
+    return {
+      runs: runs.map((r) => {
+        const { completionPromise, ...rest } = r;
+        void completionPromise;
+        return rest;
+      }),
+    };
+  }
+
+  private stopWorkflowRun(
+    runId: string,
+    sessionId?: string,
+  ): { success: boolean } {
+    const entry = this.requireSession(sessionId);
+    entry.agent.stopWorkflowRun(runId);
+    return { success: true };
+  }
+
   // ── Permissions ───────────────────────────────────────────────
 
   private async setPermissionMode(
@@ -867,6 +937,25 @@ export class AgentBridge {
       onTasksChange: (tasks: Task[]) => {
         this.emit("tasksChange", { tasks }, ctx.registeredSessionId);
       },
+      onBackgroundTasksChange: (tasks: BackgroundTask[]) => {
+        const summaries: BackgroundTaskSummary[] = tasks.map((t) => ({
+          id: t.id,
+          type: t.type,
+          status: t.status,
+          startTime: t.startTime,
+          endTime: t.endTime,
+          command: t.command,
+          description: t.description,
+          exitCode: t.exitCode,
+          runtime: t.runtime,
+          outputPath: t.outputPath,
+        }));
+        this.emit(
+          "backgroundTasksChange",
+          { tasks: summaries },
+          ctx.registeredSessionId,
+        );
+      },
       onSessionIdChange: (newSessionId: string) => {
         const oldSessionId = ctx.registeredSessionId;
         // Emit with the OLD sessionId so the client's router can deliver it
@@ -922,6 +1011,13 @@ export class AgentBridge {
       onCompactBlockAdded: (content: string) => {
         this.emit("compactBlockAdded", { content }, ctx.registeredSessionId);
       },
+      onCompactionStateChange: (isCompacting: boolean) => {
+        this.emit(
+          "compactionStateChange",
+          { isCompacting },
+          ctx.registeredSessionId,
+        );
+      },
     };
   }
 

package/src/stdio/protocol.ts

@@ -86,7 +86,12 @@ export type RequestMethod =
   | "listMarketplaces"
   | "addMarketplace"
   | "removeMarketplace"
-  | "updateMarketplace";
+  | "updateMarketplace"
+  | "compact"
+  | "getBackgroundTaskOutput"
+  | "stopBackgroundTask"
+  | "getWorkflowRuns"
+  | "stopWorkflowRun";
 
 // ── Client → Server notification methods ────────────────────────
 
@@ -116,7 +121,9 @@ export type ServerNotificationMethod =
   | "notificationMessageAdded"
   | "permissionRequest"
   | "authUrl"
-  | "compactBlockAdded";
+  | "compactBlockAdded"
+  | "compactionStateChange"
+  | "backgroundTasksChange";
 
 // ── Helper: is this a request (has id)? ─────────────────────────
 

package/src/utils/worktree.ts

@@ -17,13 +17,20 @@ export interface WorktreeSession {
  * Create a new git worktree
  * @param name Worktree name
  * @param cwd Current working directory
+ * @param options Optional creation options
+ * @param options.baseRef "fresh" (default, origin/<default-branch>) | "head" (local HEAD)
  * @returns Worktree session details
  */
-export function createWorktree(name: string, cwd: string): WorktreeSession {
+export function createWorktree(
+  name: string,
+  cwd: string,
+  options?: { baseRef?: "fresh" | "head" },
+): WorktreeSession {
   const repoRoot = getGitMainRepoRoot(cwd);
   const worktreePath = path.join(repoRoot, ".wave", "worktrees", name);
   const branchName = `worktree-${name}`;
-  const baseBranch = getDefaultRemoteBranch(cwd);
+  const useHead = options?.baseRef === "head";
+  const baseBranch = useHead ? "HEAD" : getDefaultRemoteBranch(cwd);
 
   // Ensure parent directory exists
   const parentDir = path.dirname(worktreePath);
@@ -90,8 +97,9 @@ export function createWorktree(name: string, cwd: string): WorktreeSession {
       }
     }
     if (
-      stderr.includes("not a valid object name") ||
-      stderr.includes("unknown revision")
+      !useHead &&
+      (stderr.includes("not a valid object name") ||
+        stderr.includes("unknown revision"))
     ) {
       // Base branch not fetched yet — try fetching then retrying
       const branchNameOnly = baseBranch.split("/").pop()!;