fix: parse multiple --allowed-tools values correctly

The parseAllowedTools() function was using regex matching which only
captured the first occurrence of --allowed-tools. This caused issues
when users specified multiple space-separated quoted tools like:

  --allowed-tools "Bash(git log:*)" "Bash(git diff:*)" "Bash(gh pr:*)"

The fix uses shell-quote library (same as parse-sdk-options.ts) to
properly tokenize arguments. This handles:
- Multiple space-separated quoted tools after a single --allowed-tools
- Multiple --allowedTools flags in the same string
- Mix of comma-separated and space-separated tools
- Glob patterns (which shell-quote returns as objects)

Fixes #746

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Ashwin Bhat <ashwin-ant@users.noreply.github.com>

.github/workflows/claude.yml

@@ -36,4 +36,4 @@ jobs:
           anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
           claude_args: |
             --allowedTools "Bash(bun install),Bash(bun test:*),Bash(bun run format),Bash(bun typecheck)"
-            --model "claude-opus-4-1-20250805"
+            --model "claude-opus-4-5"

.github/workflows/sync-base-action.yml

@@ -94,5 +94,5 @@ jobs:
           echo "✅ Successfully synced \`base-action\` directory to [anthropics/claude-code-base-action](https://github.com/anthropics/claude-code-base-action)" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
           echo "- **Source commit**: [\`${GITHUB_SHA:0:7}\`](https://github.com/anthropics/claude-code-action/commit/${GITHUB_SHA})" >> $GITHUB_STEP_SUMMARY
-          echo "- **Triggered by**: ${{ github.event_name }}" >> $GITHUB_STEP_SUMMARY
+          echo "- **Triggered by**: $GITHUB_EVENT_NAME" >> $GITHUB_STEP_SUMMARY
-          echo "- **Actor**: @${{ github.actor }}" >> $GITHUB_STEP_SUMMARY
+          echo "- **Actor**: @$GITHUB_ACTOR" >> $GITHUB_STEP_SUMMARY

action.yml

@@ -127,6 +127,9 @@ outputs:
   structured_output:
     description: "JSON string containing all structured output fields when --json-schema is provided in claude_args. Use fromJSON() to parse: fromJSON(steps.id.outputs.structured_output).field_name"
     value: ${{ steps.claude-code.outputs.structured_output }}
+  session_id:
+    description: "The Claude Code session ID that can be used with --resume to continue this conversation"
+    value: ${{ steps.claude-code.outputs.session_id }}
 
 runs:
   using: "composite"
@@ -140,10 +143,12 @@ runs:
     - name: Setup Custom Bun Path
       if: inputs.path_to_bun_executable != ''
       shell: bash
+      env:
+        PATH_TO_BUN_EXECUTABLE: ${{ inputs.path_to_bun_executable }}
       run: |
-        echo "Using custom Bun executable: ${{ inputs.path_to_bun_executable }}"
+        echo "Using custom Bun executable: $PATH_TO_BUN_EXECUTABLE"
         # Add the directory containing the custom executable to PATH
-        BUN_DIR=$(dirname "${{ inputs.path_to_bun_executable }}")
+        BUN_DIR=$(dirname "$PATH_TO_BUN_EXECUTABLE")
         echo "$BUN_DIR" >> "$GITHUB_PATH"
 
     - name: Install Dependencies
@@ -182,6 +187,8 @@ runs:
     - name: Install Base Action Dependencies
       if: steps.prepare.outputs.contains_trigger == 'true'
       shell: bash
+      env:
+        PATH_TO_CLAUDE_CODE_EXECUTABLE: ${{ inputs.path_to_claude_code_executable }}
       run: |
         echo "Installing base-action dependencies..."
         cd ${GITHUB_ACTION_PATH}/base-action
@@ -190,8 +197,8 @@ runs:
         cd -
 
         # Install Claude Code if no custom executable is provided
-        if [ -z "${{ inputs.path_to_claude_code_executable }}" ]; then
+        if [ -z "$PATH_TO_CLAUDE_CODE_EXECUTABLE" ]; then
-          CLAUDE_CODE_VERSION="2.0.60"
+          CLAUDE_CODE_VERSION="2.0.70"
           echo "Installing Claude Code v${CLAUDE_CODE_VERSION}..."
           for attempt in 1 2 3; do
             echo "Installation attempt $attempt..."
@@ -210,9 +217,9 @@ runs:
           echo "Claude Code installed successfully"
           echo "$HOME/.local/bin" >> "$GITHUB_PATH"
         else
-          echo "Using custom Claude Code executable: ${{ inputs.path_to_claude_code_executable }}"
+          echo "Using custom Claude Code executable: $PATH_TO_CLAUDE_CODE_EXECUTABLE"
           # Add the directory containing the custom executable to PATH
-          CLAUDE_DIR=$(dirname "${{ inputs.path_to_claude_code_executable }}")
+          CLAUDE_DIR=$(dirname "$PATH_TO_CLAUDE_CODE_EXECUTABLE")
           echo "$CLAUDE_DIR" >> "$GITHUB_PATH"
         fi
 

base-action/action.yml

@@ -82,6 +82,9 @@ outputs:
   structured_output:
     description: "JSON string containing all structured output fields when --json-schema is provided in claude_args (use fromJSON() or jq to parse)"
     value: ${{ steps.run_claude.outputs.structured_output }}
+  session_id:
+    description: "The Claude Code session ID that can be used with --resume to continue this conversation"
+    value: ${{ steps.run_claude.outputs.session_id }}
 
 runs:
   using: "composite"
@@ -101,10 +104,12 @@ runs:
     - name: Setup Custom Bun Path
       if: inputs.path_to_bun_executable != ''
       shell: bash
+      env:
+        PATH_TO_BUN_EXECUTABLE: ${{ inputs.path_to_bun_executable }}
       run: |
-        echo "Using custom Bun executable: ${{ inputs.path_to_bun_executable }}"
+        echo "Using custom Bun executable: $PATH_TO_BUN_EXECUTABLE"
         # Add the directory containing the custom executable to PATH
-        BUN_DIR=$(dirname "${{ inputs.path_to_bun_executable }}")
+        BUN_DIR=$(dirname "$PATH_TO_BUN_EXECUTABLE")
         echo "$BUN_DIR" >> "$GITHUB_PATH"
 
     - name: Install Dependencies
@@ -115,9 +120,11 @@ runs:
 
     - name: Install Claude Code
       shell: bash
+      env:
+        PATH_TO_CLAUDE_CODE_EXECUTABLE: ${{ inputs.path_to_claude_code_executable }}
       run: |
-        if [ -z "${{ inputs.path_to_claude_code_executable }}" ]; then
+        if [ -z "$PATH_TO_CLAUDE_CODE_EXECUTABLE" ]; then
-          CLAUDE_CODE_VERSION="2.0.60"
+          CLAUDE_CODE_VERSION="2.0.70"
           echo "Installing Claude Code v${CLAUDE_CODE_VERSION}..."
           for attempt in 1 2 3; do
             echo "Installation attempt $attempt..."
@@ -135,9 +142,9 @@ runs:
           done
           echo "Claude Code installed successfully"
         else
-          echo "Using custom Claude Code executable: ${{ inputs.path_to_claude_code_executable }}"
+          echo "Using custom Claude Code executable: $PATH_TO_CLAUDE_CODE_EXECUTABLE"
           # Add the directory containing the custom executable to PATH
-          CLAUDE_DIR=$(dirname "${{ inputs.path_to_claude_code_executable }}")
+          CLAUDE_DIR=$(dirname "$PATH_TO_CLAUDE_CODE_EXECUTABLE")
           echo "$CLAUDE_DIR" >> "$GITHUB_PATH"
         fi
 

base-action/bun.lock

@@ -1,11 +1,12 @@
 {
   "lockfileVersion": 1,
+  "configVersion": 0,
   "workspaces": {
     "": {
       "name": "@anthropic-ai/claude-code-base-action",
       "dependencies": {
         "@actions/core": "^1.10.1",
-        "@anthropic-ai/claude-agent-sdk": "^0.1.52",
+        "@anthropic-ai/claude-agent-sdk": "^0.1.70",
         "shell-quote": "^1.8.3",
       },
       "devDependencies": {
@@ -26,7 +27,7 @@
 
     "@actions/io": ["@actions/io@1.1.3", "", {}, "sha512-wi9JjgKLYS7U/z8PPbco+PvTb/nRWjeoFlJ1Qer83k/3C5PHQi28hiVdeE2kHXmIL99mQFawx8qt/JPjZilJ8Q=="],
 
-    "@anthropic-ai/claude-agent-sdk": ["@anthropic-ai/claude-agent-sdk@0.1.52", "", { "optionalDependencies": { "@img/sharp-darwin-arm64": "^0.33.5", "@img/sharp-darwin-x64": "^0.33.5", "@img/sharp-linux-arm": "^0.33.5", "@img/sharp-linux-arm64": "^0.33.5", "@img/sharp-linux-x64": "^0.33.5", "@img/sharp-linuxmusl-arm64": "^0.33.5", "@img/sharp-linuxmusl-x64": "^0.33.5", "@img/sharp-win32-x64": "^0.33.5" }, "peerDependencies": { "zod": "^3.24.1" } }, "sha512-yF8N05+9NRbqYA/h39jQ726HTQFrdXXp7pEfDNKIJ2c4FdWvEjxBA/8ciZIebN6/PyvGDcbEp3yq2Co4rNpg6A=="],
+    "@anthropic-ai/claude-agent-sdk": ["@anthropic-ai/claude-agent-sdk@0.1.70", "", { "optionalDependencies": { "@img/sharp-darwin-arm64": "^0.33.5", "@img/sharp-darwin-x64": "^0.33.5", "@img/sharp-linux-arm": "^0.33.5", "@img/sharp-linux-arm64": "^0.33.5", "@img/sharp-linux-x64": "^0.33.5", "@img/sharp-linuxmusl-arm64": "^0.33.5", "@img/sharp-linuxmusl-x64": "^0.33.5", "@img/sharp-win32-x64": "^0.33.5" }, "peerDependencies": { "zod": "^3.24.1" } }, "sha512-4jpFPDX8asys6skO1r3Pzh0Fe9nbND2ASYTWuyFB5iN9bWEL6WScTFyGokjql3M2TkEp9ZGuB2YYpTCdaqT9Sw=="],
 
     "@fastify/busboy": ["@fastify/busboy@2.1.1", "", {}, "sha512-vBZP4NlzfOlerQTnba4aqZoMhE/a9HY7HRqoOPaETQcSQuWEIyZMHGfVu6w9wGtGK5fED5qRs2DteVCjOH60sA=="],
 

base-action/package.json

@@ -11,7 +11,7 @@
   },
   "dependencies": {
     "@actions/core": "^1.10.1",
-    "@anthropic-ai/claude-agent-sdk": "^0.1.52",
+    "@anthropic-ai/claude-agent-sdk": "^0.1.70",
     "shell-quote": "^1.8.3"
   },
   "devDependencies": {

base-action/src/run-claude-sdk.ts

@@ -75,28 +75,15 @@ export async function runClaudeWithSdk(
   }
 
   console.log(`Running Claude with prompt from file: ${promptPath}`);
-  console.log(
+  // Log SDK options without env (which could contain sensitive data)
-    "[DEBUG] Prompt content (first 2000 chars):",
+  const { env, ...optionsToLog } = sdkOptions;
-    prompt.substring(0, 2000),
+  console.log("SDK options:", JSON.stringify(optionsToLog, null, 2));
-  );
-  console.log("[DEBUG] Prompt length:", prompt.length);
-  console.log(
-    "[DEBUG] sdkOptions passed to query():",
-    JSON.stringify(sdkOptions, null, 2),
-  );
 
   const messages: SDKMessage[] = [];
   let resultMessage: SDKResultMessage | undefined;
 
   try {
-    console.log("[DEBUG] About to call query()...");
     for await (const message of query({ prompt, options: sdkOptions })) {
-      console.log(
-        "[DEBUG] Received message type:",
-        message.type,
-        "subtype:",
-        (message as any).subtype,
-      );
       messages.push(message);
 
       const sanitized = sanitizeSdkOutput(message, showFullOutput);
@@ -106,16 +93,8 @@ export async function runClaudeWithSdk(
 
       if (message.type === "result") {
         resultMessage = message as SDKResultMessage;
-        console.log(
-          "[DEBUG] Got result message:",
-          JSON.stringify(resultMessage, null, 2),
-        );
       }
     }
-    console.log(
-      "[DEBUG] Finished iterating query(), total messages:",
-      messages.length,
-    );
   } catch (error) {
     console.error("SDK execution error:", error);
     core.setOutput("conclusion", "failure");

base-action/src/run-claude.ts

@@ -124,6 +124,36 @@ export function prepareRunConfig(
   };
 }
 
+/**
+ * Parses session_id from execution file and sets GitHub Action output
+ * Exported for testing
+ */
+export async function parseAndSetSessionId(
+  executionFile: string,
+): Promise<void> {
+  try {
+    const content = await readFile(executionFile, "utf-8");
+    const messages = JSON.parse(content) as {
+      type: string;
+      subtype?: string;
+      session_id?: string;
+    }[];
+
+    // Find the system.init message which contains session_id
+    const initMessage = messages.find(
+      (m) => m.type === "system" && m.subtype === "init",
+    );
+
+    if (initMessage?.session_id) {
+      core.setOutput("session_id", initMessage.session_id);
+      core.info(`Set session_id: ${initMessage.session_id}`);
+    }
+  } catch (error) {
+    // Don't fail the action if session_id extraction fails
+    core.warning(`Failed to extract session_id: ${error}`);
+  }
+}
+
 /**
  * Parses structured_output from execution file and sets GitHub Action outputs
  * Only runs if --json-schema was explicitly provided in claude_args
@@ -167,22 +197,14 @@ export async function parseAndSetStructuredOutputs(
 }
 
 export async function runClaude(promptPath: string, options: ClaudeOptions) {
-  // Feature flag: use SDK path when USE_AGENT_SDK=true
+  // Feature flag: use SDK path by default, set USE_AGENT_SDK=false to use CLI
-  const useAgentSdk = process.env.USE_AGENT_SDK === "true";
+  const useAgentSdk = process.env.USE_AGENT_SDK !== "false";
   console.log(
     `Using ${useAgentSdk ? "Agent SDK" : "CLI"} path (USE_AGENT_SDK=${process.env.USE_AGENT_SDK ?? "unset"})`,
   );
 
   if (useAgentSdk) {
-    console.log(
-      "[DEBUG] Raw options passed to SDK path:",
-      JSON.stringify(options, null, 2),
-    );
     const parsedOptions = parseSdkOptions(options);
-    console.log(
-      "[DEBUG] Parsed SDK options:",
-      JSON.stringify(parsedOptions, null, 2),
-    );
     return runClaudeWithSdk(promptPath, parsedOptions);
   }
 
@@ -376,6 +398,9 @@ export async function runClaude(promptPath: string, options: ClaudeOptions) {
 
     core.setOutput("execution_file", EXECUTION_FILE);
 
+    // Extract and set session_id
+    await parseAndSetSessionId(EXECUTION_FILE);
+
     // Parse and set structured outputs only if user provided --json-schema in claude_args
     if (hasJsonSchema) {
       try {

base-action/test/structured-output.test.ts

@@ -4,7 +4,10 @@ import { describe, test, expect, afterEach, beforeEach, spyOn } from "bun:test";
 import { writeFile, unlink } from "fs/promises";
 import { tmpdir } from "os";
 import { join } from "path";
-import { parseAndSetStructuredOutputs } from "../src/run-claude";
+import {
+  parseAndSetStructuredOutputs,
+  parseAndSetSessionId,
+} from "../src/run-claude";
 import * as core from "@actions/core";
 
 // Mock execution file path
@@ -35,16 +38,19 @@ async function createMockExecutionFile(
 // Spy on core functions
 let setOutputSpy: any;
 let infoSpy: any;
+let warningSpy: any;
 
 beforeEach(() => {
   setOutputSpy = spyOn(core, "setOutput").mockImplementation(() => {});
   infoSpy = spyOn(core, "info").mockImplementation(() => {});
+  warningSpy = spyOn(core, "warning").mockImplementation(() => {});
 });
 
 describe("parseAndSetStructuredOutputs", () => {
   afterEach(async () => {
     setOutputSpy?.mockRestore();
     infoSpy?.mockRestore();
+    warningSpy?.mockRestore();
     try {
       await unlink(TEST_EXECUTION_FILE);
     } catch {
@@ -156,3 +162,66 @@ describe("parseAndSetStructuredOutputs", () => {
     );
   });
 });
+
+describe("parseAndSetSessionId", () => {
+  afterEach(async () => {
+    setOutputSpy?.mockRestore();
+    infoSpy?.mockRestore();
+    warningSpy?.mockRestore();
+    try {
+      await unlink(TEST_EXECUTION_FILE);
+    } catch {
+      // Ignore if file doesn't exist
+    }
+  });
+
+  test("should extract session_id from system.init message", async () => {
+    const messages = [
+      { type: "system", subtype: "init", session_id: "test-session-123" },
+      { type: "result", cost_usd: 0.01 },
+    ];
+    await writeFile(TEST_EXECUTION_FILE, JSON.stringify(messages));
+
+    await parseAndSetSessionId(TEST_EXECUTION_FILE);
+
+    expect(setOutputSpy).toHaveBeenCalledWith("session_id", "test-session-123");
+    expect(infoSpy).toHaveBeenCalledWith("Set session_id: test-session-123");
+  });
+
+  test("should handle missing session_id gracefully", async () => {
+    const messages = [
+      { type: "system", subtype: "init" },
+      { type: "result", cost_usd: 0.01 },
+    ];
+    await writeFile(TEST_EXECUTION_FILE, JSON.stringify(messages));
+
+    await parseAndSetSessionId(TEST_EXECUTION_FILE);
+
+    expect(setOutputSpy).not.toHaveBeenCalled();
+  });
+
+  test("should handle missing system.init message gracefully", async () => {
+    const messages = [{ type: "result", cost_usd: 0.01 }];
+    await writeFile(TEST_EXECUTION_FILE, JSON.stringify(messages));
+
+    await parseAndSetSessionId(TEST_EXECUTION_FILE);
+
+    expect(setOutputSpy).not.toHaveBeenCalled();
+  });
+
+  test("should handle malformed JSON gracefully with warning", async () => {
+    await writeFile(TEST_EXECUTION_FILE, "{ invalid json");
+
+    await parseAndSetSessionId(TEST_EXECUTION_FILE);
+
+    expect(setOutputSpy).not.toHaveBeenCalled();
+    expect(warningSpy).toHaveBeenCalled();
+  });
+
+  test("should handle non-existent file gracefully with warning", async () => {
+    await parseAndSetSessionId("/nonexistent/file.json");
+
+    expect(setOutputSpy).not.toHaveBeenCalled();
+    expect(warningSpy).toHaveBeenCalled();
+  });
+});

bun.lock

@@ -1,12 +1,13 @@
 {
   "lockfileVersion": 1,
+  "configVersion": 0,
   "workspaces": {
     "": {
       "name": "@anthropic-ai/claude-code-action",
       "dependencies": {
         "@actions/core": "^1.10.1",
         "@actions/github": "^6.0.1",
-        "@anthropic-ai/claude-agent-sdk": "^0.1.52",
+        "@anthropic-ai/claude-agent-sdk": "^0.1.70",
         "@modelcontextprotocol/sdk": "^1.11.0",
         "@octokit/graphql": "^8.2.2",
         "@octokit/rest": "^21.1.1",
@@ -36,7 +37,7 @@
 
     "@actions/io": ["@actions/io@1.1.3", "", {}, "sha512-wi9JjgKLYS7U/z8PPbco+PvTb/nRWjeoFlJ1Qer83k/3C5PHQi28hiVdeE2kHXmIL99mQFawx8qt/JPjZilJ8Q=="],
 
-    "@anthropic-ai/claude-agent-sdk": ["@anthropic-ai/claude-agent-sdk@0.1.52", "", { "optionalDependencies": { "@img/sharp-darwin-arm64": "^0.33.5", "@img/sharp-darwin-x64": "^0.33.5", "@img/sharp-linux-arm": "^0.33.5", "@img/sharp-linux-arm64": "^0.33.5", "@img/sharp-linux-x64": "^0.33.5", "@img/sharp-linuxmusl-arm64": "^0.33.5", "@img/sharp-linuxmusl-x64": "^0.33.5", "@img/sharp-win32-x64": "^0.33.5" }, "peerDependencies": { "zod": "^3.24.1" } }, "sha512-yF8N05+9NRbqYA/h39jQ726HTQFrdXXp7pEfDNKIJ2c4FdWvEjxBA/8ciZIebN6/PyvGDcbEp3yq2Co4rNpg6A=="],
+    "@anthropic-ai/claude-agent-sdk": ["@anthropic-ai/claude-agent-sdk@0.1.70", "", { "optionalDependencies": { "@img/sharp-darwin-arm64": "^0.33.5", "@img/sharp-darwin-x64": "^0.33.5", "@img/sharp-linux-arm": "^0.33.5", "@img/sharp-linux-arm64": "^0.33.5", "@img/sharp-linux-x64": "^0.33.5", "@img/sharp-linuxmusl-arm64": "^0.33.5", "@img/sharp-linuxmusl-x64": "^0.33.5", "@img/sharp-win32-x64": "^0.33.5" }, "peerDependencies": { "zod": "^3.24.1" } }, "sha512-4jpFPDX8asys6skO1r3Pzh0Fe9nbND2ASYTWuyFB5iN9bWEL6WScTFyGokjql3M2TkEp9ZGuB2YYpTCdaqT9Sw=="],
 
     "@fastify/busboy": ["@fastify/busboy@2.1.1", "", {}, "sha512-vBZP4NlzfOlerQTnba4aqZoMhE/a9HY7HRqoOPaETQcSQuWEIyZMHGfVu6w9wGtGK5fED5qRs2DteVCjOH60sA=="],
 

package.json

@@ -12,7 +12,7 @@
   "dependencies": {
     "@actions/core": "^1.10.1",
     "@actions/github": "^6.0.1",
-    "@anthropic-ai/claude-agent-sdk": "^0.1.52",
+    "@anthropic-ai/claude-agent-sdk": "^0.1.70",
     "@modelcontextprotocol/sdk": "^1.11.0",
     "@octokit/graphql": "^8.2.2",
     "@octokit/rest": "^21.1.1",

src/github/operations/branch.ts

@@ -6,13 +6,112 @@
  * - For Issues: Create a new branch
  */
 
-import { $ } from "bun";
+import { execFileSync } from "child_process";
 import * as core from "@actions/core";
 import type { ParsedGitHubContext } from "../context";
 import type { GitHubPullRequest } from "../types";
 import type { Octokits } from "../api/client";
 import type { FetchDataResult } from "../data/fetcher";
 
+/**
+ * Validates a git branch name against a strict whitelist pattern.
+ * This prevents command injection by ensuring only safe characters are used.
+ *
+ * Valid branch names:
+ * - Start with alphanumeric character (not dash, to prevent option injection)
+ * - Contain only alphanumeric, forward slash, hyphen, underscore, or period
+ * - Do not start or end with a period
+ * - Do not end with a slash
+ * - Do not contain '..' (path traversal)
+ * - Do not contain '//' (consecutive slashes)
+ * - Do not end with '.lock'
+ * - Do not contain '@{'
+ * - Do not contain control characters or special git characters (~^:?*[\])
+ */
+export function validateBranchName(branchName: string): void {
+  // Check for empty or whitespace-only names
+  if (!branchName || branchName.trim().length === 0) {
+    throw new Error("Branch name cannot be empty");
+  }
+
+  // Check for leading dash (prevents option injection like --help, -x)
+  if (branchName.startsWith("-")) {
+    throw new Error(
+      `Invalid branch name: "${branchName}". Branch names cannot start with a dash.`,
+    );
+  }
+
+  // Check for control characters and special git characters (~^:?*[\])
+  // eslint-disable-next-line no-control-regex
+  if (/[\x00-\x1F\x7F ~^:?*[\]\\]/.test(branchName)) {
+    throw new Error(
+      `Invalid branch name: "${branchName}". Branch names cannot contain control characters, spaces, or special git characters (~^:?*[\\]).`,
+    );
+  }
+
+  // Strict whitelist pattern: alphanumeric start, then alphanumeric/slash/hyphen/underscore/period
+  const validPattern = /^[a-zA-Z0-9][a-zA-Z0-9/_.-]*$/;
+
+  if (!validPattern.test(branchName)) {
+    throw new Error(
+      `Invalid branch name: "${branchName}". Branch names must start with an alphanumeric character and contain only alphanumeric characters, forward slashes, hyphens, underscores, or periods.`,
+    );
+  }
+
+  // Check for leading/trailing periods
+  if (branchName.startsWith(".") || branchName.endsWith(".")) {
+    throw new Error(
+      `Invalid branch name: "${branchName}". Branch names cannot start or end with a period.`,
+    );
+  }
+
+  // Check for trailing slash
+  if (branchName.endsWith("/")) {
+    throw new Error(
+      `Invalid branch name: "${branchName}". Branch names cannot end with a slash.`,
+    );
+  }
+
+  // Check for consecutive slashes
+  if (branchName.includes("//")) {
+    throw new Error(
+      `Invalid branch name: "${branchName}". Branch names cannot contain consecutive slashes.`,
+    );
+  }
+
+  // Additional git-specific validations
+  if (branchName.includes("..")) {
+    throw new Error(
+      `Invalid branch name: "${branchName}". Branch names cannot contain '..'`,
+    );
+  }
+
+  if (branchName.endsWith(".lock")) {
+    throw new Error(
+      `Invalid branch name: "${branchName}". Branch names cannot end with '.lock'`,
+    );
+  }
+
+  if (branchName.includes("@{")) {
+    throw new Error(
+      `Invalid branch name: "${branchName}". Branch names cannot contain '@{'`,
+    );
+  }
+}
+
+/**
+ * Executes a git command safely using execFileSync to avoid shell interpolation.
+ *
+ * Security: execFileSync passes arguments directly to the git binary without
+ * invoking a shell, preventing command injection attacks where malicious input
+ * could be interpreted as shell commands (e.g., branch names containing `;`, `|`, `&&`).
+ *
+ * @param args - Git command arguments (e.g., ["checkout", "branch-name"])
+ */
+function execGit(args: string[]): void {
+  execFileSync("git", args, { stdio: "inherit" });
+}
+
 export type BranchInfo = {
   baseBranch: string;
   claudeBranch?: string;
@@ -53,14 +152,19 @@ export async function setupBranch(
         `PR #${entityNumber}: ${commitCount} commits, using fetch depth ${fetchDepth}`,
       );
 
+      // Validate branch names before use to prevent command injection
+      validateBranchName(branchName);
+
       // Execute git commands to checkout PR branch (dynamic depth based on PR size)
-      await $`git fetch origin --depth=${fetchDepth} ${branchName}`;
+      // Using execFileSync instead of shell template literals for security
-      await $`git checkout ${branchName} --`;
+      execGit(["fetch", "origin", `--depth=${fetchDepth}`, branchName]);
+      execGit(["checkout", branchName, "--"]);
 
       console.log(`Successfully checked out PR branch for PR #${entityNumber}`);
 
       // For open PRs, we need to get the base branch of the PR
       const baseBranch = prData.baseRefName;
+      validateBranchName(baseBranch);
 
       return {
         baseBranch,
@@ -118,8 +222,9 @@ export async function setupBranch(
 
       // Ensure we're on the source branch
       console.log(`Fetching and checking out source branch: ${sourceBranch}`);
-      await $`git fetch origin ${sourceBranch} --depth=1`;
+      validateBranchName(sourceBranch);
-      await $`git checkout ${sourceBranch}`;
+      execGit(["fetch", "origin", sourceBranch, "--depth=1"]);
+      execGit(["checkout", sourceBranch, "--"]);
 
       // Set outputs for GitHub Actions
       core.setOutput("CLAUDE_BRANCH", newBranch);
@@ -138,11 +243,13 @@ export async function setupBranch(
 
     // Fetch and checkout the source branch first to ensure we branch from the correct base
     console.log(`Fetching and checking out source branch: ${sourceBranch}`);
-    await $`git fetch origin ${sourceBranch} --depth=1`;
+    validateBranchName(sourceBranch);
-    await $`git checkout ${sourceBranch}`;
+    validateBranchName(newBranch);
+    execGit(["fetch", "origin", sourceBranch, "--depth=1"]);
+    execGit(["checkout", sourceBranch, "--"]);
 
     // Create and checkout the new branch from the source branch
-    await $`git checkout -b ${newBranch}`;
+    execGit(["checkout", "-b", newBranch]);
 
     console.log(
       `Successfully created and checked out local branch: ${newBranch}`,

src/modes/agent/parse-tools.ts

@@ -1,22 +1,55 @@
-export function parseAllowedTools(claudeArgs: string): string[] {
+import { parse as parseShellArgs, type ParseEntry } from "shell-quote";
-  // Match --allowedTools or --allowed-tools followed by the value
-  // Handle both quoted and unquoted values
-  const patterns = [
-    /--(?:allowedTools|allowed-tools)\s+"([^"]+)"/, // Double quoted
-    /--(?:allowedTools|allowed-tools)\s+'([^']+)'/, // Single quoted
-    /--(?:allowedTools|allowed-tools)\s+([^\s]+)/, // Unquoted
-  ];
 
-  for (const pattern of patterns) {
+/**
-    const match = claudeArgs.match(pattern);
+ * Extract the string value from a shell-quote ParseEntry.
-    if (match && match[1]) {
+ * Handles both plain strings and glob patterns (which are returned as objects).
-      // Don't return if the value starts with -- (another flag)
+ */
-      if (match[1].startsWith("--")) {
+function entryToString(entry: ParseEntry): string | null {
-        return [];
+  if (typeof entry === "string") {
+    return entry;
+  }
+  // Handle glob patterns - shell-quote returns { op: "glob", pattern: "..." }
+  if (typeof entry === "object" && "op" in entry && entry.op === "glob") {
+    return (entry as { op: "glob"; pattern: string }).pattern;
+  }
+  return null;
+}
+
+export function parseAllowedTools(claudeArgs: string): string[] {
+  if (!claudeArgs?.trim()) return [];
+
+  const result: string[] = [];
+
+  // Use shell-quote to properly tokenize the arguments
+  // This handles quoted strings, escaped characters, etc.
+  const rawArgs = parseShellArgs(claudeArgs);
+
+  for (let i = 0; i < rawArgs.length; i++) {
+    const entry = rawArgs[i];
+    if (!entry) continue;
+    const arg = entryToString(entry);
+    if (!arg) continue;
+
+    // Match both --allowedTools and --allowed-tools
+    if (arg === "--allowedTools" || arg === "--allowed-tools") {
+      // Collect all subsequent non-flag values as tools
+      while (i + 1 < rawArgs.length) {
+        const nextEntry = rawArgs[i + 1];
+        if (!nextEntry) break;
+        const toolArg = entryToString(nextEntry);
+
+        // Stop if we hit another flag or a non-parseable entry
+        if (!toolArg || toolArg.startsWith("--")) {
+          break;
+        }
+
+        // Split by comma in case tools are comma-separated within a single value
+        const tools = toolArg.split(",").map((t) => t.trim());
+        result.push(...tools.filter((t) => t.length > 0));
+        i++;
       }
-      return match[1].split(",").map((t) => t.trim());
     }
   }
 
-  return [];
+  return result;
 }

test/modes/parse-tools.test.ts

@@ -37,8 +37,9 @@ describe("parseAllowedTools", () => {
 
   test("handles duplicate --allowedTools flags", () => {
     const args = "--allowedTools --allowedTools mcp__github__*";
-    // Should not match the first one since the value is another flag
+    // Should skip the first one since the value is another flag
-    expect(parseAllowedTools(args)).toEqual([]);
+    // and parse the second one correctly
+    expect(parseAllowedTools(args)).toEqual(["mcp__github__*"]);
   });
 
   test("handles typo --alloedTools", () => {
@@ -84,4 +85,50 @@ describe("parseAllowedTools", () => {
       "mcp__github_comment__*",
     ]);
   });
+
+  test("parses multiple space-separated quoted tools (issue #746)", () => {
+    // This is the exact format from the bug report
+    const args =
+      '--allowed-tools "Bash(git log:*)" "Bash(git diff:*)" "Bash(git fetch:*)" "Bash(gh pr:*)"';
+    expect(parseAllowedTools(args)).toEqual([
+      "Bash(git log:*)",
+      "Bash(git diff:*)",
+      "Bash(git fetch:*)",
+      "Bash(gh pr:*)",
+    ]);
+  });
+
+  test("parses multiple --allowedTools flags with different tools", () => {
+    const args =
+      '--allowedTools "Edit,Read" --model "claude-3" --allowedTools "Bash(npm install)"';
+    expect(parseAllowedTools(args)).toEqual([
+      "Edit",
+      "Read",
+      "Bash(npm install)",
+    ]);
+  });
+
+  test("parses mix of comma-separated and space-separated tools", () => {
+    const args =
+      '--allowed-tools "Bash(git log:*),Bash(git diff:*)" "Bash(git fetch:*)"';
+    expect(parseAllowedTools(args)).toEqual([
+      "Bash(git log:*)",
+      "Bash(git diff:*)",
+      "Bash(git fetch:*)",
+    ]);
+  });
+
+  test("handles complex workflow example from issue #746", () => {
+    const args =
+      '--allowed-tools "Bash(git log:*)" "Bash(git diff:*)" "Bash(git fetch:*)" "Bash(git reflog:*)" "Bash(git merge-tree:*)" "Bash(gh pr:*)" "Bash(gh api:*)"';
+    expect(parseAllowedTools(args)).toEqual([
+      "Bash(git log:*)",
+      "Bash(git diff:*)",
+      "Bash(git fetch:*)",
+      "Bash(git reflog:*)",
+      "Bash(git merge-tree:*)",
+      "Bash(gh pr:*)",
+      "Bash(gh api:*)",
+    ]);
+  });
 });

test/validate-branch-name.test.ts

@@ -0,0 +1,201 @@
+import { describe, expect, it } from "bun:test";
+import { validateBranchName } from "../src/github/operations/branch";
+
+describe("validateBranchName", () => {
+  describe("valid branch names", () => {
+    it("should accept simple alphanumeric names", () => {
+      expect(() => validateBranchName("main")).not.toThrow();
+      expect(() => validateBranchName("feature123")).not.toThrow();
+      expect(() => validateBranchName("Branch1")).not.toThrow();
+    });
+
+    it("should accept names with hyphens", () => {
+      expect(() => validateBranchName("feature-branch")).not.toThrow();
+      expect(() => validateBranchName("fix-bug-123")).not.toThrow();
+    });
+
+    it("should accept names with underscores", () => {
+      expect(() => validateBranchName("feature_branch")).not.toThrow();
+      expect(() => validateBranchName("fix_bug_123")).not.toThrow();
+    });
+
+    it("should accept names with forward slashes", () => {
+      expect(() => validateBranchName("feature/new-thing")).not.toThrow();
+      expect(() => validateBranchName("user/feature/branch")).not.toThrow();
+    });
+
+    it("should accept names with periods", () => {
+      expect(() => validateBranchName("v1.0.0")).not.toThrow();
+      expect(() => validateBranchName("release.1.2.3")).not.toThrow();
+    });
+
+    it("should accept typical branch name formats", () => {
+      expect(() =>
+        validateBranchName("claude/issue-123-20250101-1234"),
+      ).not.toThrow();
+      expect(() => validateBranchName("refs/heads/main")).not.toThrow();
+      expect(() => validateBranchName("bugfix/JIRA-1234")).not.toThrow();
+    });
+  });
+
+  describe("command injection attempts", () => {
+    it("should reject shell command substitution with $()", () => {
+      expect(() => validateBranchName("$(whoami)")).toThrow();
+      expect(() => validateBranchName("branch-$(rm -rf /)")).toThrow();
+      expect(() => validateBranchName("test$(cat /etc/passwd)")).toThrow();
+    });
+
+    it("should reject shell command substitution with backticks", () => {
+      expect(() => validateBranchName("`whoami`")).toThrow();
+      expect(() => validateBranchName("branch-`rm -rf /`")).toThrow();
+    });
+
+    it("should reject command chaining with semicolons", () => {
+      expect(() => validateBranchName("branch; rm -rf /")).toThrow();
+      expect(() => validateBranchName("test;whoami")).toThrow();
+    });
+
+    it("should reject command chaining with &&", () => {
+      expect(() => validateBranchName("branch && rm -rf /")).toThrow();
+      expect(() => validateBranchName("test&&whoami")).toThrow();
+    });
+
+    it("should reject command chaining with ||", () => {
+      expect(() => validateBranchName("branch || rm -rf /")).toThrow();
+      expect(() => validateBranchName("test||whoami")).toThrow();
+    });
+
+    it("should reject pipe characters", () => {
+      expect(() => validateBranchName("branch | cat")).toThrow();
+      expect(() => validateBranchName("test|grep password")).toThrow();
+    });
+
+    it("should reject redirection operators", () => {
+      expect(() => validateBranchName("branch > /etc/passwd")).toThrow();
+      expect(() => validateBranchName("branch < input")).toThrow();
+      expect(() => validateBranchName("branch >> file")).toThrow();
+    });
+  });
+
+  describe("option injection attempts", () => {
+    it("should reject branch names starting with dash", () => {
+      expect(() => validateBranchName("-x")).toThrow(
+        /cannot start with a dash/,
+      );
+      expect(() => validateBranchName("--help")).toThrow(
+        /cannot start with a dash/,
+      );
+      expect(() => validateBranchName("-")).toThrow(/cannot start with a dash/);
+      expect(() => validateBranchName("--version")).toThrow(
+        /cannot start with a dash/,
+      );
+      expect(() => validateBranchName("-rf")).toThrow(
+        /cannot start with a dash/,
+      );
+    });
+  });
+
+  describe("path traversal attempts", () => {
+    it("should reject double dot sequences", () => {
+      expect(() => validateBranchName("../../../etc")).toThrow();
+      expect(() => validateBranchName("branch/../secret")).toThrow(/'\.\.'$/);
+      expect(() => validateBranchName("a..b")).toThrow(/'\.\.'$/);
+    });
+  });
+
+  describe("git-specific invalid patterns", () => {
+    it("should reject @{ sequence", () => {
+      expect(() => validateBranchName("branch@{1}")).toThrow(/@{/);
+      expect(() => validateBranchName("HEAD@{yesterday}")).toThrow(/@{/);
+    });
+
+    it("should reject .lock suffix", () => {
+      expect(() => validateBranchName("branch.lock")).toThrow(/\.lock/);
+      expect(() => validateBranchName("feature.lock")).toThrow(/\.lock/);
+    });
+
+    it("should reject consecutive slashes", () => {
+      expect(() => validateBranchName("feature//branch")).toThrow(
+        /consecutive slashes/,
+      );
+      expect(() => validateBranchName("a//b//c")).toThrow(
+        /consecutive slashes/,
+      );
+    });
+
+    it("should reject trailing slashes", () => {
+      expect(() => validateBranchName("feature/")).toThrow(
+        /cannot end with a slash/,
+      );
+      expect(() => validateBranchName("branch/")).toThrow(
+        /cannot end with a slash/,
+      );
+    });
+
+    it("should reject leading periods", () => {
+      expect(() => validateBranchName(".hidden")).toThrow();
+    });
+
+    it("should reject trailing periods", () => {
+      expect(() => validateBranchName("branch.")).toThrow(
+        /cannot start or end with a period/,
+      );
+    });
+
+    it("should reject special git refspec characters", () => {
+      expect(() => validateBranchName("branch~1")).toThrow();
+      expect(() => validateBranchName("branch^2")).toThrow();
+      expect(() => validateBranchName("branch:ref")).toThrow();
+      expect(() => validateBranchName("branch?")).toThrow();
+      expect(() => validateBranchName("branch*")).toThrow();
+      expect(() => validateBranchName("branch[0]")).toThrow();
+      expect(() => validateBranchName("branch\\path")).toThrow();
+    });
+  });
+
+  describe("control characters and special characters", () => {
+    it("should reject null bytes", () => {
+      expect(() => validateBranchName("branch\x00name")).toThrow();
+    });
+
+    it("should reject other control characters", () => {
+      expect(() => validateBranchName("branch\x01name")).toThrow();
+      expect(() => validateBranchName("branch\x1Fname")).toThrow();
+      expect(() => validateBranchName("branch\x7Fname")).toThrow();
+    });
+
+    it("should reject spaces", () => {
+      expect(() => validateBranchName("branch name")).toThrow();
+      expect(() => validateBranchName("feature branch")).toThrow();
+    });
+
+    it("should reject newlines and tabs", () => {
+      expect(() => validateBranchName("branch\nname")).toThrow();
+      expect(() => validateBranchName("branch\tname")).toThrow();
+    });
+  });
+
+  describe("empty and whitespace", () => {
+    it("should reject empty strings", () => {
+      expect(() => validateBranchName("")).toThrow(/cannot be empty/);
+    });
+
+    it("should reject whitespace-only strings", () => {
+      expect(() => validateBranchName("   ")).toThrow();
+      expect(() => validateBranchName("\t\n")).toThrow();
+    });
+  });
+
+  describe("edge cases", () => {
+    it("should accept single alphanumeric character", () => {
+      expect(() => validateBranchName("a")).not.toThrow();
+      expect(() => validateBranchName("1")).not.toThrow();
+    });
+
+    it("should reject single special characters", () => {
+      expect(() => validateBranchName(".")).toThrow();
+      expect(() => validateBranchName("/")).toThrow();
+      expect(() => validateBranchName("-")).toThrow();
+    });
+  });
+});