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"

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"
@@ -195,7 +198,7 @@ runs:
 
         # Install Claude Code if no custom executable is provided
         if [ -z "$PATH_TO_CLAUDE_CODE_EXECUTABLE" ]; then
-          CLAUDE_CODE_VERSION="2.0.69"
+          CLAUDE_CODE_VERSION="2.0.70"
           echo "Installing Claude Code v${CLAUDE_CODE_VERSION}..."
           for attempt in 1 2 3; do
             echo "Installation attempt $attempt..."

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"
@@ -121,7 +124,7 @@ runs:
         PATH_TO_CLAUDE_CODE_EXECUTABLE: ${{ inputs.path_to_claude_code_executable }}
       run: |
         if [ -z "$PATH_TO_CLAUDE_CODE_EXECUTABLE" ]; then
-          CLAUDE_CODE_VERSION="2.0.69"
+          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..."

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.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
@@ -368,6 +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=="],
 

examples/test-failure-analysis.yml

@@ -53,7 +53,6 @@ jobs:
           fromJSON(steps.detect.outputs.structured_output).confidence >= 0.7
         env:
           GH_TOKEN: ${{ github.token }}
-          HEAD_BRANCH: ${{ github.event.workflow_run.head_branch }}
         run: |
           OUTPUT='${{ steps.detect.outputs.structured_output }}'
           CONFIDENCE=$(echo "$OUTPUT" | jq -r '.confidence')
@@ -65,7 +64,7 @@ jobs:
           echo "Triggering automatic retry..."
 
           gh workflow run "${{ github.event.workflow_run.name }}" \
-            --ref "$HEAD_BRANCH"
+            --ref "${{ github.event.workflow_run.head_branch }}"
 
       # Low confidence flaky detection - skip retry
       - name: Low confidence detection
@@ -84,14 +83,13 @@ jobs:
         if: github.event.workflow_run.event == 'pull_request'
         env:
           GH_TOKEN: ${{ github.token }}
-          HEAD_BRANCH: ${{ github.event.workflow_run.head_branch }}
         run: |
           OUTPUT='${{ steps.detect.outputs.structured_output }}'
           IS_FLAKY=$(echo "$OUTPUT" | jq -r '.is_flaky')
           CONFIDENCE=$(echo "$OUTPUT" | jq -r '.confidence')
           SUMMARY=$(echo "$OUTPUT" | jq -r '.summary')
 
-          pr_number=$(gh pr list --head "$HEAD_BRANCH" --json number --jq '.[0].number')
+          pr_number=$(gh pr list --head "${{ github.event.workflow_run.head_branch }}" --json number --jq '.[0].number')
 
           if [ -n "$pr_number" ]; then
             if [ "$IS_FLAKY" = "true" ]; then

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/modes/agent/parse-tools.ts

@@ -1,22 +1,55 @@
-export function parseAllowedTools(claudeArgs: string): string[] {
-  // 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
-  ];
+import { parse as parseShellArgs, type ParseEntry } from "shell-quote";
 
-  for (const pattern of patterns) {
-    const match = claudeArgs.match(pattern);
-    if (match && match[1]) {
-      // Don't return if the value starts with -- (another flag)
-      if (match[1].startsWith("--")) {
-        return [];
+/**
+ * Extract the string value from a shell-quote ParseEntry.
+ * Handles both plain strings and glob patterns (which are returned as objects).
+ */
+function entryToString(entry: ParseEntry): string | null {
+  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
-    expect(parseAllowedTools(args)).toEqual([]);
+    // Should skip the first one since the value is another flag
+    // 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:*)",
+    ]);
+  });
 });