Create fix-ci.md

Add file permission detection to github-file-ops-server.ts to properly preserve file modes (regular, executable, symlink) when committing files through the GitHub API. This ensures executable scripts and other special files maintain their correct permissions.

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

Co-authored-by: Claude <noreply@anthropic.com>

.claude/commands/fix-ci.md

@@ -0,0 +1,102 @@
+---
+description: Analyze and fix CI failures by examining logs and making targeted fixes
+allowed_tools: Edit,MultiEdit,Write,Read,Glob,Grep,LS,Bash(git:*),Bash(bun:*),Bash(npm:*),Bash(npx:*),Bash(gh:*)
+---
+
+# Fix CI Failures
+
+You are tasked with analyzing CI failure logs and fixing the issues. Follow these steps:
+
+## Context Provided
+
+$ARGUMENTS
+
+## Important Context Information
+
+Look for these key pieces of information in the arguments:
+
+- **Failed CI Run URL**: Link to the failed CI run
+- **Failed Jobs**: List of jobs that failed
+- **PR Number**: The PR number to comment on
+- **Branch Name**: The fix branch you're working on
+- **Base Branch**: The original PR branch
+- **Error logs**: Detailed logs from failed jobs
+
+## Step 1: Analyze the Failure
+
+Parse the provided CI failure information to understand:
+
+- Which jobs failed and why
+- The specific error messages and stack traces
+- Whether failures are test-related, build-related, or linting issues
+
+## Step 2: Search and Understand the Codebase
+
+Use search tools to locate the failing code:
+
+- Search for the failing test names or functions
+- Find the source files mentioned in error messages
+- Review related configuration files (package.json, tsconfig.json, etc.)
+
+## Step 3: Apply Targeted Fixes
+
+Make minimal, focused changes:
+
+- **For test failures**: Determine if the test or implementation needs fixing
+- **For type errors**: Fix type definitions or correct the code logic
+- **For linting issues**: Apply formatting using the project's tools
+- **For build errors**: Resolve dependency or configuration issues
+- **For missing imports**: Add the necessary imports or install packages
+
+Requirements:
+
+- Only fix the actual CI failures, avoid unrelated changes
+- Follow existing code patterns and conventions
+- Ensure changes are production-ready, not temporary hacks
+- Preserve existing functionality while fixing issues
+
+## Step 4: Commit and Push Changes
+
+After applying ALL fixes:
+
+1. Stage all modified files with `git add -A`
+2. Commit with: `git commit -m "Fix CI failures: [describe specific fixes]"`
+3. Document which CI jobs/tests were addressed
+4. **CRITICAL**: Push the branch with `git push origin HEAD` - You MUST push the branch after committing
+
+## Step 5: Create PR Comment
+
+After successfully pushing the fixes, create a comment on the original PR to notify about the auto-fix:
+
+1. Extract the PR number, branch name, and base branch from the context provided
+2. Use gh CLI to create a comment with the fix information
+3. Include a link to create a pull request from the fix branch
+
+Use this command format (replace placeholders with actual values):
+```bash
+gh pr comment PR_NUMBER --body "## 🤖 CI Auto-Fix Available
+
+Claude has analyzed the CI failures and prepared fixes.
+
+[**→ Create pull request to fix CI**](https://github.com/OWNER/REPO/compare/BASE_BRANCH...FIX_BRANCH?quick_pull=1)
+
+_This fix was generated automatically based on the failed CI run._"
+```
+
+## Step 6: Verify Fixes Locally
+
+Run available verification commands:
+
+- Execute the failing tests locally to confirm they pass
+- Run the project's lint command (check package.json for scripts)
+- Run type checking if available
+- Execute any build commands to ensure compilation succeeds
+
+## Important Guidelines
+
+- Focus exclusively on fixing the reported CI failures
+- Maintain code quality and follow the project's established patterns
+- If a fix requires significant refactoring, document why it's necessary
+- When multiple solutions exist, choose the simplest one that maintains code quality
+
+Begin by analyzing the failure details provided above.

action.yml

@@ -166,6 +166,7 @@ runs:
         DEFAULT_WORKFLOW_TOKEN: ${{ github.token }}
         ADDITIONAL_PERMISSIONS: ${{ inputs.additional_permissions }}
         USE_COMMIT_SIGNING: ${{ inputs.use_commit_signing }}
+        ALL_INPUTS: ${{ toJson(inputs) }}
 
     - name: Install Base Action Dependencies
       if: steps.prepare.outputs.contains_trigger == 'true'
@@ -177,7 +178,7 @@ runs:
         echo "Base-action dependencies installed"
         cd -
         # Install Claude Code globally
-        curl -fsSL https://claude.ai/install.sh | bash -s 1.0.83
+        curl -fsSL https://claude.ai/install.sh | bash -s 1.0.85
         echo "$HOME/.local/bin" >> "$GITHUB_PATH"
 
     - name: Setup Network Restrictions
@@ -212,6 +213,7 @@ runs:
         INPUT_CLAUDE_ENV: ${{ inputs.claude_env }}
         INPUT_FALLBACK_MODEL: ${{ inputs.fallback_model }}
         INPUT_EXPERIMENTAL_SLASH_COMMANDS_DIR: ${{ github.action_path }}/slash-commands
+        INPUT_ACTION_INPUTS_PRESENT: ${{ steps.prepare.outputs.action_inputs_present }}
 
         # Model configuration
         ANTHROPIC_MODEL: ${{ inputs.model || inputs.anthropic_model }}

base-action/action.yml

@@ -118,7 +118,7 @@ runs:
 
     - name: Install Claude Code
       shell: bash
-      run: curl -fsSL https://claude.ai/install.sh | bash -s 1.0.83
+      run: curl -fsSL https://claude.ai/install.sh | bash -s 1.0.85
 
     - name: Run Claude Code Action
       shell: bash

base-action/src/run-claude.ts

@@ -110,6 +110,10 @@ export function prepareRunConfig(
   // Parse custom environment variables
   const customEnv = parseCustomEnvVars(options.claudeEnv);
 
+  if (process.env.INPUT_ACTION_INPUTS_PRESENT) {
+    customEnv.GITHUB_ACTION_INPUTS = process.env.INPUT_ACTION_INPUTS_PRESENT;
+  }
+
   return {
     claudeArgs,
     promptPath,
@@ -142,9 +146,11 @@ export async function runClaude(promptPath: string, options: ClaudeOptions) {
   console.log(`Prompt file size: ${promptSize} bytes`);
 
   // Log custom environment variables if any
-  if (Object.keys(config.env).length > 0) {
-    const envKeys = Object.keys(config.env).join(", ");
-    console.log(`Custom environment variables: ${envKeys}`);
+  const customEnvKeys = Object.keys(config.env).filter(
+    (key) => key !== "CLAUDE_ACTION_INPUTS_PRESENT",
+  );
+  if (customEnvKeys.length > 0) {
+    console.log(`Custom environment variables: ${customEnvKeys.join(", ")}`);
   }
 
   // Output to console
@@ -169,7 +175,6 @@ export async function runClaude(promptPath: string, options: ClaudeOptions) {
       ...config.env,
     },
   });
-  console.log("yolo", process.env);
 
   // Handle Claude process errors
   claudeProcess.on("error", (error) => {

src/entrypoints/collect-inputs.ts

@@ -0,0 +1,59 @@
+import * as core from "@actions/core";
+
+export function collectActionInputsPresence(): void {
+  const inputDefaults: Record<string, string> = {
+    trigger_phrase: "@claude",
+    assignee_trigger: "",
+    label_trigger: "claude",
+    base_branch: "",
+    branch_prefix: "claude/",
+    allowed_bots: "",
+    mode: "tag",
+    model: "",
+    anthropic_model: "",
+    fallback_model: "",
+    allowed_tools: "",
+    disallowed_tools: "",
+    custom_instructions: "",
+    direct_prompt: "",
+    override_prompt: "",
+    mcp_config: "",
+    additional_permissions: "",
+    claude_env: "",
+    settings: "",
+    anthropic_api_key: "",
+    claude_code_oauth_token: "",
+    github_token: "",
+    max_turns: "",
+    use_sticky_comment: "false",
+    use_commit_signing: "false",
+    experimental_allowed_domains: "",
+  };
+
+  const allInputsJson = process.env.ALL_INPUTS;
+  if (!allInputsJson) {
+    console.log("ALL_INPUTS environment variable not found");
+    core.setOutput("action_inputs_present", JSON.stringify({}));
+    return;
+  }
+
+  let allInputs: Record<string, string>;
+  try {
+    allInputs = JSON.parse(allInputsJson);
+  } catch (e) {
+    console.error("Failed to parse ALL_INPUTS JSON:", e);
+    core.setOutput("action_inputs_present", JSON.stringify({}));
+    return;
+  }
+
+  const presentInputs: Record<string, boolean> = {};
+
+  for (const [name, defaultValue] of Object.entries(inputDefaults)) {
+    const actualValue = allInputs[name] || "";
+
+    const isSet = actualValue !== defaultValue;
+    presentInputs[name] = isSet;
+  }
+
+  core.setOutput("action_inputs_present", JSON.stringify(presentInputs));
+}

src/entrypoints/prepare.ts

@@ -13,9 +13,12 @@ import { parseGitHubContext, isEntityContext } from "../github/context";
 import { getMode, isValidMode, DEFAULT_MODE } from "../modes/registry";
 import type { ModeName } from "../modes/types";
 import { prepare } from "../prepare";
+import { collectActionInputsPresence } from "./collect-inputs";
 
 async function run() {
   try {
+    collectActionInputsPresence();
+
     // Step 1: Get mode first to determine authentication method
     const modeInput = process.env.MODE || DEFAULT_MODE;
 

src/mcp/github-file-ops-server.ts

@@ -3,8 +3,9 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { z } from "zod";
-import { readFile } from "fs/promises";
+import { readFile, stat } from "fs/promises";
 import { join } from "path";
+import { constants } from "fs";
 import fetch from "node-fetch";
 import { GITHUB_API_URL } from "../github/api/config";
 import { retryWithBackoff } from "../utils/retry";
@@ -162,6 +163,34 @@ async function getOrCreateBranchRef(
   return baseSha;
 }
 
+// Get the appropriate Git file mode for a file
+async function getFileMode(filePath: string): Promise<string> {
+  try {
+    const fileStat = await stat(filePath);
+    if (fileStat.isFile()) {
+      // Check if execute bit is set for user
+      if (fileStat.mode & constants.S_IXUSR) {
+        return "100755"; // Executable file
+      } else {
+        return "100644"; // Regular file
+      }
+    } else if (fileStat.isDirectory()) {
+      return "040000"; // Directory (tree)
+    } else if (fileStat.isSymbolicLink()) {
+      return "120000"; // Symbolic link
+    } else {
+      // Fallback for unknown file types
+      return "100644";
+    }
+  } catch (error) {
+    // If we can't stat the file, default to regular file
+    console.warn(
+      `Could not determine file mode for ${filePath}, using default: ${error}`,
+    );
+    return "100644";
+  }
+}
+
 // Commit files tool
 server.tool(
   "commit_files",
@@ -223,6 +252,9 @@ server.tool(
             ? filePath
             : join(REPO_DIR, filePath);
 
+          // Get the proper file mode based on file permissions
+          const fileMode = await getFileMode(fullPath);
+
           // Check if file is binary (images, etc.)
           const isBinaryFile =
             /\.(png|jpg|jpeg|gif|webp|ico|pdf|zip|tar|gz|exe|bin|woff|woff2|ttf|eot)$/i.test(
@@ -261,7 +293,7 @@ server.tool(
             // Return tree entry with blob SHA
             return {
               path: filePath,
-              mode: "100644",
+              mode: fileMode,
               type: "blob",
               sha: blobData.sha,
             };
@@ -270,7 +302,7 @@ server.tool(
             const content = await readFile(fullPath, "utf-8");
             return {
               path: filePath,
-              mode: "100644",
+              mode: fileMode,
               type: "blob",
               content: content,
             };