feat: add comprehensive response logging for GitHub API errors

- Log entire raw response body in text, hex, and base64 formats
- Capture complete request context including timing and memory usage
- Add detailed error response parsing with fallback handling
- Include environment and operation state context
- Special handling for 500 errors with GitHub request IDs
- Log all response headers including rate limit info

.github/workflows/claude.yml

@@ -31,6 +31,6 @@ jobs:
 
       - name: Run Claude Code
         id: claude
-        uses: anthropics/claude-code-action@beta
+        uses: ./
         with:
           anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}

check-pr-status.ts

@@ -0,0 +1,93 @@
+#!/usr/bin/env bun
+// Check the status of PR #105775
+
+const GITHUB_API_URL = "https://api.github.com";
+
+async function checkPRStatus(token: string) {
+  const headers = {
+    Accept: "application/vnd.github+json",
+    Authorization: `Bearer ${token}`,
+    "X-GitHub-Api-Version": "2022-11-28",
+  };
+
+  try {
+    // Check PR details
+    console.log("Checking PR #105775...\n");
+    const prResponse = await fetch(
+      `${GITHUB_API_URL}/repos/anthropics/anthropic/pulls/105775`,
+      { headers }
+    );
+    
+    console.log(`PR Status: ${prResponse.status}`);
+    
+    if (!prResponse.ok) {
+      if (prResponse.status === 404) {
+        console.log("PR not found - it might be in a private repo or deleted");
+      }
+      const error = await prResponse.text();
+      console.error(error);
+      return;
+    }
+    
+    const prData = await prResponse.json();
+    console.log(`Title: ${prData.title}`);
+    console.log(`State: ${prData.state}`);
+    console.log(`Branch: ${prData.head.ref}`);
+    console.log(`Base: ${prData.base.ref}`);
+    console.log(`Created: ${prData.created_at}`);
+    console.log(`Updated: ${prData.updated_at}`);
+    
+    // Check if branch still exists
+    console.log(`\nChecking if branch '${prData.head.ref}' still exists...`);
+    const branchResponse = await fetch(
+      `${GITHUB_API_URL}/repos/anthropics/anthropic/git/refs/heads/${prData.head.ref}`,
+      { headers }
+    );
+    
+    if (branchResponse.ok) {
+      const branchData = await branchResponse.json();
+      console.log(`✓ Branch exists with SHA: ${branchData.object.sha}`);
+      console.log(`  PR head SHA: ${prData.head.sha}`);
+      if (branchData.object.sha !== prData.head.sha) {
+        console.log(`  ⚠️  Branch has been updated since PR was created`);
+      }
+    } else {
+      console.log(`✗ Branch does not exist (${branchResponse.status})`);
+    }
+    
+    // Get recent comments
+    console.log(`\nFetching recent comments...`);
+    const commentsResponse = await fetch(
+      `${GITHUB_API_URL}/repos/anthropics/anthropic/issues/105775/comments?per_page=5&sort=created&direction=desc`,
+      { headers }
+    );
+    
+    if (commentsResponse.ok) {
+      const comments = await commentsResponse.json();
+      console.log(`Found ${comments.length} recent comments:`);
+      
+      comments.reverse().forEach((comment: any, index: number) => {
+        console.log(`\nComment ${index + 1}:`);
+        console.log(`  Author: ${comment.user.login}`);
+        console.log(`  Created: ${comment.created_at}`);
+        console.log(`  Body preview: ${comment.body.substring(0, 100)}...`);
+        
+        // Check if it's a claude-code-action comment
+        if (comment.body.includes("claude") || comment.user.login.includes("bot")) {
+          console.log(`  → Appears to be a Claude-related comment`);
+        }
+      });
+    }
+    
+  } catch (error) {
+    console.error("Error:", error);
+  }
+}
+
+const token = process.argv[2];
+if (!token) {
+  console.log("Usage: bun check-pr-status.ts <github-pat>");
+  process.exit(1);
+}
+
+checkPRStatus(token);

diagnose-app-permissions.ts

@@ -0,0 +1,183 @@
+#!/usr/bin/env bun
+// Diagnose why GitHub App permissions are inconsistent
+
+const GITHUB_API_URL = "https://api.github.com";
+
+async function diagnosePermissions(token: string, owner: string, repo: string) {
+  const headers = {
+    Accept: "application/vnd.github+json",
+    Authorization: `Bearer ${token}`,
+    "X-GitHub-Api-Version": "2022-11-28",
+  };
+
+  console.log(`\n=== Diagnosing GitHub App Permission Issues ===`);
+  console.log(`Repository: ${owner}/${repo}\n`);
+
+  try {
+    // 1. Check what type of token we have
+    console.log("1. Token Analysis:");
+    const authHeader = headers.Authorization;
+    if (authHeader.includes('ghs_')) {
+      console.log("✓ GitHub App installation token detected");
+    } else if (authHeader.includes('ghp_')) {
+      console.log("✓ Personal Access Token detected");
+    } else {
+      console.log("? Unknown token type");
+    }
+
+    // 2. Check rate limit headers (different for apps vs users)
+    console.log("\n2. Rate Limit Analysis:");
+    const rateLimitResponse = await fetch(`${GITHUB_API_URL}/rate_limit`, { headers });
+    if (rateLimitResponse.ok) {
+      const rateData = await rateLimitResponse.json();
+      console.log(`  Core limit: ${rateData.rate.remaining}/${rateData.rate.limit}`);
+      if (rateData.rate.limit > 5000) {
+        console.log("  → Higher limit suggests GitHub App token");
+      } else {
+        console.log("  → Standard limit suggests user token");
+      }
+    }
+
+    // 3. Test different API endpoints to find permission boundaries
+    console.log("\n3. Testing API Endpoints:");
+    
+    // Test regular content API
+    console.log("\n  a) Content API (high-level):");
+    const contentResponse = await fetch(
+      `${GITHUB_API_URL}/repos/${owner}/${repo}/contents/README.md`,
+      { headers }
+    );
+    console.log(`     GET contents: ${contentResponse.status} ${contentResponse.ok ? '✓' : '✗'}`);
+
+    // Test git database read
+    console.log("\n  b) Git Database API (read):");
+    const branchResponse = await fetch(
+      `${GITHUB_API_URL}/repos/${owner}/${repo}/branches`,
+      { headers }
+    );
+    if (branchResponse.ok) {
+      const branches = await branchResponse.json();
+      const defaultBranch = branches.find((b: any) => b.name === 'main' || b.name === 'master' || b.name === 'staging');
+      if (defaultBranch) {
+        const commitSha = defaultBranch.commit.sha;
+        
+        // Try to read commit
+        const commitResponse = await fetch(
+          `${GITHUB_API_URL}/repos/${owner}/${repo}/git/commits/${commitSha}`,
+          { headers }
+        );
+        console.log(`     GET commit: ${commitResponse.status} ${commitResponse.ok ? '✓' : '✗'}`);
+        
+        // Try to read tree
+        if (commitResponse.ok) {
+          const commitData = await commitResponse.json();
+          const treeResponse = await fetch(
+            `${GITHUB_API_URL}/repos/${owner}/${repo}/git/trees/${commitData.tree.sha}`,
+            { headers }
+          );
+          console.log(`     GET tree: ${treeResponse.status} ${treeResponse.ok ? '✓' : '✗'}`);
+        }
+      }
+    }
+
+    // Test git database write
+    console.log("\n  c) Git Database API (write):");
+    
+    // Get a base commit to test with
+    const testBranch = branches[0];
+    if (testBranch) {
+      const baseCommitResponse = await fetch(
+        `${GITHUB_API_URL}/repos/${owner}/${repo}/git/commits/${testBranch.commit.sha}`,
+        { headers }
+      );
+      
+      if (baseCommitResponse.ok) {
+        const baseCommit = await baseCommitResponse.json();
+        
+        // Try to create a blob
+        const blobResponse = await fetch(
+          `${GITHUB_API_URL}/repos/${owner}/${repo}/git/blobs`,
+          {
+            method: "POST",
+            headers: {
+              ...headers,
+              "Content-Type": "application/json",
+            },
+            body: JSON.stringify({
+              content: "test",
+              encoding: "utf-8",
+            }),
+          }
+        );
+        console.log(`     POST blob: ${blobResponse.status} ${blobResponse.ok ? '✓' : '✗'}`);
+        
+        // Try to create a tree
+        const treeResponse = await fetch(
+          `${GITHUB_API_URL}/repos/${owner}/${repo}/git/trees`,
+          {
+            method: "POST",
+            headers: {
+              ...headers,
+              "Content-Type": "application/json",
+            },
+            body: JSON.stringify({
+              base_tree: baseCommit.tree.sha,
+              tree: [{
+                path: "test-permission-check.txt",
+                mode: "100644",
+                type: "blob",
+                content: "test",
+              }],
+            }),
+          }
+        );
+        console.log(`     POST tree: ${treeResponse.status} ${treeResponse.ok ? '✓' : '✗'}`);
+        
+        if (!treeResponse.ok) {
+          const error = await treeResponse.text();
+          console.log(`     Error: ${error}`);
+        }
+      }
+    }
+
+    // 4. Check webhook/app events
+    console.log("\n4. Checking Recent Activity:");
+    const eventsResponse = await fetch(
+      `${GITHUB_API_URL}/repos/${owner}/${repo}/events?per_page=10`,
+      { headers }
+    );
+    
+    if (eventsResponse.ok) {
+      const events = await eventsResponse.json();
+      const appEvents = events.filter((e: any) => 
+        e.actor.login.includes('[bot]') || 
+        e.actor.type === 'Bot'
+      );
+      
+      console.log(`  Found ${appEvents.length} bot/app events in last 10 events`);
+      appEvents.forEach((event: any) => {
+        console.log(`  - ${event.actor.login}: ${event.type} at ${event.created_at}`);
+      });
+    }
+
+    // 5. Summary and recommendations
+    console.log("\n=== Analysis Summary ===");
+    console.log("\nPossible causes for inconsistent 500 errors:");
+    console.log("1. Race conditions with other bots (check events above)");
+    console.log("2. Token scope varies based on who triggered the action");
+    console.log("3. GitHub App needs to be reinstalled/reconfigured");
+    console.log("4. Branch-specific protection rules");
+    
+  } catch (error) {
+    console.error("\nError during diagnosis:", error);
+  }
+}
+
+const [token, owner, repo] = process.argv.slice(2);
+if (!token || !owner || !repo) {
+  console.log("Usage: bun diagnose-app-permissions.ts <token> <owner> <repo>");
+  console.log("\nThis script helps diagnose why GitHub App permissions are inconsistent.");
+  process.exit(1);
+}
+
+diagnosePermissions(token, owner, repo);

revert-test-commit.ts

@@ -0,0 +1,112 @@
+#!/usr/bin/env bun
+// Revert the test commit we just made
+
+const GITHUB_API_URL = "https://api.github.com";
+
+async function revertTestCommit(token: string) {
+  const owner = "anthropics";
+  const repo = "anthropic";
+  const branch = "monty/fixing-pipeline-runner";
+  
+  const headers = {
+    Accept: "application/vnd.github+json",
+    Authorization: `Bearer ${token}`,
+    "X-GitHub-Api-Version": "2022-11-28",
+  };
+
+  console.log(`\n=== Reverting test commit ===`);
+  console.log(`Repository: ${owner}/${repo}`);
+  console.log(`Branch: ${branch}\n`);
+
+  try {
+    // Get current branch state
+    console.log("Getting current branch reference...");
+    const refUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${branch}`;
+    const refResponse = await fetch(refUrl, { headers });
+    
+    if (!refResponse.ok) {
+      console.error(`Failed to get branch: ${refResponse.status}`);
+      return;
+    }
+
+    const refData = await refResponse.json();
+    const currentSha = refData.object.sha;
+    console.log(`Current branch SHA: ${currentSha}`);
+
+    // Get the current commit to find its parent
+    console.log("\nGetting current commit details...");
+    const commitResponse = await fetch(
+      `${GITHUB_API_URL}/repos/${owner}/${repo}/git/commits/${currentSha}`,
+      { headers }
+    );
+    
+    if (!commitResponse.ok) {
+      console.error(`Failed to get commit: ${commitResponse.status}`);
+      return;
+    }
+
+    const commitData = await commitResponse.json();
+    console.log(`Current commit message: "${commitData.message}"`);
+    
+    if (!commitData.message.includes("Debug: Test commit to reproduce 500 error")) {
+      console.log("⚠️  Current commit doesn't look like our test commit");
+      console.log("Are you sure you want to revert this?");
+      console.log("Current message:", commitData.message);
+      return;
+    }
+
+    if (commitData.parents.length === 0) {
+      console.error("Cannot revert: this appears to be the initial commit");
+      return;
+    }
+
+    const parentSha = commitData.parents[0].sha;
+    console.log(`Parent SHA: ${parentSha}`);
+
+    // Reset the branch to the parent commit
+    console.log("\nReverting branch to parent commit...");
+    const updateRefResponse = await fetch(refUrl, {
+      method: "PATCH",
+      headers: {
+        ...headers,
+        "Content-Type": "application/json",
+      },
+      body: JSON.stringify({
+        sha: parentSha,
+        force: true, // Force is needed for this kind of reset
+      }),
+    });
+
+    if (!updateRefResponse.ok) {
+      console.error(`Failed to revert: ${updateRefResponse.status}`);
+      const error = await updateRefResponse.text();
+      console.error(error);
+      return;
+    }
+
+    console.log("✅ Successfully reverted test commit!");
+    console.log(`Branch ${branch} is now back to SHA: ${parentSha}`);
+    
+    // Verify the revert
+    console.log("\nVerifying revert...");
+    const verifyResponse = await fetch(refUrl, { headers });
+    const verifyData = await verifyResponse.json();
+    
+    if (verifyData.object.sha === parentSha) {
+      console.log("✅ Revert confirmed");
+    } else {
+      console.log("⚠️  Unexpected SHA after revert:", verifyData.object.sha);
+    }
+
+  } catch (error) {
+    console.error("Error:", error);
+  }
+}
+
+const token = process.argv[2];
+if (!token) {
+  console.log("Usage: bun revert-test-commit.ts <github-pat>");
+  process.exit(1);
+}
+
+revertTestCommit(token);

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

@@ -1,12 +1,13 @@
 #!/usr/bin/env node
-// GitHub File Operations MCP Server
+// GitHub File Operations MCP Server - Enhanced with detailed error logging
 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 { join } from "path";
 import fetch from "node-fetch";
-import { GITHUB_API_URL } from "../github/api/config";
+// Import removed - define inline to ensure subprocess gets the value
+const GITHUB_API_URL = process.env.GITHUB_API_URL || "https://api.github.com";
 
 type GitHubRef = {
   object: {
@@ -51,6 +52,18 @@ const server = new McpServer({
   version: "0.0.1",
 });
 
+// Enhanced error logging helper
+function logDetailedError(prefix: string, error: any) {
+  console.error(`[${prefix}] FULL ERROR CAUGHT:`, error);
+  console.error(`[${prefix}] Error type:`, typeof error);
+  console.error(`[${prefix}] Error constructor:`, error?.constructor?.name);
+  console.error(`[${prefix}] Error stack:`, error instanceof Error ? error.stack : 'No stack trace');
+  if (error && typeof error === 'object') {
+    console.error(`[${prefix}] Error properties:`, Object.keys(error));
+    console.error(`[${prefix}] Error JSON:`, JSON.stringify(error, null, 2));
+  }
+}
+
 // Commit files tool
 server.tool(
   "commit_files",
@@ -67,6 +80,19 @@ server.tool(
     const owner = REPO_OWNER;
     const repo = REPO_NAME;
     const branch = BRANCH_NAME;
+    console.error(`[commit_files] Starting commit for ${files.length} files to ${owner}/${repo}:${branch}`);
+    console.error(`[commit_files] REPO_DIR: ${REPO_DIR}`);
+    console.error(`[commit_files] Input files:`, files);
+    console.error(`[commit_files] Environment check:`, {
+      GITHUB_TOKEN: process.env.GITHUB_TOKEN ? 'Present' : 'Missing',
+      REPO_OWNER,
+      REPO_NAME,
+      BRANCH_NAME,
+      REPO_DIR,
+      GITHUB_API_URL,
+      CWD: process.cwd(),
+    });
+    
     try {
       const githubToken = process.env.GITHUB_TOKEN;
       if (!githubToken) {
@@ -123,7 +149,12 @@ server.tool(
             ? filePath
             : join(REPO_DIR, filePath);
 
-          const content = await readFile(fullPath, "utf-8");
+          console.error(`[commit_files] Reading file: ${fullPath}`);
+          const content = await readFile(fullPath, "utf-8").catch((error) => {
+            console.error(`[commit_files] Failed to read file '${fullPath}':`, error);
+            throw new Error(`Failed to read file '${fullPath}': ${error.message || error}`);
+          });
+          console.error(`[commit_files] Successfully read file: ${fullPath} (${content.length} chars)`);
           return {
             path: filePath,
             mode: "100644",
@@ -186,24 +217,158 @@ server.tool(
 
       // 6. Update the reference to point to the new commit
       const updateRefUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${branch}`;
-      const updateRefResponse = await fetch(updateRefUrl, {
-        method: "PATCH",
-        headers: {
+      console.error(`[commit_files] Updating reference: ${updateRefUrl}`);
+      console.error(`[commit_files] New commit SHA: ${newCommitData.sha}`);
+      console.error(`[commit_files] Base SHA was: ${baseSha}`);
+      
+      // Log full request context before making the request
+      const requestBody = JSON.stringify({
+        sha: newCommitData.sha,
+        force: false,
+      });
+      const requestHeaders = {
         Accept: "application/vnd.github+json",
         Authorization: `Bearer ${githubToken}`,
         "X-GitHub-Api-Version": "2022-11-28",
         "Content-Type": "application/json",
+      };
+      
+      console.error(`[commit_files] Full request details:`, {
+        url: updateRefUrl,
+        method: 'PATCH',
+        headers: {
+          ...requestHeaders,
+          Authorization: `Bearer [TOKEN_LENGTH:${githubToken?.length || 0}]`,
         },
-        body: JSON.stringify({
-          sha: newCommitData.sha,
-          force: false,
-        }),
+        body: requestBody,
+        timestamp: new Date().toISOString(),
+        environment: {
+          NODE_VERSION: process.version,
+          PLATFORM: process.platform,
+          ARCH: process.arch,
+        },
+        previousOperations: {
+          treeCreated: treeData?.sha ? 'YES' : 'NO',
+          commitCreated: newCommitData?.sha ? 'YES' : 'NO',
+          treeSha: treeData?.sha,
+          commitSha: newCommitData?.sha,
+          baseSha: baseSha,
+        }
+      });
+      
+      // Log memory usage before request
+      const memoryBefore = process.memoryUsage();
+      console.error(`[commit_files] Memory before request:`, {
+        rss: `${(memoryBefore.rss / 1024 / 1024).toFixed(2)} MB`,
+        heapUsed: `${(memoryBefore.heapUsed / 1024 / 1024).toFixed(2)} MB`,
+      });
+      
+      let updateRefResponse;
+      const requestStartTime = Date.now();
+      
+      try {
+        updateRefResponse = await fetch(updateRefUrl, {
+          method: "PATCH",
+          headers: requestHeaders,
+          body: requestBody,
+        });
+      } catch (fetchError) {
+        const requestDuration = Date.now() - requestStartTime;
+        console.error(`[commit_files] FETCH ERROR during reference update after ${requestDuration}ms:`, fetchError);
+        logDetailedError('commit_files_fetch', fetchError);
+        throw new Error(`Network error during reference update after ${requestDuration}ms: ${fetchError?.message || 'Unknown fetch error'}`);
+      }
+      
+      const requestDuration = Date.now() - requestStartTime;
+      console.error(`[commit_files] Request completed in ${requestDuration}ms`);
+      console.error(`[commit_files] Response received at: ${new Date().toISOString()}`);
+
+      console.error(`[commit_files] Update reference response status: ${updateRefResponse.status}`);
+      console.error(`[commit_files] Response headers:`, Object.fromEntries(updateRefResponse.headers.entries()));
+      
+      // Log specific important headers
+      console.error(`[commit_files] Key response headers:`, {
+        'x-github-request-id': updateRefResponse.headers.get('x-github-request-id'),
+        'x-ratelimit-remaining': updateRefResponse.headers.get('x-ratelimit-remaining'),
+        'x-ratelimit-reset': updateRefResponse.headers.get('x-ratelimit-reset'),
+        'content-type': updateRefResponse.headers.get('content-type'),
+        'content-length': updateRefResponse.headers.get('content-length'),
+        'server': updateRefResponse.headers.get('server'),
       });
       
       if (!updateRefResponse.ok) {
-        const errorText = await updateRefResponse.text();
+        console.error(`[commit_files] ERROR RESPONSE - Status: ${updateRefResponse.status} ${updateRefResponse.statusText}`);
+        
+        // Capture the entire raw response body
+        let responseArrayBuffer;
+        let responseText = '';
+        let responseHex = '';
+        let responseBase64 = '';
+        
+        try {
+          // Clone the response so we can read it multiple ways
+          const clonedResponse = updateRefResponse.clone();
+          
+          // Get raw bytes
+          responseArrayBuffer = await updateRefResponse.arrayBuffer();
+          const responseBytes = new Uint8Array(responseArrayBuffer);
+          
+          // Convert to text (with error handling for non-UTF8)
+          responseText = new TextDecoder('utf-8', { fatal: false }).decode(responseBytes);
+          
+          // Convert to hex for debugging binary responses
+          responseHex = Array.from(responseBytes.slice(0, 1000)) // First 1000 bytes to avoid huge logs
+            .map(b => b.toString(16).padStart(2, '0'))
+            .join(' ');
+          
+          // Convert to base64
+          responseBase64 = Buffer.from(responseBytes).toString('base64');
+          
+          console.error(`[commit_files] COMPLETE ERROR RESPONSE:`);
+          console.error(`[commit_files] ===== RESPONSE BODY (TEXT) =====`);
+          console.error(responseText);
+          console.error(`[commit_files] ===== END RESPONSE BODY =====`);
+          console.error(`[commit_files] Response body length: ${responseBytes.length} bytes`);
+          console.error(`[commit_files] Response body (first 1000 bytes as hex): ${responseHex}${responseBytes.length > 1000 ? '...' : ''}`);
+          console.error(`[commit_files] Response body (base64): ${responseBase64}`);
+          
+          // Try to parse as JSON if it looks like JSON
+          if (responseText.trim().startsWith('{') || responseText.trim().startsWith('[')) {
+            try {
+              const parsedError = JSON.parse(responseText);
+              console.error(`[commit_files] Parsed error object:`, JSON.stringify(parsedError, null, 2));
+            } catch (e) {
+              console.error(`[commit_files] Response looks like JSON but failed to parse:`, e);
+            }
+          }
+          
+        } catch (readError) {
+          console.error(`[commit_files] CRITICAL: Failed to read error response:`, readError);
+          logDetailedError('commit_files_response_read', readError);
+          responseText = `Failed to read response: ${readError}`;
+        }
+        
+        // Log memory state after error
+        const memoryAfter = process.memoryUsage();
+        console.error(`[commit_files] Memory after error:`, {
+          rss: `${(memoryAfter.rss / 1024 / 1024).toFixed(2)} MB`,
+          heapUsed: `${(memoryAfter.heapUsed / 1024 / 1024).toFixed(2)} MB`,
+        });
+        
+        // Special handling for 500 errors
+        if (updateRefResponse.status === 500) {
+          const requestId = updateRefResponse.headers.get('x-github-request-id');
+          console.error(`[commit_files] ===== GITHUB 500 ERROR DETAILS =====`);
+          console.error(`[commit_files] GitHub Request ID: ${requestId}`);
+          console.error(`[commit_files] This is an internal GitHub server error`);
+          console.error(`[commit_files] The error may be transient - consider retrying`);
+          console.error(`[commit_files] Note: Tree (${treeData?.sha}) and commit (${newCommitData?.sha}) were created successfully`);
+          console.error(`[commit_files] Only the reference update failed`);
+          console.error(`[commit_files] ===================================`);
+        }
+        
         throw new Error(
-          `Failed to update reference: ${updateRefResponse.status} - ${errorText}`,
+          `Failed to update reference: ${updateRefResponse.status} - ${responseText || 'No response body'}`,
         );
       }
 
@@ -229,18 +394,21 @@ server.tool(
         ],
       };
     } catch (error) {
+      logDetailedError('commit_files', error);
+      
       const errorMessage =
         error instanceof Error ? error.message : String(error);
-      return {
-        content: [
-          {
-            type: "text",
-            text: `Error: ${errorMessage}`,
-          },
-        ],
-        error: errorMessage,
-        isError: true,
-      };
+      console.error(`[commit_files] Final error message being thrown: "${errorMessage}"`);
+      
+      // Ensure we're throwing a proper Error object with a message
+      if (!errorMessage || errorMessage === 'undefined' || errorMessage === '[object Object]') {
+        console.error(`[commit_files] WARNING: Error message is undefined or object, using fallback`);
+        const fallbackMessage = error instanceof Error && error.stack 
+          ? `Failed to commit files: ${error.stack.split('\n')[0]}`
+          : 'Failed to commit files: Unknown error occurred';
+        throw new Error(fallbackMessage);
+      }
+      throw new Error(errorMessage);
     }
   },
 );
@@ -380,7 +548,17 @@ server.tool(
 
       // 6. Update the reference to point to the new commit
       const updateRefUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${branch}`;
-      const updateRefResponse = await fetch(updateRefUrl, {
+      console.error(`[delete_files] Updating reference: ${updateRefUrl}`);
+      console.error(`[delete_files] New commit SHA: ${newCommitData.sha}`);
+      console.error(`[delete_files] Base SHA was: ${baseSha}`);
+      console.error(`[delete_files] Request body:`, JSON.stringify({
+        sha: newCommitData.sha,
+        force: false,
+      }));
+      
+      let updateRefResponse;
+      try {
+        updateRefResponse = await fetch(updateRefUrl, {
           method: "PATCH",
           headers: {
             Accept: "application/vnd.github+json",
@@ -393,9 +571,48 @@ server.tool(
             force: false,
           }),
         });
+      } catch (fetchError) {
+        console.error(`[delete_files] FETCH ERROR during reference update:`, fetchError);
+        logDetailedError('delete_files_fetch', fetchError);
+        throw new Error(`Network error during reference update: ${fetchError?.message || 'Unknown fetch error'}`);
+      }
+
+      console.error(`[delete_files] Update reference response status: ${updateRefResponse.status}`);
+      console.error(`[delete_files] Response headers:`, Object.fromEntries(updateRefResponse.headers.entries()));
       
       if (!updateRefResponse.ok) {
-        const errorText = await updateRefResponse.text();
+        let errorText;
+        try {
+          errorText = await updateRefResponse.text();
+        } catch (textError) {
+          console.error(`[delete_files] Failed to read error response text:`, textError);
+          errorText = 'Unable to read error response';
+        }
+        
+        console.error(`[delete_files] Update reference error body: "${errorText}"`);
+        console.error(`[delete_files] Error body length: ${errorText?.length}`);
+        console.error(`[delete_files] Error body type: ${typeof errorText}`);
+        
+        // Log additional debugging info for 500 errors
+        if (updateRefResponse.status === 500) {
+          const requestId = updateRefResponse.headers.get('x-github-request-id');
+          console.error(`[delete_files] GitHub Request ID: ${requestId}`);
+          console.error(`[delete_files] This appears to be an internal GitHub error`);
+          console.error(`[delete_files] Token was valid for tree/commit creation but failed for ref update`);
+          console.error(`[delete_files] Branch protection rules or permissions might be an issue`);
+        }
+        
+        // Parse error if it's JSON
+        let parsedError;
+        try {
+          if (errorText && errorText.trim().startsWith('{')) {
+            parsedError = JSON.parse(errorText);
+            console.error(`[delete_files] Parsed error:`, parsedError);
+          }
+        } catch (e) {
+          console.error(`[delete_files] Error text is not JSON`);
+        }
+        
         throw new Error(
           `Failed to update reference: ${updateRefResponse.status} - ${errorText}`,
         );
@@ -423,18 +640,21 @@ server.tool(
         ],
       };
     } catch (error) {
+      logDetailedError('delete_files', error);
+      
       const errorMessage =
         error instanceof Error ? error.message : String(error);
-      return {
-        content: [
-          {
-            type: "text",
-            text: `Error: ${errorMessage}`,
-          },
-        ],
-        error: errorMessage,
-        isError: true,
-      };
+      console.error(`[delete_files] Final error message being thrown: "${errorMessage}"`);
+      
+      // Ensure we're throwing a proper Error object with a message
+      if (!errorMessage || errorMessage === 'undefined' || errorMessage === '[object Object]') {
+        console.error(`[delete_files] WARNING: Error message is undefined or object, using fallback`);
+        const fallbackMessage = error instanceof Error && error.stack 
+          ? `Failed to delete files: ${error.stack.split('\n')[0]}`
+          : 'Failed to delete files: Unknown error occurred';
+        throw new Error(fallbackMessage);
+      }
+      throw new Error(errorMessage);
     }
   },
 );

src/mcp/install-mcp-server.ts

@@ -35,6 +35,7 @@ export async function prepareMcpConfig(
             REPO_NAME: repo,
             BRANCH_NAME: branch,
             REPO_DIR: process.env.GITHUB_WORKSPACE || process.cwd(),
+            GITHUB_API_URL: process.env.GITHUB_API_URL || "https://api.github.com",
           },
         },
       },

test-with-new-branch.ts

@@ -0,0 +1,261 @@
+#!/usr/bin/env bun
+// Test script that creates a new branch to test the commit_files flow
+// Run with: bun test-with-new-branch.ts <github-pat> <owner> <repo>
+
+const GITHUB_API_URL = "https://api.github.com";
+
+async function testCommitFilesWithNewBranch(token: string, owner: string, repo: string) {
+  const headers = {
+    Accept: "application/vnd.github+json",
+    Authorization: `Bearer ${token}`,
+    "X-GitHub-Api-Version": "2022-11-28",
+  };
+
+  // Create a unique branch name for testing
+  const timestamp = Date.now();
+  const testBranch = `claude-debug-500-test-${timestamp}`;
+
+  console.log(`\n=== Testing commit_files flow ===`);
+  console.log(`Repository: ${owner}/${repo}`);
+  console.log(`Test branch: ${testBranch}\n`);
+
+  try {
+    // First, get the default branch to branch from
+    console.log("Getting repository info...");
+    const repoResponse = await fetch(
+      `${GITHUB_API_URL}/repos/${owner}/${repo}`,
+      { headers }
+    );
+    
+    if (!repoResponse.ok) {
+      console.error(`Cannot access repository: ${repoResponse.status}`);
+      const error = await repoResponse.text();
+      console.error(error);
+      return;
+    }
+    
+    const repoData = await repoResponse.json();
+    const defaultBranch = repoData.default_branch;
+    console.log(`✓ Default branch: ${defaultBranch}`);
+
+    // Get the SHA of the default branch
+    console.log(`\nGetting ${defaultBranch} branch SHA...`);
+    const defaultBranchResponse = await fetch(
+      `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${defaultBranch}`,
+      { headers }
+    );
+    
+    if (!defaultBranchResponse.ok) {
+      console.error(`Cannot get default branch: ${defaultBranchResponse.status}`);
+      return;
+    }
+    
+    const defaultBranchData = await defaultBranchResponse.json();
+    const baseSha = defaultBranchData.object.sha;
+    console.log(`✓ Base SHA: ${baseSha}`);
+
+    // Create a new branch
+    console.log(`\nCreating test branch: ${testBranch}...`);
+    const createBranchResponse = await fetch(
+      `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs`,
+      {
+        method: "POST",
+        headers: {
+          ...headers,
+          "Content-Type": "application/json",
+        },
+        body: JSON.stringify({
+          ref: `refs/heads/${testBranch}`,
+          sha: baseSha,
+        }),
+      }
+    );
+    
+    if (!createBranchResponse.ok) {
+      console.error(`Failed to create branch: ${createBranchResponse.status}`);
+      const error = await createBranchResponse.text();
+      console.error(error);
+      return;
+    }
+    
+    console.log(`✓ Created test branch: ${testBranch}`);
+    
+    // Now replicate the commit_files flow
+    console.log("\n--- Starting commit_files flow ---");
+    
+    // Step 1: Get the branch reference (should be same as baseSha)
+    console.log("\nStep 1: Getting branch reference...");
+    const refUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${testBranch}`;
+    const refResponse = await fetch(refUrl, { headers });
+    
+    if (!refResponse.ok) {
+      console.error(`Failed: ${refResponse.status}`);
+      return;
+    }
+
+    const refData = await refResponse.json();
+    console.log(`✓ Branch SHA: ${refData.object.sha}`);
+
+    // Step 2: Get the base commit
+    console.log("\nStep 2: Getting base commit...");
+    const commitUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/commits/${baseSha}`;
+    const commitResponse = await fetch(commitUrl, { headers });
+    
+    if (!commitResponse.ok) {
+      console.error(`Failed: ${commitResponse.status}`);
+      return;
+    }
+
+    const commitData = await commitResponse.json();
+    const baseTreeSha = commitData.tree.sha;
+    console.log(`✓ Base tree SHA: ${baseTreeSha}`);
+
+    // Step 3: Create a new tree
+    console.log("\nStep 3: Creating new tree...");
+    const treeUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/trees`;
+    
+    const testFileContent = `# Test file for debugging 500 error
+# Created at: ${new Date().toISOString()}
+# This simulates the commit_files operation from claude-code-action
+
+def test_function():
+    # This simulates fixing a code issue
+    result = "Fixed code"
+    return result
+`;
+
+    const treeBody = {
+      base_tree: baseTreeSha,
+      tree: [{
+        path: "test-debug-500.py",
+        mode: "100644",
+        type: "blob",
+        content: testFileContent,
+      }],
+    };
+
+    const treeResponse = await fetch(treeUrl, {
+      method: "POST",
+      headers: {
+        ...headers,
+        "Content-Type": "application/json",
+      },
+      body: JSON.stringify(treeBody),
+    });
+    
+    if (!treeResponse.ok) {
+      console.error(`Failed to create tree: ${treeResponse.status}`);
+      const error = await treeResponse.text();
+      console.error(error);
+      return;
+    }
+
+    const treeData = await treeResponse.json();
+    console.log(`✓ Tree SHA: ${treeData.sha}`);
+
+    // Step 4: Create commit
+    console.log("\nStep 4: Creating commit...");
+    const newCommitUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/commits`;
+    const commitBody = {
+      message: "Test: Debugging 500 error in commit_files",
+      tree: treeData.sha,
+      parents: [baseSha],
+    };
+
+    const newCommitResponse = await fetch(newCommitUrl, {
+      method: "POST",
+      headers: {
+        ...headers,
+        "Content-Type": "application/json",
+      },
+      body: JSON.stringify(commitBody),
+    });
+
+    if (!newCommitResponse.ok) {
+      console.error(`Failed to create commit: ${newCommitResponse.status}`);
+      const error = await newCommitResponse.text();
+      console.error(error);
+      return;
+    }
+
+    const newCommitData = await newCommitResponse.json();
+    console.log(`✓ Commit SHA: ${newCommitData.sha}`);
+
+    // Step 5: Update reference (this is where the 500 error happens)
+    console.log("\nStep 5: Updating branch reference (the critical step)...");
+    const updateRefUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${testBranch}`;
+    const updateBody = {
+      sha: newCommitData.sha,
+      force: false,
+    };
+
+    console.log(`URL: PATCH ${updateRefUrl}`);
+    console.log(`Body: ${JSON.stringify(updateBody)}`);
+    
+    const startTime = Date.now();
+    const updateRefResponse = await fetch(updateRefUrl, {
+      method: "PATCH",
+      headers: {
+        ...headers,
+        "Content-Type": "application/json",
+      },
+      body: JSON.stringify(updateBody),
+    });
+    const duration = Date.now() - startTime;
+
+    console.log(`\nStatus: ${updateRefResponse.status} (took ${duration}ms)`);
+    console.log(`Headers:`, {
+      'x-ratelimit-remaining': updateRefResponse.headers.get('x-ratelimit-remaining'),
+      'x-github-request-id': updateRefResponse.headers.get('x-github-request-id'),
+    });
+
+    if (!updateRefResponse.ok) {
+      console.error(`\n✗ FAILED: ${updateRefResponse.status}`);
+      const errorText = await updateRefResponse.text();
+      console.error(`Error body: "${errorText}"`);
+      
+      if (updateRefResponse.status === 500) {
+        console.error(`\n🔍 500 ERROR REPRODUCED!`);
+        console.error(`This confirms the issue exists with PAT as well.`);
+        console.error(`GitHub Request ID: ${updateRefResponse.headers.get('x-github-request-id')}`);
+      }
+    } else {
+      console.log(`\n✓ SUCCESS: Branch updated!`);
+      console.log(`The 500 error might be specific to certain conditions.`);
+      
+      // Cleanup: delete the test branch
+      console.log(`\nCleaning up test branch...`);
+      const deleteResponse = await fetch(
+        `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${testBranch}`,
+        {
+          method: "DELETE",
+          headers,
+        }
+      );
+      
+      if (deleteResponse.ok) {
+        console.log(`✓ Test branch deleted`);
+      }
+    }
+
+  } catch (error) {
+    console.error(`\nUnexpected error:`, error);
+  }
+}
+
+// Main execution
+const [token, owner, repo] = process.argv.slice(2);
+
+if (!token || !owner || !repo) {
+  console.log("Usage: bun test-with-new-branch.ts <github-pat> <owner> <repo>");
+  console.log("");
+  console.log("Examples:");
+  console.log("  bun test-with-new-branch.ts ghp_xxx myorg myrepo");
+  console.log("  bun test-with-new-branch.ts ghp_xxx anthropics anthropic");
+  console.log("");
+  console.log("This creates a test branch and replicates the commit_files flow.");
+  process.exit(1);
+}
+
+console.log("Starting test with new branch...");
+testCommitFilesWithNewBranch(token, owner, repo);