diff --git a/src/create-prompt/index.ts b/src/create-prompt/index.ts
index 0a6c385..f622dec 100644
--- a/src/create-prompt/index.ts
+++ b/src/create-prompt/index.ts
@@ -434,9 +434,27 @@ ${
   eventData.eventName === "pull_request_review_comment"
     ? `<comment_tool_info>
 IMPORTANT: For this inline PR review comment, you have been provided with ONLY the mcp__github__update_pull_request_comment tool to update this specific review comment.
+
+Tool usage example for mcp__github__update_pull_request_comment:
+{
+  "owner": "${context.repository.split("/")[0]}",
+  "repo": "${context.repository.split("/")[1]}",
+  "commentId": ${eventData.commentId || context.claudeCommentId},
+  "body": "Your comment text here"
+}
+All four parameters (owner, repo, commentId, body) are required.
 </comment_tool_info>`
     : `<comment_tool_info>
 IMPORTANT: For this event type, you have been provided with ONLY the mcp__github__update_issue_comment tool to update comments.
+
+Tool usage example for mcp__github__update_issue_comment:
+{
+  "owner": "${context.repository.split("/")[0]}",
+  "repo": "${context.repository.split("/")[1]}",
+  "commentId": ${context.claudeCommentId},
+  "body": "Your comment text here"
+}
+All four parameters (owner, repo, commentId, body) are required.
 </comment_tool_info>`
 }
 
@@ -547,6 +565,9 @@ Important Notes:
 - Use this spinner HTML when work is in progress: <img src="https://github.com/user-attachments/assets/5ac382c7-e004-429b-8e35-7feb3e8f9c6f" width="14px" height="14px" style="vertical-align: middle; margin-left: 4px;" />
 ${eventData.isPR && !eventData.claudeBranch ? `- Always push to the existing branch when triggered on a PR.` : `- IMPORTANT: You are already on the correct branch (${eventData.claudeBranch || "the created branch"}). Never create new branches when triggered on issues or closed/merged PRs.`}
 - Use mcp__github_file_ops__commit_files for making commits (works for both new and existing files, single or multiple). Use mcp__github_file_ops__delete_files for deleting files (supports deleting single or multiple files atomically), or mcp__github__delete_file for deleting a single file. Edit files locally, and the tool will read the content from the same path on disk.
+  Tool usage examples:
+  - mcp__github_file_ops__commit_files: {"files": ["path/to/file1.js", "path/to/file2.py"], "message": "feat: add new feature"}
+  - mcp__github_file_ops__delete_files: {"files": ["path/to/old.js"], "message": "chore: remove deprecated file"}
 - Display the todo list as a checklist in the GitHub comment and mark things off as you go.
 - REPOSITORY SETUP INSTRUCTIONS: The repository's CLAUDE.md file(s) contain critical repo-specific setup instructions, development guidelines, and preferences. Always read and follow these files, particularly the root CLAUDE.md, as they provide essential context for working with the codebase effectively.
 - Use h3 headers (###) for section titles in your comments, not h1 headers (#).
diff --git a/src/mcp/github-file-ops-server.ts b/src/mcp/github-file-ops-server.ts
index 8bc1bfb..19834c9 100644
--- a/src/mcp/github-file-ops-server.ts
+++ b/src/mcp/github-file-ops-server.ts
@@ -4,6 +4,7 @@ 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";
 
@@ -36,6 +37,7 @@ type GitHubNewCommit = {
 const REPO_OWNER = process.env.REPO_OWNER;
 const REPO_NAME = process.env.REPO_NAME;
 const BRANCH_NAME = process.env.BRANCH_NAME;
+const REPO_DIR = process.env.REPO_DIR || process.cwd();
 
 if (!REPO_OWNER || !REPO_NAME || !BRANCH_NAME) {
   console.error(
@@ -71,18 +73,9 @@ server.tool(
         throw new Error("GITHUB_TOKEN environment variable is required");
       }
 
-      // Convert absolute paths to relative if they match CWD
-      const cwd = process.cwd();
       const processedFiles = files.map((filePath) => {
         if (filePath.startsWith("/")) {
-          if (filePath.startsWith(cwd)) {
-            // Strip CWD from absolute path
-            return filePath.slice(cwd.length + 1);
-          } else {
-            throw new Error(
-              `Path '${filePath}' must be relative to repository root or within current working directory`,
-            );
-          }
+          return filePath.slice(1);
         }
         return filePath;
       });
@@ -126,7 +119,11 @@ server.tool(
       // 3. Create tree entries for all files
       const treeEntries = await Promise.all(
         processedFiles.map(async (filePath) => {
-          const content = await readFile(filePath, "utf-8");
+          const fullPath = filePath.startsWith("/")
+            ? filePath
+            : join(REPO_DIR, filePath);
+
+          const content = await readFile(fullPath, "utf-8");
           return {
             path: filePath,
             mode: "100644",
@@ -232,13 +229,16 @@ server.tool(
         ],
       };
     } catch (error) {
+      const errorMessage =
+        error instanceof Error ? error.message : String(error);
       return {
         content: [
           {
             type: "text",
-            text: `Error: ${error instanceof Error ? error.message : String(error)}`,
+            text: `Error: ${errorMessage}`,
           },
         ],
+        error: errorMessage,
         isError: true,
       };
     }
@@ -423,13 +423,16 @@ server.tool(
         ],
       };
     } catch (error) {
+      const errorMessage =
+        error instanceof Error ? error.message : String(error);
       return {
         content: [
           {
             type: "text",
-            text: `Error: ${error instanceof Error ? error.message : String(error)}`,
+            text: `Error: ${errorMessage}`,
           },
         ],
+        error: errorMessage,
         isError: true,
       };
     }
diff --git a/src/mcp/install-mcp-server.ts b/src/mcp/install-mcp-server.ts
index 7c271cf..462967d 100644
--- a/src/mcp/install-mcp-server.ts
+++ b/src/mcp/install-mcp-server.ts
@@ -34,6 +34,7 @@ export async function prepareMcpConfig(
             REPO_OWNER: owner,
             REPO_NAME: repo,
             BRANCH_NAME: branch,
+            REPO_DIR: process.env.GITHUB_WORKSPACE || process.cwd(),
           },
         },
       },