diff --git a/src/mcp/github-file-ops-server.ts b/src/mcp/github-file-ops-server.ts
index 8bc1bfb..80f579b 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 +73,11 @@ server.tool(
         throw new Error("GITHUB_TOKEN environment variable is required");
       }
 
-      // Convert absolute paths to relative if they match CWD
-      const cwd = process.cwd();
+      // Process file paths - keep them as-is for now
       const processedFiles = files.map((filePath) => {
+        // Remove leading slash if present to ensure relative paths
         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 +121,12 @@ 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");
+          // Construct the full path using REPO_DIR
+          const fullPath = filePath.startsWith('/') 
+            ? filePath 
+            : join(REPO_DIR, filePath);
+          
+          const content = await readFile(fullPath, "utf-8");
           return {
             path: filePath,
             mode: "100644",
@@ -232,13 +232,15 @@ 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 +425,15 @@ 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..dacae25 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(),  // Use GitHub workspace directory
           },
         },
       },