diff --git a/src/github/operations/branch-cleanup.ts b/src/github/operations/branch-cleanup.ts
index 88de6de..612ef90 100644
--- a/src/github/operations/branch-cleanup.ts
+++ b/src/github/operations/branch-cleanup.ts
@@ -1,6 +1,8 @@
 import type { Octokits } from "../api/client";
 import { GITHUB_SERVER_URL } from "../api/config";
 import { $ } from "bun";
+import { resignCommits } from "./resign-commits";
+import { parseGitHubContext } from "../context";
 
 export async function checkAndCommitOrDeleteBranch(
   octokit: Octokits,
@@ -101,7 +103,48 @@ export async function checkAndCommitOrDeleteBranch(
           shouldDeleteBranch = true;
         }
       } else {
-        // Only add branch link if there are commits
+        // Branch has commits
+        console.log(
+          `Branch ${claudeBranch} has ${comparison.total_commits} commits`,
+        );
+
+        // First, check for any uncommitted changes
+        try {
+          const gitStatus = await $`git status --porcelain`.quiet();
+          const hasUncommittedChanges =
+            gitStatus.stdout.toString().trim().length > 0;
+
+          if (hasUncommittedChanges) {
+            console.log(
+              "Found uncommitted changes after commits, committing them...",
+            );
+
+            // Add all changes
+            await $`git add -A`;
+
+            // Commit any remaining changes
+            const runId = process.env.GITHUB_RUN_ID || "unknown";
+            const commitMessage = `Auto-commit: Save remaining changes from Claude\n\nRun ID: ${runId}`;
+            await $`git commit -m ${commitMessage}`;
+
+            // Push the changes
+            await $`git push origin ${claudeBranch}`;
+
+            console.log(
+              "✅ Successfully committed and pushed remaining changes",
+            );
+          }
+        } catch (gitError) {
+          console.error("Error checking for remaining changes:", gitError);
+        }
+
+        // Re-sign all commits made by Claude if commit signing is enabled
+        if (useCommitSigning) {
+          const context = parseGitHubContext();
+          await resignCommits(claudeBranch, baseBranch, octokit, context);
+        }
+
+        // Add branch link since there are commits
         const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${claudeBranch}`;
         branchLink = `\n[View branch](${branchUrl})`;
       }
diff --git a/src/github/operations/resign-commits.ts b/src/github/operations/resign-commits.ts
new file mode 100644
index 0000000..fb701b2
--- /dev/null
+++ b/src/github/operations/resign-commits.ts
@@ -0,0 +1,159 @@
+import type { Octokits } from "../api/client";
+import type { GitHubContext } from "../context";
+import { $ } from "bun";
+
+interface CommitInfo {
+  sha: string;
+  message: string;
+  author: {
+    name: string;
+    email: string;
+    date: string;
+  };
+  files: string[];
+}
+
+/**
+ * Get all commits made by claude[bot] on the current branch that aren't on the base branch
+ */
+async function getClaudeCommits(baseBranch: string): Promise<CommitInfo[]> {
+  try {
+    // Get commits that are on current branch but not on base branch
+    const output =
+      await $`git log ${baseBranch}..HEAD --pretty=format:"%H|%an|%ae|%aI|%B%x00" --name-only`.quiet();
+    const rawCommits = output.stdout
+      .toString()
+      .trim()
+      .split("\x00")
+      .filter((c) => c);
+
+    const commits: CommitInfo[] = [];
+
+    for (const rawCommit of rawCommits) {
+      const lines = rawCommit.trim().split("\n");
+      if (lines.length === 0) continue;
+
+      const firstLine = lines[0];
+      if (!firstLine) continue;
+
+      const parts = firstLine.split("|");
+      if (parts.length < 4) continue;
+
+      const [sha, authorName, authorEmail, date, ...rest] = parts;
+
+      // Find where the file list starts (after empty line)
+      let messageEndIndex = rest.findIndex((line) => line === "");
+      if (messageEndIndex === -1) messageEndIndex = rest.length;
+
+      const message = rest.slice(0, messageEndIndex).join("\n");
+      const files = rest.slice(messageEndIndex + 1).filter((f) => f);
+
+      // Only include commits by claude[bot]
+      if (
+        authorName &&
+        authorEmail &&
+        (authorName === "claude[bot]" || authorEmail.includes("claude"))
+      ) {
+        commits.push({
+          sha: sha || "",
+          message,
+          author: {
+            name: authorName,
+            email: authorEmail,
+            date: date || new Date().toISOString(),
+          },
+          files,
+        });
+      }
+    }
+
+    return commits.reverse(); // Return in chronological order
+  } catch (error) {
+    console.error("Error getting Claude commits:", error);
+    return [];
+  }
+}
+
+/**
+ * Re-create commits using GitHub API to get them signed
+ */
+export async function resignCommits(
+  branch: string,
+  baseBranch: string,
+  client: Octokits,
+  context: GitHubContext,
+): Promise<boolean> {
+  try {
+    console.log(
+      `Checking for unsigned commits by Claude on branch ${branch}...`,
+    );
+
+    // Get all commits made by Claude
+    const claudeCommits = await getClaudeCommits(baseBranch);
+
+    if (claudeCommits.length === 0) {
+      console.log("No commits by Claude found to re-sign");
+      return false;
+    }
+
+    console.log(`Found ${claudeCommits.length} commits by Claude to re-sign`);
+
+    // Get the base commit (last commit before Claude's commits)
+    const baseCommitOutput = await $`git rev-parse ${baseBranch}`.quiet();
+    const baseCommitSha = baseCommitOutput.stdout.toString().trim();
+
+    // Create a mapping of old SHA to new SHA
+    const shaMapping = new Map<string, string>();
+    let currentParentSha = baseCommitSha;
+
+    for (const commit of claudeCommits) {
+      console.log(
+        `Re-signing commit: ${commit.sha.substring(0, 7)} - ${commit.message.split("\n")[0]}`,
+      );
+
+      // Get the tree SHA for this commit
+      const treeOutput = await $`git rev-parse ${commit.sha}^{tree}`.quiet();
+      const treeSha = treeOutput.stdout.toString().trim();
+
+      // Create the commit via API (which will sign it)
+      const { data: newCommit } = await client.rest.git.createCommit({
+        owner: context.repository.owner,
+        repo: context.repository.repo,
+        message: commit.message,
+        tree: treeSha,
+        parents: [currentParentSha],
+        author: {
+          name: commit.author.name,
+          email: commit.author.email,
+          date: commit.author.date,
+        },
+      });
+
+      console.log(`  Created signed commit: ${newCommit.sha.substring(0, 7)}`);
+      shaMapping.set(commit.sha, newCommit.sha);
+      currentParentSha = newCommit.sha;
+    }
+
+    // Update the branch to point to the new commit
+    console.log(`Updating branch ${branch} to point to signed commits...`);
+    await client.rest.git.updateRef({
+      owner: context.repository.owner,
+      repo: context.repository.repo,
+      ref: `heads/${branch}`,
+      sha: currentParentSha,
+      force: true,
+    });
+
+    // Pull the updated branch locally
+    console.log("Pulling signed commits locally...");
+    await $`git fetch origin ${branch}`;
+    await $`git reset --hard origin/${branch}`;
+
+    console.log(`✅ Successfully re-signed ${claudeCommits.length} commits`);
+    return true;
+  } catch (error) {
+    console.error("Error re-signing commits:", error);
+    // Don't fail the action if we can't re-sign
+    return false;
+  }
+}
diff --git a/src/mcp/github-file-ops-server.ts b/src/mcp/github-file-ops-server.ts
index e3da6f4..40f8a91 100644
--- a/src/mcp/github-file-ops-server.ts
+++ b/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 +163,35 @@ 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 +253,9 @@ 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 +294,7 @@ server.tool(
             // Return tree entry with blob SHA
             return {
               path: filePath,
-              mode: "100644",
+              mode: fileMode,
               type: "blob",
               sha: blobData.sha,
             };
@@ -270,7 +303,7 @@ server.tool(
             const content = await readFile(fullPath, "utf-8");
             return {
               path: filePath,
-              mode: "100644",
+              mode: fileMode,
               type: "blob",
               content: content,
             };