@@ -1484,6 +1484,7 @@ function createHandlers(server, appendSafeOutput, config = {}) {
     }
 
     const prHeadBaseline = resolvePRHeadBaselineForPush(entry.branch, itemRepo, effectivePushPRNumber, server);
+    const incrementalBaseRef = prHeadBaseline?.sha || prHeadBaseline?.ref || `refs/remotes/origin/${entry.branch}`;
     if (prHeadBaseline?.headRepo && prHeadBaseline.headRepo.toLowerCase() !== itemRepo.toLowerCase() && prHeadBaseline.headRepo.toLowerCase() !== configuredHeadRepo.toLowerCase()) {
       return {
         content: [
@@ -1556,10 +1557,9 @@ function createHandlers(server, appendSafeOutput, config = {}) {
     // only local refs (no extra fetch); a detection miss simply preserves the
     // existing behavior.
     if (!useBundle && !patchFormatExplicit && entry.branch) {
-      const rangeBaseRef = prHeadBaseline?.sha || prHeadBaseline?.ref || `refs/remotes/origin/${entry.branch}`;
-      const hasMerges = hasMergeCommitsInRange(rangeBaseRef, entry.branch, { cwd: repoCwd || undefined });
+      const hasMerges = hasMergeCommitsInRange(incrementalBaseRef, entry.branch, { cwd: repoCwd || undefined });
       if (hasMerges) {
-        server.debug(`push_to_pull_request_branch: detected merge commit(s) in incremental range ${rangeBaseRef}..${entry.branch}; auto-switching to bundle transport (set patch-format: am to override).`);
+        server.debug(`push_to_pull_request_branch: detected merge commit(s) in incremental range ${incrementalBaseRef}..${entry.branch}; auto-switching to bundle transport (set patch-format: am to override).`);
         useBundle = true;
       }
     }
@@ -1604,8 +1604,7 @@ function createHandlers(server, appendSafeOutput, config = {}) {
         if (!pushPinnedSha) {
           server.debug("Incremental allowed-files check skipped: branch SHA not pinned (non-bundle path)");
         } else {
-          const incrementalBase = prHeadBaseline?.sha || prHeadBaseline?.ref || `refs/remotes/origin/${entry.branch}`;
-          const agentFiles = execGitSync(["log", "--name-only", "--pretty=format:", `${incrementalBase}..${pushPinnedSha}`, "--"], { cwd: pushGitCwd })
+          const agentFiles = execGitSync(["log", "--ancestry-path", "--name-only", "--pretty=format:", `${incrementalBaseRef}..${pushPinnedSha}`, "--"], { cwd: pushGitCwd })
             .toString()
             .split("\n")
             .map(s => s.trim())
 
@@ -2619,6 +2619,8 @@ describe("safe_outputs_handlers", () => {
         fs.writeFileSync(path.join(repoDir, "agent.js"), "console.log('agent');\n");
         execSync("git add agent.js", { cwd: repoDir, stdio: "pipe" });
         execSync("git commit -m 'agent script'", { cwd: repoDir, stdio: "pipe" });
+        execSync("git rm agent.js", { cwd: repoDir, stdio: "pipe" });
+        execSync("git commit -m 'revert agent script'", { cwd: repoDir, stdio: "pipe" });
 
         process.env.GITHUB_BASE_REF = "main";
         process.env.GITHUB_WORKSPACE = repoDir;
@@ -2637,6 +2639,33 @@ describe("safe_outputs_handlers", () => {
         }
       });
 
+      it("does not reject disallowed files merged from the updated base branch", async () => {
+        const { repoDir } = createRepoWithDisallowedHistoryFile();
+        execSync("git checkout main", { cwd: repoDir, stdio: "pipe" });
+        fs.writeFileSync(path.join(repoDir, "upstream.js"), "console.log('upstream');\n");
+        execSync("git add upstream.js", { cwd: repoDir, stdio: "pipe" });
+        execSync("git commit -m 'update base branch'", { cwd: repoDir, stdio: "pipe" });
+        execSync("git checkout feature/work", { cwd: repoDir, stdio: "pipe" });
+        execSync("git merge --no-ff main -m 'merge updated base'", { cwd: repoDir, stdio: "pipe" });
+
+        process.env.GITHUB_BASE_REF = "main";
+        process.env.GITHUB_WORKSPACE = repoDir;
+        const localHandlers = createHandlers(mockServer, mockAppendSafeOutput, {
+          push_to_pull_request_branch: { allowed_files: ["*.md"] },
+        });
+        try {
+          const result = await localHandlers.pushToPullRequestBranchHandler({ branch: "feature/work" });
+          if (result.isError) {
+            const data = JSON.parse(result.content[0].text);
+            expect(data.error).not.toContain("allowed-files configuration");
+            expect(data.disallowed_files).toBeUndefined();
+          }
+        } finally {
+          delete process.env.GITHUB_BASE_REF;
+          process.env.GITHUB_WORKSPACE = testWorkspaceDir;
+        }
+      });
+
       it("does not block when agent files are within allowed_files", async () => {
         const repoDir = path.join(testWorkspaceDir, "allowed-files-ok-repo");
         fs.mkdirSync(repoDir, { recursive: true });
 
@@ -5,7 +5,7 @@ const { createHash } = require("node:crypto");
 const fs = require("node:fs");
 const os = require("node:os");
 const path = require("node:path");
-const { test } = require("node:test");
+import { test } from "vitest";
 const { canonical } = require("./work_queue_codec.cjs");
 const { main: planCompaction, planFor } = require("./work_queue_compaction_plan.cjs");
 const { isRetryablePublicationError, main: apply, PLAN_MAX_BYTES, readPlan } = require("./work_queue_compaction_apply.cjs");