diff --git a/service/src/service/file-authorization.test.ts b/service/src/service/file-authorization.test.ts
index 4d98c59f..fa60d4c8 100644
--- a/service/src/service/file-authorization.test.ts
+++ b/service/src/service/file-authorization.test.ts
@@ -304,6 +304,106 @@ describe('resolveOutputBucketSessionKey', () => {
 });
 
 describe('authorizeRequestedFiles', () => {
+  test('coalesces repeated destinations while preserving distinct names for one object', async () => {
+    const req = request({ tenantId: TENANT_ID, userId: USER_ID });
+    const sessionKey = resolveSessionKey(req, { kind: 'user', id: USER_ID });
+    const alias = validFile({ name: 'extract/Transport_Phenomena/appendix-a1b2c3.pdf' });
+    const inherited = { ...alias, name: 'extract/Transport Phenomena/appendix.pdf' };
+    await expect(authorizeRequestedFiles({
+      req, files: [alias, inherited, { ...alias }, { ...inherited }], store: ownedStore(sessionKey),
+    })).resolves.toEqual([alias, inherited]);
+  });
+
+  test('keeps distinct destinations even when their object ids match', async () => {
+    const req = request({ tenantId: TENANT_ID, userId: USER_ID });
+    const sessionKey = resolveSessionKey(req, { kind: 'user', id: USER_ID });
+    const files = [
+      validFile(),
+      validFile({ id: 'file_abcdefghijklmnop', name: 'inputs/second.csv' }),
+      validFile({ storage_session_id: 'sess_abcdefghijklmnop', name: 'inputs/third.csv' }),
+    ];
+    const store = ownedStore(sessionKey);
+    for (const file of files) {
+      store.set(`session:${file.storage_session_id}`, sessionKey);
+      store.set(`upload:${sessionKey}${file.storage_session_id}${file.id}`, 'true');
+    }
+    await expect(authorizeRequestedFiles({ req, files, store })).resolves.toEqual(files);
+  });
+
+  test('selects the last distinct user ref per path without letting an earlier echo replace it', async () => {
+    const req = request({ tenantId: TENANT_ID, userId: USER_ID });
+    const sessionKey = resolveSessionKey(req, { kind: 'user', id: USER_ID });
+    const earlier = validFile({ name: 'report.py' });
+    const replacement = validFile({
+      name: earlier.name, id: 'file_abcdefghijklmnop', storage_session_id: 'sess_abcdefghijklmnop',
+    });
+    const unrelated = validFile({ id: 'file_0000000000000000', name: 'report.csv' });
+    const store = ownedStore(sessionKey, earlier);
+    for (const file of [replacement, unrelated]) {
+      store.set(`session:${file.storage_session_id}`, sessionKey);
+      store.set(`upload:${sessionKey}${file.storage_session_id}${file.id}`, 'true');
+    }
+    for (const files of [
+      [earlier, unrelated, replacement],
+      [earlier, unrelated, replacement, { ...earlier }],
+    ]) {
+      await expect(authorizeRequestedFiles({ req, files, store })).resolves.toEqual([unrelated, replacement]);
+    }
+    await expect(authorizeRequestedFiles({
+      req, files: [replacement, unrelated, earlier], store,
+    })).resolves.toEqual([unrelated, earlier]);
+    const alias = { ...earlier, name: 'original-report.py' };
+    await expect(authorizeRequestedFiles({
+      req, files: [earlier, alias, replacement, { ...earlier }], store,
+    })).resolves.toEqual([alias, replacement]);
+  });
+
+  test('authorizes superseded user refs before selecting a destination', async () => {
+    const req = request({ tenantId: TENANT_ID, userId: USER_ID });
+    const sessionKey = resolveSessionKey(req, { kind: 'user', id: USER_ID });
+    for (const unauthorized of [
+      validFile({ storage_session_id: 'sess_abcdefghijklmnop' }),
+      validFile({ id: 'file_abcdefghijklmnop' }),
+    ]) {
+      for (const files of [[unauthorized, validFile()], [validFile(), unauthorized]]) {
+        await expectAuthError(authorizeRequestedFiles({
+          req, files, store: ownedStore(sessionKey),
+        }), 403);
+      }
+    }
+  });
+
+  test('preserves shared input collisions for the sandbox to reject', async () => {
+    const req = request({ tenantId: TENANT_ID, userId: USER_ID });
+    const userSessionKey = resolveSessionKey(req, { kind: 'user', id: USER_ID });
+    for (const scope of [
+      { kind: 'skill' as const, resource_id: SKILL_ID, version: 1 },
+      { kind: 'agent' as const, resource_id: AGENT_ID },
+    ]) {
+      const shared = validFile({ ...scope, storage_session_id: 'sess_abcdefghijklmnop' });
+      const otherShared = { ...shared, id: 'file_abcdefghijklmnop' };
+      const sharedKey = resolveSessionKey(req, { kind: scope.kind, id: scope.resource_id, version: scope.version });
+      const store = ownedStore(userSessionKey);
+      store.set(`session:${shared.storage_session_id}`, sharedKey);
+      for (const file of [shared, otherShared]) {
+        store.set(`upload:${sharedKey}${file.storage_session_id}${file.id}`, 'true');
+      }
+      for (const files of [[shared, validFile()], [validFile(), shared], [shared, otherShared]]) {
+        await expect(authorizeRequestedFiles({ req, files, store })).resolves.toEqual(files);
+      }
+    }
+  });
+
+  test('still rejects an unauthorized scope on a duplicate object', async () => {
+    const req = request({ tenantId: TENANT_ID, userId: USER_ID });
+    const sessionKey = resolveSessionKey(req, { kind: 'user', id: USER_ID });
+    await expectAuthError(authorizeRequestedFiles({
+      req,
+      files: [validFile(), validFile({ kind: 'agent', resource_id: AGENT_ID })],
+      store: ownedStore(sessionKey),
+    }), 403);
+  });
+
   test('allows files owned by the resolved user sessionKey', async () => {
     const req = request({ tenantId: TENANT_ID, userId: USER_ID });
     const sessionKey = resolveSessionKey(req, { kind: 'user', id: USER_ID });
diff --git a/service/src/service/file-authorization.ts b/service/src/service/file-authorization.ts
index 4afa2c85..1b46ade0 100644
--- a/service/src/service/file-authorization.ts
+++ b/service/src/service/file-authorization.ts
@@ -269,5 +269,22 @@ export async function authorizeRequestedFiles(args: {
     }
   }
 
-  return requestedFiles;
+  // Deduplicate authorized refs by object and destination, preserving aliases.
+  const seenReferences = new Set<string>();
+  const uniqueReferences = requestedFiles.filter(file => {
+    const identity = `${file.storage_session_id}\0${file.id}\0${file.name}`;
+    if (seenReferences.has(identity)) return false;
+    seenReferences.add(identity);
+    return true;
+  });
+
+  // Last distinct user ref wins each path; exact echoes cannot undo replacements.
+  // Shared skill/agent inputs retain the sandbox's destination conflict checks.
+  const selectedUserFiles = new Map<string, t.RequestFile>();
+  for (const file of uniqueReferences) {
+    if (file.kind === 'user') selectedUserFiles.set(file.name, file);
+  }
+  return uniqueReferences.filter(file =>
+    file.kind !== 'user' || selectedUserFiles.get(file.name) === file,
+  );
 }
diff --git a/service/src/service/programmatic-input-limit.test.ts b/service/src/service/programmatic-input-limit.test.ts
new file mode 100644
index 00000000..fe7ba594
--- /dev/null
+++ b/service/src/service/programmatic-input-limit.test.ts
@@ -0,0 +1,96 @@
+import { expect, test } from 'bun:test';
+import { resolve } from 'path';
+
+test('selected-workspace replay caps authorized, coalesced inputs', async () => {
+  // Keep infrastructure mocks isolated from other suites. Cancellation stops
+  // accepted requests after validation, before any execution state is written.
+  const probe = Bun.spawn([process.execPath, '-e', `
+    import { mock } from 'bun:test';
+    import assert from 'node:assert/strict';
+    import { BRIDGE_WORKSPACE_PROGRAMMATIC_MAX_INPUT_FILES as limit,
+      BRIDGE_WORKSPACE_PROGRAMMATIC_MAX_FILES as totalLimit } from '../packages/code/src/protocol';
+    const passthrough = (_req, _res, next) => next();
+    mock.module('./src/middleware/limits', () => ({
+      executionLimiter: passthrough, cancellationLimiter: passthrough,
+    }));
+    mock.module('./src/lifecycle', () => ({
+      checkServiceStartUp: () => false, checkServiceShutDown: () => false,
+    }));
+    mock.module('./src/request-disconnect', () => ({
+      observeRequestDisconnect: () => ({
+        signal: AbortSignal.abort(), isDisconnected: () => false, dispose() {},
+      }),
+    }));
+    const stored = new Map();
+    mock.module('./src/queue', () => ({
+      pyQueue: {}, pyQueueEvents: {}, jobCancellationRegistry: {},
+      getExecutionQueueBinding() { throw new Error('must not enqueue'); },
+      getExistingExecutionJob() { throw new Error('must not look up jobs'); },
+      connection: {
+        defineCommand() {},
+        get: async key => stored.get(key) ?? null,
+        exists: async key => stored.has(key) ? 1 : 0,
+      },
+    }));
+    const { env } = await import('./src/config');
+    env.PTC_MODE = 'replay';
+    env.SANDBOX_BACKEND = 'remote-bridge';
+    env.BRIDGE_DYNAMIC_WORKERS = true;
+    const { resolveSessionKey } = await import('./src/session-key');
+    const { default: router } = await import('./src/service/programmatic-router');
+    const handler = router.stack.find(layer => layer.route?.path === '/exec/programmatic').route.stack.at(-1).handle;
+    const auth = { userId: 'user_123', tenantId: 'tenant_abc' };
+    const sessionKey = resolveSessionKey({ codeApiAuthContext: auth }, { kind: 'user', id: auth.userId });
+    function file(index, name = 'input-' + index + '.txt') {
+      const result = {
+        id: 'file_' + String(index).padStart(16, '0'), resource_id: 'rsrc_1234567890123456',
+        storage_session_id: 'sess_1234567890123456', name, kind: 'user',
+      };
+      stored.set('session:' + result.storage_session_id, sessionKey);
+      stored.set('upload:' + sessionKey + result.storage_session_id + result.id, 'true');
+      return result;
+    }
+    async function request(files) {
+      const req = {
+        body: { code: 'ls', language: 'bash', tools: [], files },
+        header: name => name === 'X-LibreChat-Code-Workspace-ID' ? 'workspace-1' : undefined,
+        codeApiPrincipal: { ...auth, principalSource: 'none', codeWorkerId: 'worker-1' },
+        codeApiAuthContext: auth,
+      };
+      const res = { status(code) { this.statusCode = code; return this; }, json(body) { this.body = body; return this; } };
+      await handler(req, res);
+      return { req, res };
+    }
+    assert.equal(limit + 2, totalLimit, 'main and history reserve two slots');
+    const boundary = Array.from({ length: limit }, (_, index) => file(index));
+    const replacement = file(limit, boundary[0].name);
+    for (const [inputs, expected] of [
+      [boundary, boundary],
+      [[...boundary, boundary[0]], boundary],
+      [[...boundary, replacement, boundary[0]], [...boundary.slice(1), replacement]],
+    ]) {
+      const { req, res } = await request(inputs);
+      assert.equal(res.statusCode, 200, JSON.stringify(res.body));
+      assert.equal(res.body.error, 'Programmatic execution request cancelled');
+      assert.deepEqual(req.body.files, expected);
+    }
+    const { res: oversized } = await request([...boundary, file(limit + 1)]);
+    assert.equal(oversized.statusCode, 400);
+    assert.equal(oversized.body.error, 'Selected-workspace execution allows at most ' + limit + ' input files; main and replay history occupy two reserved slots');
+    for (const unauthorized of [
+      { ...boundary[0], kind: 'agent' },
+      { ...boundary[0], storage_session_id: 'sess_abcdefghijklmnop' },
+    ]) {
+      const { res } = await request([unauthorized, ...boundary]);
+      assert.equal(res.statusCode, 403);
+      assert.equal(res.body.error, 'Unauthorized file reference');
+    }
+    console.log('PROGRAMMATIC_INPUT_LIMIT_OK');
+    process.exit(0);
+  `], { cwd: resolve(__dirname, '../..'), stdout: 'pipe', stderr: 'pipe' });
+  const [exitCode, stdout, stderr] = await Promise.all([
+    probe.exited, new Response(probe.stdout).text(), new Response(probe.stderr).text(),
+  ]);
+  expect(exitCode, `${stdout}\n${stderr}`).toBe(0);
+  expect(stdout).toContain('PROGRAMMATIC_INPUT_LIMIT_OK');
+}, 15000);
diff --git a/service/src/service/programmatic-router.ts b/service/src/service/programmatic-router.ts
index 1063fbfe..85d7e2c8 100644
--- a/service/src/service/programmatic-router.ts
+++ b/service/src/service/programmatic-router.ts
@@ -509,9 +509,6 @@ async function handleReplayInitial(
         req.body as t.ProgrammaticRequestBody;
   let timeout: number;
   try {
-        if (workspaceId != null && Array.isArray(files) && files.length > BRIDGE_WORKSPACE_PROGRAMMATIC_MAX_INPUT_FILES) {
-          throw new Error(`Selected-workspace execution allows at most ${BRIDGE_WORKSPACE_PROGRAMMATIC_MAX_INPUT_FILES} input files; main and replay history occupy two reserved slots`);
-        }
         timeout = workspaceId != null
           ? normalizeSelectedWorkspaceProgrammaticTimeoutMs(
               (req.body as t.ProgrammaticRequestBody).timeout,
@@ -602,6 +599,13 @@ async function handleReplayInitial(
     return;
   }
 
+  if (workspaceId != null && authorizedFiles.length > BRIDGE_WORKSPACE_PROGRAMMATIC_MAX_INPUT_FILES) {
+    res.status(400).json({
+      error: `Selected-workspace execution allows at most ${BRIDGE_WORKSPACE_PROGRAMMATIC_MAX_INPUT_FILES} input files; main and replay history occupy two reserved slots`,
+    });
+    return;
+  }
+
   /* Output bucket: hardcoded user-private. See router.ts /exec for the
    * full rationale; same gate, same shape. */
   let sessionKey: string;