diff --git a/packages/amplify-category-auth/src/index.js b/packages/amplify-category-auth/src/index.js
index 75e014aea0e..dbdc94d2258 100644
--- a/packages/amplify-category-auth/src/index.js
+++ b/packages/amplify-category-auth/src/index.js
@@ -68,8 +68,10 @@ async function add(context, skipNextSteps = false) {
 async function transformCategoryStack(context, resource) {
   if (resource.service === AmplifySupportedService.COGNITO) {
     if (canResourceBeTransformed(resource.resourceName)) {
-      await generateAuthStackTemplate(context, resource.resourceName);
+      generateAuthStackTemplate(context, resource.resourceName);
     }
+  } else if (resource.service === 'S3') {
+    // Not yet implemented
   }
 }
 
diff --git a/packages/amplify-e2e-core/src/init/initProjectHelper.ts b/packages/amplify-e2e-core/src/init/initProjectHelper.ts
index 94d91c15af7..bf1b418ba0b 100644
--- a/packages/amplify-e2e-core/src/init/initProjectHelper.ts
+++ b/packages/amplify-e2e-core/src/init/initProjectHelper.ts
@@ -348,39 +348,6 @@ export function initNewEnvWithProfile(cwd: string, s: { envName: string }): Prom
   });
 }
 
-export function updatedInitNewEnvWithProfile(cwd: string, s: { envName: string }): Promise<void> {
-  addCircleCITags(cwd);
-
-  return new Promise((resolve, reject) => {
-    spawn(getCLIPath(), ['init'], {
-      cwd,
-      stripColors: true,
-      env: {
-        CLI_DEV_INTERNAL_DISABLE_AMPLIFY_APP_CREATION: '1',
-      },
-    })
-      .wait('Do you want to use an existing environment?')
-      .sendConfirmNo()
-      .wait('Enter a name for the environment')
-      .sendLine(s.envName)
-      .wait('Choose your default editor:')
-      .sendCarriageReturn()
-      .wait('Using default provider  awscloudformation')
-      .wait('Select the authentication method you want to use:')
-      .sendCarriageReturn()
-      .wait('Please choose the profile you want to use')
-      .sendCarriageReturn()
-      .wait(/Try "amplify add api" to create a backend API and then "amplify (push|publish)" to deploy everything/)
-      .run((err: Error) => {
-        if (!err) {
-          resolve();
-        } else {
-          reject(err);
-        }
-      });
-  });
-}
-
 export function amplifyInitSandbox(cwd: string, settings: {}): Promise<void> {
   const s = { ...defaultSettings, ...settings };
   let env;
diff --git a/packages/amplify-e2e-core/src/utils/index.ts b/packages/amplify-e2e-core/src/utils/index.ts
index a0555c3cb35..e0e795c628c 100644
--- a/packages/amplify-e2e-core/src/utils/index.ts
+++ b/packages/amplify-e2e-core/src/utils/index.ts
@@ -24,7 +24,6 @@ export * from './sleep';
 export * from './transformConfig';
 export * from './admin-ui';
 export * from './hooks';
-export * from './transform-current-project-to-git-pulled-project';
 
 // run dotenv config to update env variable
 config();
diff --git a/packages/amplify-e2e-core/src/utils/transform-current-project-to-git-pulled-project.ts b/packages/amplify-e2e-core/src/utils/transform-current-project-to-git-pulled-project.ts
deleted file mode 100644
index d3ebc473c8b..00000000000
--- a/packages/amplify-e2e-core/src/utils/transform-current-project-to-git-pulled-project.ts
+++ /dev/null
@@ -1,26 +0,0 @@
-import { pathManager } from 'amplify-cli-core';
-import * as fs from 'fs-extra';
-import glob from 'glob';
-
-/**
- *
- * @param projRoot : string
- * deleting files matching .gitignore regex
- */
-export const transformCurrentProjectToGitPulledProject = (projRoot: string) => {
-  const gitIgnoreFilePath = pathManager.getGitIgnoreFilePath(projRoot);
-  const regexArray = fs.readFileSync(gitIgnoreFilePath, 'utf-8').split('\n');
-  regexArray.forEach(str => {
-    const dirPath = glob.sync(str, {
-      cwd: projRoot,
-      absolute: true,
-    });
-    dirPath.forEach(file => {
-      if (fs.existsSync(file) && fs.lstatSync(file).isDirectory()) {
-        fs.removeSync(file);
-      } else {
-        fs.unlinkSync(file);
-      }
-    });
-  });
-};
diff --git a/packages/amplify-e2e-tests/src/__tests__/init-special-case.test.ts b/packages/amplify-e2e-tests/src/__tests__/init-special-case.test.ts
index 7c319e2131e..c3dd50918fd 100644
--- a/packages/amplify-e2e-tests/src/__tests__/init-special-case.test.ts
+++ b/packages/amplify-e2e-tests/src/__tests__/init-special-case.test.ts
@@ -1,18 +1,5 @@
-import { category } from '@aws-amplify/amplify-category-auth';
-import {
-  addAuthWithDefault,
-  amplifyPushAuth,
-  createNewProjectDir,
-  deleteProject,
-  deleteProjectDir,
-  getBackendAmplifyMeta,
-  getParameters,
-  getTeamProviderInfo,
-  initJSProjectWithProfile,
-  initNewEnvWithProfile,
-  transformCurrentProjectToGitPulledProject,
-} from 'amplify-e2e-core';
 import * as specialCaseInit from '../init-special-cases';
+import { createNewProjectDir, getBackendAmplifyMeta, deleteProject, deleteProjectDir } from 'amplify-e2e-core';
 
 describe('amplify init', () => {
   let projRoot: string;
@@ -34,29 +21,4 @@ describe('amplify init', () => {
     expect(AuthRoleName).toBeIAMRoleWithArn(AuthRoleArn);
     expect(DeploymentBucketName).toBeAS3Bucket(DeploymentBucketName);
   });
-
-  it('test init on a git pulled project', async () => {
-    const envName = 'dev';
-    const resourceName = 'authConsoleTest';
-    await initJSProjectWithProfile(projRoot, { disableAmplifyAppCreation: false, name: resourceName, envName });
-    await addAuthWithDefault(projRoot, {});
-    await amplifyPushAuth(projRoot);
-    let teamInfo = getTeamProviderInfo(projRoot);
-    expect(teamInfo).toBeDefined();
-    let appId = teamInfo[envName].awscloudformation.AmplifyAppId;
-    let stackName = teamInfo[envName].awscloudformation.StackName;
-    expect(stackName).toBeDefined();
-    expect(appId).toBeDefined();
-    expect(teamInfo[envName].categories.auth).toBeDefined();
-    /**
-     * simulate git clone by deleteing files based on .gitignore
-     */
-    transformCurrentProjectToGitPulledProject(projRoot);
-
-    // to not crash
-    expect(await initNewEnvWithProfile(projRoot, { envName })).not.toThrow();
-
-    // check parameters.json exists
-    expect(getParameters(projRoot, category, resourceName)).not.toThrow();
-  });
 });
diff --git a/packages/amplify-provider-awscloudformation/src/initialize-env.ts b/packages/amplify-provider-awscloudformation/src/initialize-env.ts
index 1239e65f531..c050bacbe53 100644
--- a/packages/amplify-provider-awscloudformation/src/initialize-env.ts
+++ b/packages/amplify-provider-awscloudformation/src/initialize-env.ts
@@ -13,8 +13,6 @@ import { pullHooks } from './utils/hooks-manager';
 import { buildOverridesEnabledResources } from './build-override-enabled-resources';
 
 export async function run(context: $TSContext, providerMetadata: $TSMeta) {
-  await buildOverridesEnabledResources(context);
-
   if (context.exeInfo && context.exeInfo.isNewEnv) {
     return context;
   }
@@ -117,4 +115,6 @@ export async function run(context: $TSContext, providerMetadata: $TSMeta) {
   if (hasMigratedResources) {
     stateManager.setCurrentMeta(undefined, amplifyMeta);
   }
+
+  await buildOverridesEnabledResources(context);
 }