final Intent activityIntent = new Intent(context, MainActivity.class);
activityIntent.putExtra("smsChallenge", smsText);
activityIntent.putExtra("smsSenderNumber", senderMobilNumber);
activityIntent.addFlags(Intent.FLAG_ACTIVITY_NEW_TASK);
activityIntent.addFlags(Intent.FLAG_ACTIVITY_CLEAR_TOP);
context.startActivity(activityIntent);

Bundle extras = getIntent().getExtras();
if (extras != null) {
    smsChallenge = extras.getString("smsChallenge");
    extras.remove("smsChallenge");
}

getIntent().removeExtra("smsChallenge");

public YourActivity extends Activity {

 private boolean extrasClearedOut;
 private SharedPreferences mPrefs;
 private static String EXTRA_CLEAR_OUT = "extras_cleared_out";

 public void onCreate(Bundle savedInstanceState) {
     mPrefs = PreferenceManager.getDefaultSharedPreferences(getBaseContext());

     extrasClearedOut = mPrefs.getBoolean(EXTRA_CLEAR_OUT, false);

     if (savedInstanceState != null && savedInstanceState.getBoolean(EXTRA_CLEAR_OUT, false))  {
         extrasClearedOut = true;
     }

     Intent intent = getIntent();
     if (extrasClearedOut) {
       // ignore the extras in the intent.

     }

     else {
       // Read and use the extras in the intent.
     }
 }

 protected void onNewIntent (Intent intent)  {
    super.onNewIntent(intent);
    setIntent(intent);

    if (extrasClearedOut) {
       // ignore the extras in the intent.
    }
    else {
       // Read and use the extras in the intent.
    }
 }

 public void someMethod(...) {
    extrasClearedOut = true;
 }

 protected void onSaveInstanceState (Bundle outState) {
    super.onSaveInstanceState(outState);
    outState.putBoolean(EXTRA_CLEAR_OUT, extrasClearedOut);
 }

 public void onDestroy()
 {
    final Editor edit = mPrefs.edit();
    edit.putBoolean(EXTRA_CLEAR_OUT, extrasClearedOut);
    edit.commit();
 }

}

private void removeExtraFromBundle(String key){
    Bundle bundle = getArguments();
    if(bundle != null){
        String value = null;
        value = bundle.getString(key);
        if(value != null){
            bundle.remove(key);
        }
    }
}

final Intent activityIntent = new Intent(context, MainActivity.class);
activityIntent.putExtra("smsChallenge", smsText);
activityIntent.putExtra("smsSenderNumber", senderMobilNumber);
activityIntent.putExtra("nonce", UUID.randomUUID().toString);
activityIntent.addFlags(Intent.FLAG_ACTIVITY_NEW_TASK);
activityIntent.addFlags(Intent.FLAG_ACTIVITY_CLEAR_TOP);
context.startActivity(activityIntent);

public void onCreate(final Bundle savedInstanceState) {
    super.onCreate(savedInstanceState);
    Intent = getIntent();
    smsChallenge = intent.getStringExtra("smsChallenge", null);
    String nonce = intent.getStringExtra("nonce", null);
    if (nonce == null) {
      // should not happen, but do something sane here
    }
    SharedPreferences sp = PreferenceManager.getDefaultPreferences(this);
    if (nonce.equals(sp.getString("nonce", null)) {
      // app was restarted
    } else {
      // app was started from a shiny fresh intent
      sp.edit().putString("nonce", nonce).commit();
    }
}

final Intent activityIntent = new Intent(context, MainActivity.class);

final Intent activityIntent = new Intent(context.getApplicationContext(), MainActivity.class);

public void onCreate(Bundle savedInstanceState) {
    super.onCreate(savedInstanceState);

    // The Intent provided by getIntent() (and its extras) will persist through a restore
    // via savedInstance.  Because of this, restoring this activity from a
    // an instance that was originally started with extras (deep-link or
    // pre-defined destination) may cause un-desired behavior
    // (ie...infinite loop of sending the user directly to somewhere else because of a
    // pre-defined alternate destination in the Intent's extras).
    //
    // To get around this, if restoring from savedInstanceState, we explicitly
    // set a new Intent *** to override the original Intent that started the activity.***
    // Note...it is still possible to re-use the original Intent values...simply
    // set them in the savedInstanceState Bundle in onSavedInstanceState.
    if (savedInstanceState != null) {
        // Place savedInstanceState Bundle as the Intent "extras"
        setIntent(new Intent().putExtras(savedInstanceState));
    }

    processIntent(getIntent())
}

private void processIntent(Intent intent) {
    if (getIntent().getExtras() == null) {
        // Protection condition
        return;
    }

    doSomething(intent.getExtras.getString("SOMETHING_I_REALLY_NEED_TO_PERSIST"));

    final String somethingIDontWantToPersist =
        intent.getExtras.getString("SOMETHING_I_DONT_WANT_TO_PERSIST");

    if(somethingIDontWantToPersist != null) {
        doSomething(somethingIDontWantToPersist);
    }
}

@Override
public void onSaveInstanceState(Bundle savedInstanceState) {
    // Save selective extras from original Intent...
    savedInstanceState.putString("SOMETHING_I_REALLY_NEED_TO_PERSIST", "persistedValued");
    super.onSaveInstanceState(savedInstanceState);
}