java.lang.RuntimeException: Unable to instantiate activity ComponentInfo - NFC access

I have seen a number of questions similar to this one, but they seem to be specific to the classes and packages that they use. I tried some of the solutions, but did not help me. I get the following error:

03-27 14:30:08.604: D/AndroidRuntime(8057): Shutting down VM
03-27 14:30:08.604: W/dalvikvm(8057): threadid=1: thread exiting with uncaught exception (group=0x41c02c80)
03-27 14:30:08.604: E/AndroidRuntime(8057): FATAL EXCEPTION: main
03-27 14:30:08.604: E/AndroidRuntime(8057): Process: org.nick.nfc.seaccess, PID: 8057
03-27 14:30:08.604: E/AndroidRuntime(8057): java.lang.RuntimeException: Unable to instantiate activity ComponentInfo{org.nick.nfc.seaccess/org.nick.nfc.seaccess.MainActivity}: java.lang.ClassNotFoundException: Didn't find class "org.nick.nfc.seaccess.MainActivity" on path: DexPathList[[zip file "/system/framework/com.android.nfc_extras.jar", zip file 

Any idea, how I should address it?

Here is the beginning of the main activity:

public class MainActivity extends Activity implements OnClickListener {

    private static final String TAG = MainActivity.class.getSimpleName();

    private Button gpInfoButton;
    private Button emvInfoButton;
    private Button walletInfoButton;

    private TextView infoText;

    private Terminal terminal;
    private CardConnection seConn;

    @Override
    public void onCreate(Bundle savedInstanceState) {
...

Here is my activity tag from my manifest. I have seem sometimes folks add the full package name to the manifest. Shall I do this and see what happens?

    <activity
            android:name=".MainActivity"
            android:configChanges="keyboard|keyboardHidden|orientation|screenLayout|uiMode|screenSize|s    mallestScreenSize"
            android:label="@string/title_activity_main" >
        <intent-filter>
            <action android:name="android.intent.action.MAIN" />

            <category android:name="android.intent.category.LAUNCHER" />
        </intent-filter>
    </activity>

I found a link that states the issue may be with how I have edited an xml file, which holds certificates. I have pasted the file below; removed the certs. Do you see any issue with it?

<?xml version="1.0" encoding="utf-8"?>
<resources xmlns:xliff="urn:oasis:names:tc:xliff:document:1.2">
<!-- Applications granted NFCEE access on user builds
    See packages/apps/Nfc/etc/sample_nfcee_access.xml for full documentation.
 -->
    <!--  Google wallet release signature -->
    <signer android:signature="308205bd852e" />

<!-- Sequent Wallet signature -->
<signer android:signature="30820243badc1df9d"/>
<!-- android-se-access signature-->
    <signer
android:signature="3082044cbd852e">
<package android:name="org.nic.nfc.seaccess"/>

</signer>
</resources>

Here is a view of the project workspace

I just saw something in the logs, which I wanted to add to this thread. Seems like the is a "-1", and "-2" next to the package name. Is that supposed to be there, or is that the cause of my issue? Here are the log messages I am talking about:

03-27 22:55:10.884: E/AndroidRuntime(9436): Caused by:     java.lang.ClassNotFoundException: Didn't find class "org.nick.nfc.seaccess.MainActivity"     on path: DexPathList[[zip file "/system/framework    /com.android.nfc_extras.jar", zip file "/data/app/org.nick.nfc.seaccess-    1.apk"],nativeLibraryDirectories=[/data/app-lib/org.nick.nfc.seaccess-1, /vendor/lib,     /system/lib]]
03-27 22:58:02.104: E/AndroidRuntime(9880): Caused by:     java.lang.ClassNotFoundException: Didn't find class "org.nick.nfc.seaccess.MainActivity"     on path: DexPathList[[zip file "/system/framework    /com.android.nfc_extras.jar", zip file "/data/app/org.nick.nfc.seaccess-    2.apk"],nativeLibraryDirectories=[/data/app-lib/org.nick.nfc.seaccess-2, /vendor/lib,         /system/lib]]