CheckInvisible.cls

/*
  An entire class that has all the logic commented out
  other than two lines that simply return a value of null.
  The developer might have simply deleted or deactivated 
  the class if no longer needed.
  Here, I abreviated the commented-out code with elipses, but
  in my org, many lines of code existed in the block comment.
*/

public with sharing class CheckInvisible {
/*
  public static void TestInvis1() {
  ... 75 lines of code
  }
  public static void TestInvis2() {
  ... 80 lines of code
  }
*/
	public static pagereference CheckInvis1() {
		//CheckInvisible.TestInvis1();
		return null;
	}
	public static pagereference CheckInvis2() {
		//CheckInvisible.TestInvis2();
		return null;
	}
}

CheckInvisible.cls-meta.xml

<?xml version="1.0" encoding="UTF-8"?>
<ApexClass xmlns="http://soap.sforce.com/2006/04/metadata">
    <apiVersion>36.0</apiVersion>
    <status>Deleted</status>
</ApexClass>

CheckInvisibleTest.cls

@isTest
public class CheckInvisibleTest {
    static testMethod void Test1() {
        //CheckInventories.TestInvs1();
        CheckInvisible.CheckInvis1();
    }
    static testMethod void Test2() {
        //CheckInventories.TestInvs2();
        CheckInvisible.CheckInvis2();
    }
}

CheckInvisibleTest.cls-meta.xml

<?xml version="1.0" encoding="UTF-8"?>
<ApexClass xmlns="http://soap.sforce.com/2006/04/metadata">
    <apiVersion>36.0</apiVersion>
    <status>Deleted</status>
</ApexClass>

package.xml

<?xml version="1.0" encoding="UTF-8"?>
<Package xmlns="http://soap.sforce.com/2006/04/metadata">
    <fullName>boatAnchor</fullName>
    <description>test removing bad classes</description>
    <packageType>UNMANAGED</packageType>
    <types>
        <members>CheckInvisible</members>
        <members>CheckInvisibleTest</members>
        <name>ApexClass</name>
    </types>
    <version>36.0</version>
</Package>