To understand above sentence, lets take an example if I want to instrument class "com.my.target.Klass1" and some where in agent jar file itself we made a reference to Klass1 object by saying
"Klass1.class"
then this class will not be called for transformation by registered ClassFileTransformer in the agent.
In my case I wanted "Klass1" name so I added code in ClassFileTransformer implementation as below:
String klassObject = Klass1.class.getName();
and when I made agent jar and wanted to use it for instrumentation, this class (Klass1.class) was no where to be seen. I struggle for hours and noticed that all other classes were called in by ClassFileTransformer implementation and only "Klass1" class was not. I had to change above code not to refer to class object directly. So I removed "Klass1.class" statement and replaced it with complete class name as below
String klassObject = "com.my.target.Klass1";
Now it worked like a charm...