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Mitch McConnellMitch McConnell 

Apex code coverage not showing internal classes

I am at my wit's end.  I am trying to increase our code coverage for a custom controller extension, and cannot seem to get it to work at all.   The controller class contains several internal classes that are used to manage its data representation.   What I mean is that although my test class clearly instantiates the controller (and passes), when I look at what that does, it shows the internal class as not being covered at all, even when by inspection you can see that it would be.

Also, the developer console (yes, I know it is awful, but that is the tool we have) doesn't update even when I add a line of code to the test that clearly executes a statement (in this case, just an assignment).

Has anyone else seen this type of behavior?  
Out of curiosity, what is the API version of your test class?  How many lines total is your test class?  Are you running your test synchronously or asynchronously?
Mitch McConnellMitch McConnell
The API version is 35.  The test class has 230 lines of code.  Our "Test execution options" has only "Independent Auto-Number Sequence" checked.  Since "Disable Parallel Apex Testing" is unchecked, I assume we are running async tests.