It depends of your project's structure I guess ...

Well I am not an expert, but as my tests on this behavior ran, when you put

<whitelist>
   <directory suffix=".php">../application/</directory>

every single file in the application folder will be parsed, the .svn files,
the .random_extension files, etc, even if you've excluded them in a
<exclude> afterwards

In fact, you shouldn't even need to exclude
<directory suffix=".phtml">../application/</directory>
since you asked to allow only .php files on your whitelist

But are you saying your unittesting is slow only with these filters ? You
don't seem to include any lib (unless your libs are in your application
folder)

But basically, I recommand you to whitelist only folders you really want to
test
E.g. 


<whitelist>
   <directory suffix=".php">../application/models</directory>
   <directory suffix=".php">../application/modules/frontend</directory>
   <directory suffix=".php">../application/modules/backend</directory>
   etc.

Then if you have a "../application/my_bullshit_and_stuff" directory, it
won't even be parsed by phpunit
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