Pro tip: PHPUnit's test suite "exclude" nodes don't do wildcard expansion. Took me longer than I'd like to admit figuring this out.

nope.xml

<phpunit>
    <testsuites>
        <testsuite name="Unit">
            <directory>../src/*/Bundle/*Bundle/Tests</directory>
            <exclude>src/*/Bundle/*Bundle/Tests/Functional</exclude>
        </testsuite>
</phpunit>

yep.xml

<phpunit>
    <testsuites>
        <testsuite name="Unit Tests">
            <directory>../src/*/Bundle/*Bundle/Tests</directory>
            <exclude>src/MyProject/Bundle/MyFirstBundle/Tests/Functional</exclude>
            <exclude>src/MyProject/Bundle/MySecondBundle/Tests/Functional</exclude>
            <exclude>src/MyProject/Bundle/MyThirdBundle/Tests/Functional</exclude>
            <exclude>src/MyProject/Bundle/MyNthBundle/Tests/Functional</exclude>
        </testsuite>
    </testsuites>
</phpunit>

So.. maybe someone changed it as this is what my phpunit file looks like, and it works as intended:

    <filter>
        <whitelist processUncoveredFilesFromWhitelist="true">
            <directory suffix=".php">./HCI</directory>
            <exclude>
                <directory suffix=".php">./HCI/*/Routes</directory>
            </exclude>
        </whitelist>
    </filter>
    <logging>
        <log type="coverage-html" target="./report" charset="UTF-8"
            yui="true" highlight="true"
            lowUpperBound="50" highLowerBound="80" />
    </logging

ok, thanks... lol
took me a few hours to figure it out