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>

Thx for sharing.
Also I'd like to add that exclude are ignored if a path is added within the command line.

Someone should probably do something about this lol

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