At this moment the PHP Plugin awaits that, for example, that pdepend log file has a name pdepend.xml and is located in target/logs/.
And it is impossible to tell sonar, that it has name php_depend.xml and it is located in _build/logs.
Now I can set these parameters only in pom.xml. In earlier versions of plugin (0.2, 0.3) it was possible to set it on Sonar configuration page.
This affects all tools (codesniffer, pdepend, phpmd, phpunit and phpunit coverage report).