If I run the command...
pmd -d MyClass.java -f yahtml -P outputDir=.\issues\pmd\ -R rulesets/java/empty.xml
...I get an error to the effect that the system cannot find the path =.\issues\pmd\MyClass.html -- as though it were including the = as part of the path. This is on Windows 7, if that makes any difference. I have tried with and without the beginning .\ and got the same result.
It also seems to output the usage/help text multiple times in addition to the actual error message whenever I run into an issue with my parameters such as this, and I'm not sure if that's normal or not. (Similarly, if I run just "pmd" and get the usage options it ends with an exception about not having specified dir, and I'm not sure if that's normal or not either -- probably ought to be its own bug report, although it hardly deserves one since it's inconsequential.)
Discussion: How to use linkPrefix and linePrefix in the HTML renderer
So, I have determined that this is due the the "=" being included in the property value and isn't specific to outputDir. If I set the linkPrefix on the html renderer, the links begin with "=" before the prefix.
this will be fixed with the next release.