Directories for APT generated classes causes issues since 4.4.0

The conversion to absolute paths introduced in version 4.4.0 with the PR #218 causes issues in our Eclipse IDE setup, which leads from our previous relative paths to absolute one in `.settings/org.eclipse.jdt.apt.core.prefs` which Eclipse itself turns to relative ones by removing the first slash from the absolute path while creating the corresponding entries in `.classpath`. Can we ensure that relative paths remain as is?

Start by reviewing PR #218 and the generated `.settings/org.eclipse.jdt.apt.core.prefs` and `.classpath` entries described in the issue. Trace where APT generated-class directories are converted to absolute paths; done means relative paths remain relative and Eclipse no longer rewrites them incorrectly.

Written by the indexing model from the issue text.