Make file paths relative to the configuration file path
A very raw and simple approach.
 I believe you would be loading the properties from the configuration file.

Properties prop = new Properties();
prop.load(new FileInputStream("somepath/config.properties")); 


Hence I assume you know the path of your config file. 

Now simple iterate over your properties and set them again. 

for(String name : getProperty.getNames()) {
   String propValue = prop.getProperty(name);
   //TODO if(propValue == relative)
   setProperty(name, somepath + propValue);
}