If in a JDeveloper application you point to artifacts in a file based MDS residing in a Windows folder for example "d:\projects\MDS", then JDeveloper will create an new entry in the adf-config.xml file (that you can find in Application Resources -> Descriptors -> ADF META-INF) pointing to the absolute location of that folder:
The problem with this is that if you have other colleagues that use Linux instead of Window, it's not possible to make it work for both by defining some relative location (as you could do with ant), like "../../projects/MDS", so now what?
As in most cases, the solution is so simple that I successfully missed it many times: use an environment variable! What worked was creating an environment variable with name MDS_HOME, and after that I could use it like this:
I have not yet fully tested if this works for everything, like deploying with ant, but if it doesn't I expect you can easily fix that by modifying the ant-sca-compile.xml file in your JDeveloper installation folder by adding a property "mds_home" in there as well.