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In 2.0.x the output directory is based on the SourceSet name, by default this would be 'main' but if you were to create a custom SourceSet name just for your XJC you should achieve some control over the output directory, even if you can't fully specify it.
Strategy suggestion in lieu of feature:
Gradle allows easy sub-project creation, so structuring your larger project requirement around any pre or post processing for XJC could be done at the project level, meaning a project's only aim could be to package an output that another project consumes. This 2nd project reprocesses and the output from this project is the real output you are after.
I am assuming you want more control over outputDirectory because of some additional process only to affected XJC output or to manage many processes separately (in a single project) and keep them apart.
It is not clear how using a sub-project (while additional work for you to setup) does not address that concern.
In version 1.4.3 there was an outputDirectory option - how can I set that in 2.0?
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