When I run mvn clean install, the pax:eclipse goal gets executed. However, files are not copied to my target/pax-eclipse folder.

the only files in "target/pax-eclipse" will be embedded/inlined files _not_ found in "target/classes"

If I later run mvn pax:clean pax:eclipse, then the files get embedded.

yes, because clean removes files from "target/classes" and because you don't do a compile or install then they aren't replaced - therefore "target/pax- eclipse" will contain the difference,
ie. the entire contents of the bundle

How can I ensure that the files get embedded during a regular build (i.e. so I don't have to build twice).

one thing you forgot to mention: _why_ do you need these files in "target/pax-eclipse" ?

this folder is only needed to keep PDE happy, you shouldn't need every single file in it

Right.

The reason is that this bundle exports packages from an inlined bundle. If the target/pax-eclipse directory is not included, then Eclipse gives me an error like:

  "Package 'stuart.is.so.smart' does not exist in this plug-in

The error is there because the manifest says that the bundle exports this package, but (I suppose) PDE doesn't find it.


Cheers,
=David



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