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-invoke "Import XML Schema ..." in new wsdl wizard/add ws operation dialog in the designer => one can use schemas defined in project source roots ($PROJECT/src/java, $PROJECT/) only - this is quite restrictive and annoying since one can have his schemas in some other folder to not mix them with java sources or on some arbitrary place on the disk (we could copy these schemas to eg. xml-resources/xml-schemas or to the same location where the new WSDL will be placed/is in this case)
project source roots are only $PROJECT/src/java and $PROJECT/test (instead of $PROJECT/) by default
Reassigning to xml/wsdl
It has been designed to work with Netbeans project system. I'm not sure why would you keep some files not under src or test if they are indeed part of the source.
On a second thought, the import wizard has been designed to pick schemas from project roots. I do understand the limitations, hence marking this as an enhancement.