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wsimport problem when using catalogs

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We had been using a flat schema directory and wsimport was working fine. I broke the schemas out into separate directories and created a catalog using systemSuffix entries to map the schemas to a new path relative to the catalog. I tested the catalog with Oxygen and Eclipse XML editor. Validation works fine, the tools correctly found the relocated schemas (tested using validate ). However when using wsimport I get a lot of errors similar to the following:

[ERROR] 'UnsupportedMessageFailure' is already defined
line 440 of file:/data/catalog.work/wsdefs/foo/ServiceMessageTypes.xsd

[ERROR] (related to above error) the first definition appears here
line 436 of file:/data/catalog.work/wsdefs/foo/ServiceMessageTypes.xsd

The second line number points to the start of the UnsupportedMessageFailure element and and the first line number points to the start of the following element. This is a consistent problem across many of the elements. The fact that errors reference the relocated schemas tell me the catalog is being interpreted. The catalog entries all looks as follows:

<systemSuffix systemIdSuffix="ServiceMessageTypes.xsd" uri="./foo/ServiceMessageTypes.xsd"/>

Schemas/wsdls all work fine with wsimport in a flat directory without catalogs Any help or pointers are appreciated.
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