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See GlassFish bug https://wsit.dev.java.net/issues/show_bug.cgi?id=1131 There is a regression in configuration for web projects when WS clients are used. The wsit configuration files are being generated in wrong directory for web projects: WEB-INF folder instead of META-INF.
Fixed in web-main.
Changeset: http://hg.netbeans.org/web-main/rev/2c8f1924351f
Fixed.
Also transplanted to 6.7: http://hg.netbeans.org/release67/rev/aeee3343ad3f
v.