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After creating and building an EE 6 web app (for example), target/endorsed/javax-endorsed-apis-6.0.jar is created. This should immediately affect ClassPath.BOOT but it seems that an IDE restart is required.
core-main #d9e9ead25f38
Integrated into 'main-golden', will be available in build *201103090000* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main/rev/d9e9ead25f38 User: Jesse Glick <jglick@netbeans.org> Log: #190621: ClassPath.BOOT not refreshed eagerly after target/endorsed created