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I released QSTools 1.2.5.Final with some updates on bom-check goal that avoids ClassPath resolution: withClassPathResolution(false) and also reads the exclusion list from pom.xml.
Commit: https://github.com/jboss-developer/maven-qstools-plugin/commit/e4ffbe93b1e4cdbef519d6e9e1c42beb8c8aca0f