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If delete .settings/org.eclipse.wst.common.component update maven project generate new empty file without <wb-module deploy-name="deploy-name"> <wb-resource deploy-path="/" source-path="/src/main/java"/> <wb-resource deploy-path="/" source-path="/src/main/resources"/> </wb-module>
The component file is generated and configured when m2e-wtp installs the project Facet(s). If the relevant facet hasn't changed, then it won't try anything. Your solutions for now : 1 - please don't delete org.eclipse.wst.common.component ;-) 2 - delete project from workspace then delete .project, .classpath, .settings/*, reimport as a maven project.
another workaround is edit generated .settings/org.eclipse.wst.common.component add <wb-module> xml tag and update maven project