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How do I turn off the Java code helpers, especially the JPA helper. When I do a Maven update, Kepler often runs for long periods of time - sometimes an hour or more. It usually seems to be related to the JPA helper. Even better would be if 'Project...Build' didn't always require a 'Maven...Update' and if the 'Maven...Update' didn't always reset the project facet to 'JPA'.
Moving to M2E
Have you tried increasing Eclipse memory settings? https://wiki.eclipse.org/FAQ_How_do_I_increase_the_heap_size_available_to_Eclipse%3F It's hard to tell what really is happening in your situation given the lack of context, but if JPA tooling really is causing performance issues, and you have it reenabled after each project configuration update, it means you have m2e-wtp' JPA integration installed. You can disable it globally in the workspace, in Preferences > Maven > Java EE integration or add <m2e.jpa.activation>false</m2e.jpa.activation> in the properties section of your pom.xml. See https://wiki.eclipse.org/M2E-WTP/New_and_Noteworthy/1.0.0#Enable.2FDisable_the_JAX-RS.2FJPA.2FJSF_Configurators_at_the_pom.xml_level