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When a scrub happens the entire contents of the build directory are wiped out. When using eclipse to work on tomcat projects this is a nusance. The build directory is set to the WEB-INF/classes dir, which also contains config files etc. It would be nice to have an option to srub or not, or to have it only scrub .class files.
In 2.1-M4, a preference got added to control this behavior. Preferences>Java>Compiler>Other>Allow to clean output folder Is it enough for your need ?
Reopen if the option is not sufficient.