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JNDI already provides a mechanism for separating out such configuration. See https://github.com/mwoodiupui/DSpace/tree/DS-1494 for a sketch of such an approach.
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search.user and search.password configurations in dspace/config/modules/authentication-ldap.cfg are sensitive pieces of information, and it should be possible to keep them in a central location. This requires changing /build.properties, /dspace/pom.xml, and /dspace/config/modules/authentication-ldap.cfg.
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