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If you're using startManagedWeblogic.cmd it wont use anything related to nodemanager, unless your using nodemanager to call it with startscriptenabled. We use boot.properties for username/pass startup options. We do not store it in the data directory but in the servers/server_name/security directory. Might need to create the dir. Does this help ?
The files under
will be used by nodemanager while starting the servers. You should configure nodemanager and use it to start the managed servers. See : http://docs.oracle.com/cd/E24329_01/web.1211/e21050/starting_nodemgr.htm#NODEM209 for more information. Also take a look at this : http://docs.oracle.com/cd/E24329_01/web.1211/e21050/java_nodemgr.htm#i1068413 for configuring nodemanager.properties to enable the StartScriptEnabled and StartScriptName