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1. Create a MIFOS_CONF environment variable that points to a directory where you want to store your custom files.
2. If using a custom deploymifosDB.properties file in v1.1.x or v.1.2.x, add these custom values to a new local.properties file.    
   1. Reference 
   - http://www.mifos.org/developers/wiki/MigratingToPostV12DatabaseConfiguration
   1. Migrating to Post-v1.2 Database Configuration
3. If using a custom Application Configuration file, move this file to the location referenced by MIFOS_CONF.
4. If using a custom loggerconfiguration.xml file, move this file to the location referenced by MIFOS_CONF.