Autoconfig

Autoconfig is tool/utility to reconfigure your Oracle Application configuration files using context (XML file) and template files, more information here and here 
This post covers steps to run Autoconfig in Oracle Apps R12 (steps are similar to 11i, only change is location of autoconfig script and log files)
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A) Running Autoconfig on R12 environment Application Tier
1. Login as user owning application tierfor R12 (usually applmgr)
2. Set environment variable by executing env file $INSTALL_BASE/ apps/ apps_st/ appl/ APPL[$SID]_[$hostname].env
3. cd $ADMIN_SCRIPTS_HOME  (or $INSTALL_BASE/apps/$CONTEXT_NAME/ admin/ scripts)
4. run adautocfg.sh (Autoconfig script)
./adautocfg.sh5. Supply apps password when prompted.
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B) Running Autoconfig on R12 environment Database Tier
1.Login as user owning database tier for R12 (usually oracle)
2. Set environment variable by executing env file $INSTALL_BASE/ db/ tech_st/ [11.1.0 or 10.2.0]/ [$SID]_[$hostname].env
3. cd $ORACLE_HOME/ appsutil/ scripts/ $CONTEXT_NAME
4. run adautocfg.sh (Autoconfig script)
./adautocfg.sh
5. Supply apps password when prompted