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From the downloaded distribution, extract the /database/upgrade folder.  This folder includes a number of migration*.sql files which upgrades the FlexDeploy schemas.  You will need to execute these scripts from the version of FlexDeploy you currently have, up to the latest version.  And they must be executed in that order.  For example, if you are upgrading from FlexDeploy 3.7.1 to FlexDeploy 4.0.3, you will need to execute migration3.7.1_to_4.0.0.sql,  then migration4.0.0_to_4.0.1.sql, then migration4.0.1_to_4.0.2.sql, and finally, migration4.0.2_to_4.0.3.sql. 

These scripts should be executed as system, sys, or another user which has privileges to create objects in other schemas, performs grants, etc.  You can load and execute these scripts using other tools such as Toad or SQL Developer, but the instructions here are for using the sqlplus client.

export ORACLE_HOME=<your Oracle Home directory>
export ORACLE_SID=<the SID of your database>
spool migration4.0.3.out (change for each script execution so logs are preserved)
$ORACLE_HOME/bin/sqlpus (login as sys or system when prompted)
SQL> <<execute scripts as shown above>>

export ORACLE_HOME=<your Oracle Home directory>
export ORACLE_SID=<the SID of your database>
spool migration4.0.3.out (change for each script execution so logs are preserved)
$ORACLE_HOME/bin/sqlpus system@<tnsname>
SQL> <<execute scripts as shown above>>

For example,