When building multi module projects, aggregator will be built first, and modules will be built in an order based on the dependencies between them.
You can add the following plugin to your aggregator(it's the parent pom you mentioned in the question) pom.xml to solve your problem. I choose initialize for this to be executed, but You could have choose install also. Check out lifecycle. Imported thing here this code will be executed when a maven command that is later in the lifecycle is issued. (Ex: If You choose install as the phase, and execute mvn package this wont be executed.)
<build>
<plugins>
<plugin>
<artifactId>exec-maven-plugin</artifactId>
<groupId>org.codehaus.mojo</groupId>
<version>1.6.0</version>
<executions>
<execution>
<id>Run Script</id>
<phase>initialize</phase>
<goals>
<goal>exec</goal>
</goals>
<configuration>
<executable>bootstrap.sh</executable>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>