How to change settings of the persistence.xml file through an external file?

I believe the best solution is to tell your connection settings in Tomcat, not the project. Following Tomcat 7 documentation :

Within Context of your application, create Resource (attention to name: jdbc/TestDB ):

<Context>
    <Resource name="jdbc/TestDB" auth="Container" type="javax.sql.DataSource"
               maxActive="100" maxIdle="30" maxWait="10000"
               username="javauser" password="javadude" driverClassName="com.mysql.jdbc.Driver"
               url="jdbc:mysql://localhost:3306/javatest"/>
</Context>

On your web.xml :

<web-app xmlns="http://java.sun.com/xml/ns/j2ee"
         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
         xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee
         http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"
         version="2.4">
    <description>MySQL Test App</description>
    <resource-ref>
        <description>DB Connection</description>
        <res-ref-name>jdbc/TestDB</res-ref-name>
        <res-type>javax.sql.DataSource</res-type>
        <res-auth>Container</res-auth>
    </resource-ref>
</web-app>

On your persistence.xml :

<persistence-unit name="TestUnit" transaction-type="JTA">
    <provider>org.hibernate.ejb.HibernatePersistence</provider>
    <jta-data-source>jdbc/TestDB</jta-data-source>
    <!-- Demais configurações pertinentes -->
</persistence-unit>

In this way, your project will always be the same. What will change is the configuration of your server / container.

The Persistence.createEntityManagerFactory method has an overload that you can pass a Map with the settings of persistence.xml, there you load them from wherever you like (eg a configuration file);

Map properties = new HashMap();

properties.put("javax.persistence.jdbc.driver", "oracle.jdbc.OracleDriver");
properties.put("javax.persistence.jdbc.url", "jdbc:oracle:thin:@localhost:1521:ORCL");
properties.put("javax.persistence.jdbc.user", "user-name");
properties.put("javax.persistence.jdbc.password", "password");

Persistence.createEntityManagerFactory("unit-name", properties);