Reconfigure Project: persistence.xml, context.xml,web.xml and ,tomcat: server.xml

I have a test project which works fine with Mysql 5.6.10 as it is set up on a windows 7 laptop. I have successfully configured it with Tomcat and Hibernate JPA with DERBY database which is not the database I wish to work with. MySQL server 5.6 is running fine on my laptop. I want MySQL 5.6 to work properly in this Hibernate JPA /Tomcat environment. I have several other working projects projects with Tomcat including a mssql server app on this workstation which I got to work by simply copying the [login to view URL] file to the tomcat/lib folder and setting [login to view URL] file to address the connections for that. Hibernate 4.5.1 JPA environment works differently for some reason with MySQL than it does with Derby. I do not know why the pooling configuration is such a problem with MySQL. I would appreciate some assistance on this project: Here is my current problem: I get the following error: From the Tomcat(Catalina 7.035) log below: INFO: Undeploying context [/mywebapp] May 27, 2014 3:27:14 PM [login to view URL] deployWAR INFO: Deploying web application archive C:\apache\apache-tomcat-7.0.35\webapps\[login to view URL] 15:27:19,955 WARN HibernatePersistence:58 - HHH015016: Encountered a deprecated [login to view URL] [[login to view URL]]; use [[login to view URL]] instead. 15:27:19,957 WARN HibernatePersistence:58 - HHH015016: Encountered a deprecated [login to view URL] [[login to view URL]]; use [[login to view URL]] instead. 15:27:19,958 WARN HibernatePersistence:58 - HHH015016: Encountered a deprecated [login to view URL] [[login to view URL]]; use [[login to view URL]] instead. In the code this appears to happen at this line: private static EntityManagerFactory emf = [login to view URL]("myDatabaseConfig"); (Please remember I got this working completely with Derby I will include the working [login to view URL] file as well When I use the browser I go to http://localhost:8080/mywebapp/[login to view URL] and get: see added file: I used rtf files for easy access Please let me know if you can help me on this. I will pay for the job done. Peferably you have done this configuration before. I included the working derby [login to view URL] file as reference point Upon okay I can upload the project and the links to install the MySQL database , tomcat server etc should you need that.(Also the Jre7update55 [login to view URL] file had to be changed to allow access to ports needed. I can send that as well. I would like to get started as soon as possible