sorry I didn't reply so long, but my previous tomcat was messed with tests and many attempts, now I did everything from start with clean tomcat installation and confirm context xml disappears.
steps to reproduce
1) make dir C:\tomcat_test
2) download apache-tomcat-7.0.39.zip and unpack it in C:\tomcat_test
3) in C:\tomcat_test unpack attached jdbc.7z
4) start tomcat with startup.bat
4) in c:\tomcat_test\jdbc> call ant deploy-war
org.apache.jasper.JasperException: An exception occurred processing JSP page /select.jsp at line 22 .....
javax.servlet.ServletException: javax.naming.NameNotFoundException: Name [jdbc/Test] is not bound in this Context. Unable to find [jdbc].
6) into C:\tomcat_test\apache-tomcat-7.0.39\conf\Catalina\localhost insert attached jdbc.xml
7) close tomcat console
8) start tomcat with startup.bat
9) again open result is OK, config works fine, error is caused by lack of h2 jar (org.apache.jasper.JasperException: javax.servlet.ServletException: org.apache.tomcat.dbcp.dbcp.SQLNestedException: Cannot load JDBC driver class 'org.h2.Driver')
10) now in notepad++ open C:\tomcat_test\jdbc\src\main\webapp\select.jsp, change title to <title>Simple jsp page 2</t>
11) as in 4) in c:\tomcat_test\jdbc> call ant deploy-war
jdbc.xml disappeared from C:\tomcat_test\apache-tomcat-7.0.39\conf\Catalina\localhost , go to 5) result is the same as in 5)
I run it on windows 7 64 bit