Web.xml files can be stored in two places in WebSphere storage

A WebSphere question, first of all, I'm not really familiar with the directory structure of WebSphere, and if I know the directory structure of it, I don't make this mistake:
We do application projects need to be published to WebSphere, the project manager let me for the application as a whole, the requirements are: when the system run batch time does not allow users to log on to the system; began to prepare, and write a filter to configure how my filter does not work, so I adjusted the position of the filter, found that the filter is effective and can be used by the application itself struts2, This will cause problems with my filter before it is added to the struts2 filter: If my filter takes effect, it will not pass through the struts2 filter, and when I return to the page it is reported as a struts2 filter error. After a period of time I have no way, and after a period of reflection, I decided to modify the Struts2 filter, starting also do not know where to start, so began to see Struts2 source code, It is found that the distributor dispatch can be modified: Before the Distributor is distributed to determine if the time is running batch time let it jump to the fixed page (login page), after the modification finally succeeded. My debug server is tomcat5.5 no problem, and yesterday we posted it to WebSphere and found it was working. In the evening I was delighted to be home, and suddenly a colleague called me and said that he had modified the configuration information for the related time in Web.xml the configuration information did not take effect after restarting the server.
     this morning I started looking for a problem and found that no matter how it was modified it does not work, after talking to colleagues: the idea is that WebSphere should have a cache directory and look for other places to store the Web.xml. Then use Find command to look for Web.xml file, suddenly the screen appears two prefixes and our application name the same Web.xml file, one is we know in advance directory (... /appserver/profiles/appsrv01/installedapps/loopbacknode01cell/), and the other is (config/cells/loopbacknode01cell/ application/) directory, in order to describe the convenience I put the previous directory name called Directory one, the following directory name is called directory two. After repeated testing found that only modified directory two of the following Web.xml file and restart the server after the application will not take effect, directory one of the configuration file does not work, so the problem is resolved.