Sometimes you want to test quick changes to single files deployed on WebSphere without having to upload a whole new EAR, WAR, or even individual file. (I wish the individual file upload process was simpler and safer.)

If you have command-line access to the server, you can edit or upload many of those files in place under their deploy location, typically something like:

<websphere-install-root>/profiles/AppSrv01/installedApps/<ear-name>/...

However, for web.xml, the copy that resides under this location does not actually make use of your changes. Instead, the copy under this location does:

<websphere-install-root>/profiles/AppSrv01/config/cells/<cellname>/applications/<ear-name>/deployments/<application-name>/<war-name>/WEB-INF

Update: it appears that in web application 3.0 web.xml files, there can be a web_merged.xml file which also must be edited to make changes.

Also see this StackOverflow question: Websphere application modify web.xml doesn’t work