- When you install a package, you basically overwrite(default behavior) all path(filter) includes in the package definition. If you want to change package merge technique, you can do it indicating in advance properties that you wanna merge the content from the package and existing in the case of conflict.
- the filter.xml can not be deleted from the zip, all those files are necessary to install correctly
With maven, you normally build and deploy the apps(all packages generated during the build process) and each package has been generating thru each Maven plugins which also contains their own configuration(filter, and other more advanced configurations).
You also have to carefully manage what kinds of thing include in your maven plugins, for example, site and dam definition which it normally used for the first deployment(first stage of the project) but after that, you NEVER have to use your normal app build otherwise you blow up all existing content(you should separate thru definition maven profile to separate each part of your application such as service, design, dam, site, etc.