Entropy allows you to automatically remove files from an archive based on their names. The most common use for this is to remove the pesky .DS_Store files that are automatically generated by Mac OS X and accidentally get included in archives. These files are non-essential and often confusing for people who encounter them on other platforms.
By default, only .DS_Store files are removed. However, can define your own set of files to ignore. This is very easy to accomplish in Entropy — open Entropy's Preferences and click on the "Filters" section. There, you can define your own rules for removing files.
Archives are automatically filtered when they are saved. You can also filter them manually by selecting the "Clean" option from the File menu.