Sometimes files need to be edited before being packaged up. The regular expression feature is the only method to do this now and sometimes it is far to limited to do the sorts of things some plugins need to do. For example, the JBOSS plugin removes passwords from configuration files that are stored as XML documents. Using a real XML parser would be a better tool than passing the document text through some regular expressions.
If there was a way to get direct access to the file and change it only in the archived version that would allow the use of other file editing tools.