Editing the contents of this directory is not reccommended. Plugins may install additional files here, but you should not modify anything. If you wish to override files in the /lib/ dir you can do so in the appropriate cfg dir of your repository. For example, if a file exists in both eprints3/lib/static/style and eprints3/archives/ARCHIVEID/cfg/static/style then only the one under archives/ will be used.
An exception is phrases. Phrases are over-ridden by phrase-id not by filename. To override a phrase, just place a phrase with the same phraseid in any file in your archive cfg/lang/.../phrases/ directory.