The AUFS file system, part of what gives us C-Groups, now called containers, now called Dockers, etc, but it is the onion-style file system that gives Dockers (we’re gonna just settle on calling them dockers) their magical powers.
This can lead to some very unexpected results, for example deleting a file in container “X” will appear to delete it. However let’s presume the previous base box “A” had the file and you want to make an new image and container from “A”. You might presume that file “abc” was deleted from all of the layers. But with AUFS that isn’t how works. You either keep layering up (meaning build your new site as a container from an image of the latest container you were working on.
This layering is a critically important concept to fully understand if you are working with dockers and the aufs file system. Rather than take my amateur explanation of it, I’ll refer you to the full docs on and let you go from there. Just *please* don’t overlook file system layers in AUFs when trouble shooting issues with containers.