Right now, files are simple objects stored in an array. This is nice and simple, but also a bit of a mess. It allows duplicate filenames forces us to use regex to find files in a given directory, and so on. Instead, we should use Path::Resolver (or something) to build a simple virtual filesystem.
Then we could have filename changes detect conflicts immediately, we could have $file->replace_with( $other_file ), and other nice improvements.