Boxer
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Support compressed .boxer bundles or inner .harddisk containers.
ZIP files are essentially a small single-file read/write filesystem, with NeXT (thus Cocoa, thus macOS) supporting use of ZIP archives as the container for "file bundles", not just unpacked directories. (Ex: iWork '07 files.) It would massively reduce the overhead of maintenance (offsite backup) and poor Spotlight metadata indexing to permit zipped bundle use. This would result in a single file per application or game, not potentially thousands.
Though, yes, this would be with the trade-off of modifying a small file within that DOS environment (e.g. creating a save game) invalidating the entire .boxer
bundle, but that happens far more rarely than adding a new package to the archive. Even if the .boxer overall bundle can't be sourced from ZIP, could the .harddisk / .cdrom / .floppy inner bundles be?
My library is extensive—just under a terabyte of DOS software, alone, still to be processed. A small subset of 182 games from childhood totalling 16GB are actually comprised of 25,692 individual files, or an average of 141 files per game.