Is there the opposite of chunking? If chunking is the ability to split large files into multiple files and interpret them as one file, can you merge whole directories into one file and have rclone interpret them individually? This is mostly for those providers that have a file/object limit
Check out this issue: Streaming archive/unarchive capabilities · Issue #2815 · rclone/rclone · GitHub
This has a beta in it which lets you transparently use a .zip file. Is that what you are thinking of?
This might be pretty similar to solve the problem. It seems like it's own backend instead of embedded alongside other files, but it might work!
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