I thought with cow file systems programs didn't have to explicitly reflink since normal copies are already reflinks?
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This isn't a basic copy of a whole file. This is creating a new file from a portion of an existing file.
A normal copy consists of a program reading from one file and writing to another. There is no way for the filesystem to do a reflink in that case, it just sees that the program is reading and writing stuff. In order to do a reflink, the program must tell the filesystem what data should be "copied" to where using FICLONE or FICLONERANGE. Though some programs will do that by default if possible nowadays when copying files or when moving files between different subvolumes on the same partition, including the Coreutils cp, mv and install commands and some GUI file managers.
Are there downsides to using reflinks, like alignment and read performance issues?
Compatibility shouldn't be an issue, ie it should be relatively simple and safe to have a fallback that copy when reflink isn't available.