Things like ADS provide a way to store data about a file which doesn't have an integrated mechanism to store metadata (e.g., EXIF). Keeping it in a separate name and using an alternative API call makes sense from a compatibility and a simplicity point-of-view.
No it doesn't. It increases the complexity of every program that deals with the file, makes both the files and the accessing programs less portable, hides things from the user they may need to know (mystery program behavior anyone?) and generally just puts a spanner in the works.
Things like ADS provide a way to store data about a file which doesn't have an integrated mechanism to store metadata (e.g., EXIF). Keeping it in a separate name and using an alternative API call makes sense from a compatibility and a simplicity point-of-view.
No it doesn't. Storing the "metadata" under a separate name/label (ie. in a file with a related file name) may make sense but using a separate OS call doesn't because the OS is providing no additional service. OS calls are expensive and non-portable and should be kept to a minimum. If you insist on trying to hide such attributes from calling programs then it should be a compatibility layer on top of the OS, not in the OS itself.
Users largely don't care if metadata is lost because a file is copied to an incompatible filesystem on a flash drive, synced to Dropbox, emailed to a friend, or maybe even printed out.
Actually they do. So-called metadata is often just as important as the data itself for everything from backups (users are going to be real happy if they discover their data missing because the incremental backup lost it due to bad file dates) to file names (users are real happy when they try to type in or copy some file name/label in their native language and the OS comes back with some cryptic error message) to sorting (users are real happy if they have to deal with a thousand out of order items due faulty character set handling). As just one example amongst many VFAT's poor preservation of metadata like file hierarchies, character sets and links has caused problems for millions.
but losing the 200 page thesis is unacceptable.
Losing all user data is unacceptable, whether it's called metadata or not. You're right that some data is more important than others but metadata is there for a reason and deleting it causes all sorts of user-visible furfies. And that is bad. Computer interfaces are unusable enough as it is without introducing even more problems.
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Are you one of those programmers who expect their users to be mind readers? Think about how your code is going to be used step-by-step!