For example in many regulated domains such as human subjects research files must be approved and only approved files may be used. "Is this version of the consent document the version that the IRB approved?" Well let's see... (1) file modification date is after the approval date and (2) checksums do not match.
Not to mention that writing a single byte of content to a filesystems marks the entire blob as needing backup.
The fact is the filesystem is the user's database, save is commit, and it should be under the users control because application developers do not have the faintest idea about user context.