
I would suggest this could be a major issue, it just depends if your business consists purely of chucking out new stuff all the time or if you have to occasionally go back to the archive to either support or update something you did a few years before. Or if you just value the knowledge that has been accumulated over the years.
And it really isn't difficult to manage 'security' by validating the file contents as you go. It just takes some extra thought in the implementation; unfortunately it frequently appears that most people don't go through any 'what if' cycle in their code design but they just bang out the first thing that works with a properly formatted file and leave it at that.
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Lets say, for example, that 10 years ago I generated some documentation for a product/project. I followed all the rules and stored it away in the retrieval system along with all the drawings, code etc. etc. Any paper copies that existed may have been archived, but have probably just had the signature sheet scanned and stored (in the retrieval system) and have been shredded to save on storage.
Then the customer returns, wanting an update to their system and/or a replacement for the hardware someone flew into the ground.
I go back to the system, and pull all the files. I can still read and use the dxf, vhdl, C and other files are still fine. But for some reason I can't get at any of the documentation, even though it was saved in Word, and I'm trying to import it back into the latest flavour of Word... (replace Word with old/new software of your choice, this is just an example)
Obviously you could argue that it's worth storing documents in plain text, or in multiple formats, but then you end up with all kinds of formatting and layout problems, missing content (e.g. diagrams) and other glitches. Plus they aren't the document that was signed off. Or you could scan the document and store it all as TIFs, only downsides being you can't edit the document any more and the storage requirements are usually bigger.
(Obviously anything *really* special will be supported by the original machines for the service life of the program: it's not a problem using special files when you still have the original gear they were created on 20 years before!)
I've had to do this sort of thing a few times and while updating the documents to the latest template can be a pain, at least I can read them, usually without having to dig out some obsolete hardware and a few old install disks from around the place.
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The other issue to consider is that depending on how update cycles are managed you might find you've gone from horribly obsolete to the latest flavour in a couple of weeks. Imagine how f*cked you'd be if documents you created a couple of months previously on your old system were suddenly unreadable.
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So in the real world formats becoming obsolete, especially in a relatively short time can be a problem. Obviously it can be managed but that is something that potentially takes a lot of thought.