Once again, a question has come up on the Bacula users' list about restoring just the registry of a Windows box that has corrupted its SOFTWARE registry hive to the point that it won't boot.
I put it to you that of all the "innovative" ideas that Microsoft has built into Windows over the years, the Windows Registry is the worst. It is opaque, it is fragile, it is difficult to back up, clean out or repair, you can pretty much only repair it from Windows itself which means that it's almost impossible to repair it when — not if — Windows corrupts it, and all kinds of noxious things can be buried inside it by malware. Not only does Windows periodically outright corrupt the registry, but from the first time you boot a new Windows installation the registry starts accumulating cruft and droppings that gradually bog the machine down and introduce cryptic malfunctions with no readily determinable cause. Things that worked yesterday just stop working for no apparent reason.
Combine with opaque hexadecimal-string registry key names created by various things, so that you can't even tell what some random leftover registry key belongs to or whether it's still in use, and it's a recipe for disaster. That disaster has been ongoing for fifteen years now, and there's no end in sight.
The saddest part about the whole thing is that Microsoft actually believed that this massive, opaque, monolithic, unmaintainable monstrosity would be an improvement.
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Oh, and when you dump it, it still contains opaque hash keys.
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I would really prefer something that properly wrappers an install and will then gut all the crap the installed program spews on.
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Utilities exist to back it up, restore it, and repair it. Heck, if I recall, there are command line utilities built into Windows to do a lot of that. The trick is that it's not common knowledge what they are or how to use them.
I haven't honestly had too many registry fragility issues, but ones introduced by applications can be rolled back as long as you install using any number of freeware configuration-change monitors.
One thing I will agree with is that Microsoft's use of UUIDs and similar for system keys gets overly arcane. OTOH, not sure I like Apple's plists all that much either, and Unix's use of rc/conf files is awesome, but often a little opaque and confusing too.
The one thing I'll give Unix is that changing a whole-system config usually has to be a proactive thing, so the SA knows what changes are there. Unless you're using SuSE's YaST, then it's a crapshoot. :)
Basically, every config system I've used is annoying in some way. But what I think you're really bumping up against isn't a bad config system as much as it is that Windows users generally aren't trained or inclined (or forced) to manage their system in the way that Unix admins do.
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Third-party registry cleaner tools exist, too. I've tried several. Some are fairly reliable. But all of them warn up front that beyond a certain point, they're guessing when it comes to repairing bitrot or removing keys that they don't think anything owns any more, and that if it hoses your registry, you're on your own.
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http://www.larshederer.homepage.t-online.de/erunt/
Registry backup, restore, and optimization tools for Windows NT/2000/2003/XP. (Also works on Vista and 7, with some minor workarounds.)