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By "server crash", I meant the machine (server or workstation) where the code is running, stops because of hardware failure, or power failure, or you knock the off-switch, or even because an administrator accidently kills your process while cleaning up zombies at 4 am. Ie. Events that you cannot detect from within your script.
The basic mechanism to avoid this is to make a backup of the original before overwirting it with the modified version. The are several different sequences of copying, renaming, deleting and overwriting that you can use. Some of these are "better" than others, but I've yet to see one that completly eliminates the risks, though they reduce the window for failure to the point of reasonable risk.
For a couple of neat way to use $^I (see Perlvar and perlrun -i) to get perl to backup your files for you, see My pattern for "in-place edit" for many files and Put your inplace-edit backup files into a subdir, both from Merlyn.
Perhaps the best way to be safe, is to make a copy of the directory structure, run your script against that, and then copy the directory structure over the original when your sure it has been successful. Perhaps you are already doing (or intending to do) this, in which case you can ignore this advise.
The other thing I noticed in your script is that every file will be over written regardless of whether any actual changes were made or not. This is likely to give you problems when you come to verify that the changes made where correct, or worse, make it hard to undo any mistakes as you won't know whether 1 file or every file was changed.
There are many, many ways of writing your script, and many different philosophies on the best way to do it. Perhaps the best advice I can give you, is to sit down with your code, mentally or physically on paper, work through each step of the process and imagine what state your files will be left in if a powercut occurs at each step. Decide how much of a risk that presents in your system, and how much effort you should expend to prevent it from happening.
Examine what is said, not who speaks."Efficiency is intelligent laziness." -David Dunham
"When I'm working on a problem, I never think about beauty. I think only how to solve the problem. But when I have finished, if the solution is not beautiful, I know it is wrong." -Richard Buckminster Fuller