Difficult to answer without context. (Although I lean towards "by hand")
Consider and older app with thousands of files and millions of lines. Unless you're intimately familiar with it, I'd recommend letting an IDE do the heavy lifting of refactoring.
Ultimately, the right way is the one that works best for the developer and project in question. I'd rather the dev use the tools they are familiar with and are productive with rather than forcing them to do it my perceived "right" way.
And by "by hand", I'm assuming still includes using tools such as grep, find, sed, etc.
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Difficult to answer without context. (Although I lean towards "by hand")
Consider and older app with thousands of files and millions of lines. Unless you're intimately familiar with it, I'd recommend letting an IDE do the heavy lifting of refactoring.
Ultimately, the right way is the one that works best for the developer and project in question. I'd rather the dev use the tools they are familiar with and are productive with rather than forcing them to do it my perceived "right" way.
And by "by hand", I'm assuming still includes using tools such as grep, find, sed, etc.