Customize functions
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My approach breaks down the functionality into classes; and then put each class in one file.
If you have a lot of functions, I would do the same - split them into thematically separate files and include them only when needed.
If you are working with classes, you can use the PHP autoloader functionality , which will automatically load any PHP files needed to instantiate a specific class.
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I prefer to use several different files - usually one group of "functions" each.
Benefits:
- smaller files: easier to work with the IDE
- several files: one developer can work with one function, in one file, another development for another function, in another file; limits the risks of conflicts (yes, even with SVN and equivalents)
- you only need to include what you need
(And if you expand your question to classes: one class for each file, structured in directories and using autoloading to include the required files)
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