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While I have little hesitation in creating a patch directory structure within an the related extension or settings extension for the instance of that site installation there is a bit of work in keeping track of these modifications or patches for future upgrades.
This makes patching fairly simple to repeat. Sometimes I use a patch file, sometimes I only use instances of the modified file and original file.
Path: [ Patch Base Path] + [ Version of eZ] + [ Relative Stock Path]
Example of extension's which include kernel patches and or patch directory structure. (...)
Still, I can't remember if my tests in modifying the include_path were successful, I don't remember using it regularly after my first encounter with it.
The idea being you can add a file path to the php include path configuration variable which should allow you to be able to in affect override a specific stock file without having to actualy replace the stock file.
Example of the php.ini setting requirered to override a stock eZ publish file (kernel or lib) (...)
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