Just because you think that you have to do it doesn’t remove the fact that it is very not smart to do it. The plugin code is built to be used as a plugin and not as a theme, and while you can copy parts of the code and use them in the theme there can not be any simple way to make sure there is no dependency left somewhere in the code.
The easiest way to do this kind of things is to check that a plugin is active and force its activation if it isn’t (and you can’t trust your client not to deactivate it).
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