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I'm looking for some guidance on the ideal modman folder structure.

I'm a developer that owns a store so all my development is for a single store. I have my own custom theme and frequently customise extentions - both via theme overrides and code changes. I use svn.

My .modman dir has a theme dir and a dir for each extension. In the old pre-modman days i would copy the extensions theme file to my theme (just as i would a core magento one that needed to be overridden) and then edit that, but now i have modman and svn i'm wondering if i should now just directly edit the extensions theme files - after all i have history and merging updates via vendor branches would be easier. For core theme files i would just continue to copy the file into my theme and edit it there. Any thoughts, previous experiences or guidance?

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If there is any chance you will find use for the module outside of the single store environment and if the modification isn't specific to the scope of the extension itself, I would personally continue treating the extensions like 3rd party / core module and copy any files you wish to modify to your theme.

If the modules are custom written for the store and will never be used elsewhere I'd say just stick with whatever you're most comfortable with. There's much less benefit to be gained from modman in this sort of situation. Arguably the main advantage would be the ability to cleanly remove a module when you're done with it. In which case modifying the templates in the extension dir might make the most sense as you can then remove all trace of it with a single command.

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