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I think this is best described using an image.
enter image description here

So it dawned on me that perhaps this isn't the best or most logical way to organise files.
The way it is currently, as you can see is just a dumping ground. The only reason complexify has it's own folder is that it's a submodule in Git.

So should I be using a /lib folder with jquery & jqueryui and perhaps a /plugins with all the plugins in? Where would my files live?

Are there any accepted practises for file structure in this situation where you have a core library, a number of plugins and then some of your own code?

PS, I realised just now I have two copies of jQueryUI.

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closed as not constructive by Walter, Dynamic, Mark Trapp, Jim G., ChrisF Oct 6 '12 at 21:50

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up vote 3 down vote accepted

yes, put 3rd party not-your-code files in directories so you can keep them separate from your files. A common naming convention is 'lib' or 'libs' with each 3rd party library in its own sub-directory (so you can directly update the files from their own source repo with a little more control).

You can put your files anywhere you like then, usually in the root.

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Great, so I'm thinking along the right lines :) – user15256 Aug 7 '12 at 14:38
+1 Exactly. Organize JS just like the rest of your code. – Matt S Aug 7 '12 at 14:49