How to organize a Rails App
For the first time I'm creating a quite complex Rails app.
I'd like to know what's the best way to organize that app by folders. Until now, I'd do everything under one app (all the models, controllers, etC) but reading some open source code I realize that they put everything under different apps.
Like for example Spree Commerce. They have a general folder and inside that they have different apps (API, core, admin, etc). How is that done and is that the best way to do it?
I'd like to get pointed to the best way to do it (a book, blog, anything) so I can understand how I can architect my app for future maintenance.
As an aside I think the title of your question is a little confusing. Rails, by using convention over configuration, defines 'how to organise a Rails app'. I think your question is rather about how to architect your application as opposed to anything Rails-specific. Maybe tweak the title?
That aside, without knowing any more detail about your project it's a tricky question to answer, but I'll give it a go.
All applications should start off simple, if you believe (like I do) that you should start by building the simplest thing that could possibly work. Given this, since you're using Rails, then in all likelihood the simplest thing would be to structure your app as a vanilla Rails 3 application. This will probably (I say 'probably' because I don't know any specifics about the app) allow you to get a beta version of your app up and running pretty quickly without worrying about complexities which at this stage in the development of your project are not a problem.
If you need to create an XML or JSON-based API then Rails makes this really easy using the standard framework, which will allow you to spend more time thinking about the API design than how to code it, and it's the API design which is the most important thing to get right in the first instance.
Similarly, your Admin site can be part of the same app just in a different namespace. If you find later down the line that you want it as a separate app, you can do this (maybe you could use the awesome API you designed to facilitate this), but why bother designing it with this added complexity (and hence extended development time) in the first place if you don't have a good reason for doing so?
Once you have your app up and running and people are starting to use it, you start to get a picture of where the bottlenecks are and where the design could be improved. At this stage, if there's a need, you can start to move parts of the app to scalable solutions, such as running your API as a standalone service, introducing caching, changing data stores and other improvements and optimisations.
Even if your app is as wildly successful (and I hope it is!) then re-architecting your application whist continuing to run the existing service is still entirely possible, as Twitter have proved. Just stick to Knuth's statement and you'll be alright.
Regarding reading material, that's a tricky one. For me a lot of the XP and agile development classics taught me a huge amount about how to approach program and app design. I'd also check this StackOverflow topic for book inspiration.