About the include path in Zendstuido the differences between the files that are entered and those that are in project engineering

The difference between the files included in the include path in Zendstuido and the files in the project engineering
The problem is that when you use Zendstudio to create a new ZF2 project, we can select which libraries to include in the process, including the default included Zend Framework and some JS libraries, after selecting the JS and ZF Library new item, you can find in the project file, We can find the source file of the Zend Framework, but there is no JS library file. What is the difference between the JS library and the ZF library? Why contains the JS library files can not be found, if I want to use the JS library methods and objects, in the case does not include JS file, directly call it?
------to solve the idea----------------------
Any time the JS file is for the browser, with what tools you use, in what directory development irrelevant
As long as you can ensure that the browser can read the JS file (including CSS, pictures, streaming).

So you need to figure out the difference between a Web path and a file system path.

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