For the most part, you can choose any names you like for the folders in your project but Unity reserves some names to indicate that the contents have a special purpose. Some of these folders have an effect on the order of script compilation. Essentially, there are four separate phases of script compilation and the phase where a script will be compiled is determined by its parent folder.
This is significant in cases where a script must refer to classes defined in other scripts. The basic rule is that anything that will be compiled in a phase after the current one cannot be referenced. Anything that is compiled in the current phase or an earlier phase is fully available.
Another situation occurs when a script written in one language must refer to a class defined in another language (say, a UnityScript file that declares variables of a class defined in a C# script). The rule here is that the class being referenced must have been compiled in a earlier phase.
The phases of compilation are as follows:
Phase 1: Runtime scripts in folders called Standard Assets, Pro Standard Assets and Plugins.
Phase 2: Editor scripts in folders called Editor that are anywhere inside top-level folders called Standard Assets, Pro Standard Assets and Plugins.
Phase 3: All other scripts that are not inside a folder called Editor.
Phase 4: All remaining scripts (ie, the ones that are inside a folder called Editor).
A common example is where a UnityScript file needs to reference a class defined in a C# file. You can achieve this by placing the C# file inside a Plugins folder and the UnityScript file in a non-special folder. If you don’t do this, you will get an error saying the C# class cannot be found.
Note. Standard Assets work only in the Assets root folder.