Magento has an configuration option in the admin at
System -> Configuration -> Developer -> JavaScript Settings
named Merged Javascript Files.
When this setting is on, Magento will take all the javascript files it knows about, "compile" them to a minified version to product smaller files sizes, and then combine all the javascript files into a single javascript file. This way, instead of opening multiple network connections to download multiple files, Magento will open a single network connection to open one file.
So, when the documentation says that folder contains the pre-compiled versions, it means that's where the individual javascript files are stored, and where the files are loaded from when Merged Javascript Files
The term compilation comes from Computer Science. A compiler takes source code, and transforms it from one language into another language.
Traditionally, it's meant taking code from a higher level language (C, .NET, Java, etc.), and transforming it into the machine code (assembly code) that's understood by the computer chip. However, the term is generic and more modern usage includes taking the source code written in one language (Javascript) and transforms it into a different form (minified javascript).