There are many different tools and methods for rooting different devices. What exactly do these tools do and how do they work? Which files do they modify? Any information/link regarding this topic or source code for rooting tools would be a great help.
This is a very hard question, but anyway I will try to explain how it works ...
So first you need a database in which list of device and each instance is written: Link to download the files and BuildNumber.
You create an application as another PC or Android. If You create an application for the PC so it got easier because a PC is easier to fool android ...
But now the focus workings apps for android:
1) The application detects the device (eg. Using android.build.VERSION.release) and locates it in the database. Then applies the download link to download the file to the root.
2) Phase two is the hardest. I'm not sure how at this stage really goes, but I think that drugging android application, in order to get to the root file folders in which to be. As this takes place, however, so I do not know what is the secret developers of Root applications.
3) The application will overwrite existing files and if the quality is so even checks.
It is all but Step 2 is really difficult, and that how it works is you can ask just about developers from root applications.
Sorry for my engish.