Arduino IDE automatic tools
The IDE runs a "preprocessing" routine. As well as adding prototypes it also:


Adds #include &lt;Arduino.h&gt; to the start of your sketch
Removes comments (or the older versions did, I am not sure about arduino-builder)
Identifies the libraries #included in the sketch


The latter is used to build the list of -I ... directories to add to the command line. Removing of comments was chiefly to make finding functions easier for making function prototypes (though there are better ways of doing both those and arduino-builder might use them).

Can you disable it? No. Not for .ino files. However, any .cpp files added to your project are treated as vanilla C++ source code and aren't preprocessed in this way.