Clip glitching is an exploit in the game since the 1.5 'Foundation' update. It allows players to have parts clipped into each other. Before 1.5, when you put a part over a part, one of the parts would go translucent on the VAB and disappear on launch.
How to clip glitch
If two parts are placed overlapping, one will go transparent and disappear on launch. But in version 1.5, if both parts are selected and moved or long pressed, they will clip glitch and both exist on launch, allowing players to create otherwise-impossible designs like this:
You can also put engines on top of each other and make them act as one with very high TWR, as seen here.
Since the 1.5.2 update, long pressing the parts will just show info on the parts you selected, but not two or more parts to show the info. Select the parts you want to clip, and move it. An alternate option is to just use the hold and drag option. Hold a part in the blueprint that is empty. And a blue box appears, select the parts you want to clip, and move it.
Clipping engines were back; however when activating the clipped engines they explode because of heat damage.
The Part Clipping cheat was added. If on, you can just drag and drop parts on top of each other. Old clipping still works, though
The Part Clipping cheat was updated. If you place 2 parts in Symmetry mode with the cheat on overlapping each other, both would now be placed. There is also a bug when where if you place a part with symmetry mode in the center with the cheat on, two parts will be overlapping each other.