Ever seen things like this?

I have. Some "work accidents" here were caused by similar things, where people were... hum... "accidentally" thrown out of the window when I saw this kind of art.

There are a lot of practices related to ETL development. I won't go into those (there are a good amount of books on the subject). But there's an extremely useful one that I force people here to use, and you should do too:

Always set Spoon's grid size to 32
Why? It's actually very simple. 32 is the size of the icons. So instead of having a freeform placement, you'll be able to arrange the canvas in a much cleaner way, improving the legibility.

But there's even a bigger reason: You store your etl files in a version management system like git or svn, right? (Cause if you don't, you'll be prone to more... "work accidents").

With the freeform placement, even double-clicking on a step to change it's properties will slightly change it's position. Means that on the serialized file, there will be a new coordinate to that step's position. Multiply that with the number of steps, tracing differences in the etl suddenly becomes... un-tracable.

By setting the grid we're limiting a lot the unwanted geometry changes, and the differences between different version will become much narrower. Take this simple example, where I changed a field called priority from 3 to 4:

Granted - not perfect, but a huge improvement over the standard behaviour.

I created a jira issue to make this the default. Vote if you agree.