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Based on where upgrades are positioned on the inventory page of a star-ship, exo-suit, or multi-tool, additional bonuses may be awarded.
Every technology in the game belongs to a hard-coded "family". When technologies of the same "family" are placed adjacent to one another, the technologies will gain a colored border around them to indicate that it is benefiting from the adjacency bonus.
The adjacency bonus is calculated for every side of every technology, and added to total, before the tool/ship's class bonus is calculated. It is calculated by multiplying:
The hidden "bonus power" stat of the technology in possession of the side
The hidden "bonus multiplier" stat of the technology the side is facing towards.
What this basically means is that you should place as many of the same family next to each other in a box shape, making sure your best one in the family has the most others touching it. Some may benefit from a + shape, but it's not worth the disruption to your layout.
The videos at the bottom of this page may help to explain this concept further.