From the patch notes
8/21/2013 Game Update 2.3.1 Patch Notes wrote:
Crafting Skills
General
Players are now presented with a warning when Reverse Engineering gear that contains mods.
While this seems like a good idea on the surface, I'm trying to level an Armstech, and yes even though it does not matter, I want to RE to purple everything. The issue here is that a lot of the weapons include a color crystal which triggers the prompt. Even if I were not trying to RE everything and only just those things that mattered for leveling the skill or producing slots, it still creates a LOT of unnecessary prompting.
I would suggest either removing this prompt or offer a shift+rt-click type option which allows you to RE without prompting.