Different people in different situations use different ways to refine 'the thought that went behind that code'. Some like to write on paper/whiteboard, some like to draw graphs, some like to research for similar solutions on the web, some like to directly code. Time in IDE/Editor is easy to quantify, time thinking about solving the problem is not. That is strictly individual work, though. Time spent convincing the PM/stakeholder to reduce/change scope is one that is very productive but rarely quantifiable/counted.