Meta: this is probably not a question for which there is a single, objective, best answer, but I'm going to ask it here anyway because it's applicable to our jobs and non-obvious.
I spent three months last year performance-testing a system. I thought of the process as a series of experiments of the form, "Configure the system like this, using that version of the code, and run the test using these variables." I kept notes on each experiment, e.g. the date & time, software version, inputs, resulting graphs. My notes were in a Google Doc that I shared with my co-workers. After the project was over, one of my co-workers complained that it was often hard to determine which experiments I had performed. In retrospect, I could have spent more time editing my notes to make them clearer. That I didn't wasn't just a matter of laziness.
Here's what I mean. In a scientific investigation, where you formulate a hypotheses and decide on how to evaluate your data before you run your experiments, it is easy to imagine recording all your experiments in a tabular form, e.g. a row for each experiment, a column for each variable, and a column for each measurement.
Performance testing, and other kinds of software testing, is more of a discovery process than a scientific investigation. You make mistakes, encounter dead ends, and discover variables that you did not anticipate in the beginning. In a sense, the discovery process looks more like a directed graph than a table. The linear flow of a table hides the hierarchical nature of the process.
So here's the question. What is an effective way to document the chronology of a discovery process? Are there tools you have used to simplify producing the documentation?