being a hobby programmer for a couple of years, I want to step it up and try my hands in something rather sophisticated at work.

Whilst in the past, I was working here and there on some projects which were in the 10k+ LOC range, I would like to tackle this project as professional as possible.

Is there any program/service with which is being used in the designing phase of a tool/software? E.g. something where you type down the objectives, functionality, flowcharts perhaps, track time etc.? Or is all of this being done in other mediums (onenote, kanban etc.)?