Even though there aren’t any active projects for my Masters Thesis, how can I keep reflecting on it in case there are things I need to add? Make a list in a separate app?
That's what I would do, yes. Having your projects at different levels and mixed in with empty levels is likely to make it hard to see what you're actively working on right now. If you want to take action be sure that you reflect on your Areas of Focus you could have a specific project for that, or you could make it a step in your weekly review.
For me, areas of focus don't affect my Omnifocus folder/project hierarchy at all. My general organizational philosophy for my project lists is:
- Default to having all projects in one list.
- When that list gets too long (more than perhaps fifteen items) find logical groupings to use to pull out items until it's no longer too long.
Right now, my top level of folders in OmniFocus is:
Other
Shopping
Lists
Farm Projects
Home Projects
That's all. And right now I have no subfolders at all--sometimes I do.
(I should note that OmniFocus is my personal system; my work system is separate, but the philosophy is similar.)
"Other" is where projects go by default--it's the "one list".
When "Other" gets to be more than about fifteen projects, I pull some out.
For example, long ago, I pulled out the Farm Projects. (I have thirteen of those right now.)
If Farm Projects gets a little bit bigger, I'm likely to create a subfolder. Maybe "Farm Projects--The Simplification Effort" or "Farm Projects--New Perennial Beds" or "Farm Projects--Winter 21/22 Structure Changes." It will depend on what the mix of projects is at the moment that I make the folder. Edited to add: Actually, no, I won't make it as a subfolder. That is, I will, and then, as always happens, the subfolderness will annoy me, and I'll make it a peer folder instead.
Similarly, at some point I pulled out the Home Projects. (Eleven.)
Not long ago, I had a folder for Decluttering Projects, containing projects that I had pulled out of Home Projects. but I compressed my decluttering efforts into a smaller number of projects and re-merged Decluttering Projects and Home Projects.
"Lists" and "Shopping" are different. They're both Someday/Maybe--where random thoughts go by default, and where once-active projects get sent when they become Someday/Maybe projects. Logically much of Shopping isn't really Someday/Maybe--
the desire to buy a dozen eggs is an active action. But instead of "buy eggs" showing up in my list of actions, I'll instead have an action telling me to organize a grocery delivery, and as part of that organizing I'll go to the List - Shopping - Food list.
This is a little bit fuzzy--several of my Farm Projects have actions telling me to buy irrigation tubing, or to buy seeds, and those
are active actions. Whether shopping is active or inactive tends to be an "I know it when I see it" thing.
I'm babbling on. My main point was: IMO, your lists are mainly for regular, daily or several-times daily, scanning, to decide what to do. For that function, organizing those tasks into an areas of focus structure is likely to be more expensive, in terms of repeated cognitive effort, than it's worth.