Just to be clear the “one-project-per-note structure” you mention, I assume you mean the fact that you can only assign a note to a single project right?
I can understand the scenario you describe, I’ve definitely been there at times. Still, I don’t think the solution is to necessarily introduce additional hierarchies, two things can help I think.
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think about alternative ways to choose what you call a project. For example, perhaps the level of granularity is already too fine in picking the project, e.g. instead of a project for Joe, Jane, Will etc, you could create one for the team and use to tags or the title to indicate targets within the projects. Or alternatively try dividing along a different access, for example instead of marketing, sales, etc, try projects for product A, product B. etc.
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use a different workflow during the meeting, then cleanup/divide/organize afterwards. For example, I’ve created a Scratchpad project that I use to collect a variety of ideas during a meeting or busy moment, simply separating topics by using different headers. I can take notes during the meeting for all people this way without having to switch. Then at a quieter I take a few minutes to clean up and group my notes and copy them to the various projects where they ultimately belong.
A Scratchpad Project that allows you to collect and “stage” your notes during a meeting in a single place, that you then later clean up by distributing the notes over the relevant projects.
I understand that you can nevertheless always end up with some notes that kind of belong a bit to project A and a bit to project B. There I often use the ability to create internal Agenda links. I pick the project where it’s most relevant to place the note, then create an Agenda link (Edit > Copy As > Agenda Link) and paste it as a reference in a note in the other project.
As said, I don’t think we’ll introduce more hierarchies (with the except perhaps of allowing you to create subprojects, which also could partially solve this issue), as we don’t want to make the app any more complex than it currently is. But we do have some ideas to make the type of workflows we describe in the second point easier. Stay tuned!