The problem
When we kept everything on paper, organised people had filing cabinets. They stored their documents in them in a structured way so that they could find them again.
They didn't toss things into the cabinet without thought. But that is exactly what we do today with our computer's file system.
In large organisations it was someone's job to organise these cabinets. They knew what they contained and how the information should be structured. They helped you find things if you weren't sure.
The solution
This person is the Librarian and they oversee the Johnny.Decimal system.
The Librarian understands your system's structure and the type of artefacts you generate. They must be a part of the team that sets everything up. And they must own the index.
It doesn't matter if you're at home or work. Maybe you have a shared personal system with your partner -- decide which of you will take this venerable role.
If you're at work, there's usually someone in the office/on a project who would relish this task. Find them and empower them.
Benefits of having a Librarian
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They annotate the system and/or develop process documentation to guide new and existing users on what goes where, and why.
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They monitor the system, keep it neat, and proactively help people who aren't following the rules.
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They consider disputes, discuss them with the teams involved, and if required they're the final arbiter.
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They keep the index up to date. They own it, the tool in which it's hosted, and all the data it contains.
An investment that pays back many times over
As I've said, this system isn't 'free' from a time perspective. It requires an investment, which you will recoup many times over.
Consider an example from my past -- a medium-sized IT transformation project with a $10m budget. I estimate that the Librarian should be allocated funding for one day a week. More at the start, ramping down as the project matures. Larger projects scale linearly.
"Wait, isn't this already someone's job?". Maybe. But do they do it? If yes, great. You can stop reading.
If not, either get them on board so they implement this for you, or do it yourself. But stop thinking it's just going to happen.