Your notes aren't messy. Your thinking is.
You have a note called "Thoughts on Leadership." It's 1,200 words. It covers delegation, emotional intelligence, hiring philosophy, and something about servant leadership you half-remember from a podcast. You wrote it six months ago. You've opened it twice since then — once to add a sentence, once to skim it and close it because you couldn't figure out where to add the new thing you were thinking.
That note isn't a knowledge asset. It's a graveyard.
Not because the ideas inside it are bad, but because the structure is wrong. Multiple ideas are fused into a single blob, and the relationships between them are implicit rather than explicit. You can't build on it, challenge it, or connect it to anything else — because you'd have to hold the entire 1,200-word mass in working memory just to find the part you need.
The fix isn't deleting the note. It's refactoring it — changing its internal structure without losing the ideas it contains, so that both the notes and your understanding become something you can actually work with.
What software engineers already know
Martin Fowler defined refactoring in his foundational 1999 book (updated in 2018) as "a change made to the internal structure of software to make it easier to understand and cheaper to modify without changing its observable behavior." The key insight: you don't add new features during a refactoring pass. You restructure what exists so that future changes become possible.
Software teams learned this the hard way. Code that works but has poor internal structure accumulates what Ward Cunningham called technical debt — a compounding cost that makes every subsequent change harder, slower, and more error-prone. Research from the Software Improvement Group found that organizations with high technical debt spend 10-20% more on engineering to deliver identical outcomes. The debt doesn't announce itself. It just makes everything gradually harder until the system becomes a black box nobody wants to touch.
Your notes accumulate the same kind of debt. Every compound note that tries to say three things. Every vague connection you didn't make explicit. Every insight you buried inside a paragraph instead of promoting to its own atomic unit. This is cognitive debt — and like technical debt, it compounds silently. The more tangled your notes become, the less useful they are, and the less likely you are to return to them. Eventually, your knowledge system becomes a write-only archive: things go in, nothing comes out.
Refactoring is debt repayment. You take what exists, restructure it for clarity, and make the system useful again.
Restructuring is not reorganizing
There's a critical distinction most people miss. Reorganizing is moving things around: renaming files, changing folder structures, adding tags. Reorganizing changes the container. Refactoring changes the content.
When you split a compound note into three atomic notes, you aren't just moving text. You're forced to make decisions: Which idea is the actual core claim? What was supporting evidence and what was a separate argument? How do these pieces relate — is one the cause of another, or are they parallel observations?
Nancy Sommers' landmark 1980 study of revision strategies revealed exactly this difference. She compared how student writers and experienced professional writers approached revision. Students treated revision as rewording — a "thesaurus philosophy," she called it, where they swapped synonyms and trimmed sentences without changing meaning. Experienced writers, by contrast, revised the structure of their arguments. They moved sections, split ideas apart, combined weak points into stronger ones. For experienced writers, revision was recursive and generative — a way of discovering what they actually meant. As one of Sommers' professional writers put it: "More than a half, maybe as much as two-thirds of my life as a writer is rewriting."
Hemingway demonstrated the same principle in practice. He rewrote the ending of A Farewell to Arms thirty-nine times. When asked what the problem was, he said: "Getting the words right." But "getting the words right" wasn't cosmetic. Each revision was a structural experiment — a different way of organizing the emotional and narrative weight of the ending. The final version worked not because it used better vocabulary, but because its structure carried the meaning more precisely.
This is exactly what happens when you refactor a note. The act of restructuring forces you to re-examine the ideas, clarify the relationships, and surface the gaps. The output isn't just a cleaner note — it's a clearer understanding.
The cognitive science of restructuring
Piaget identified two fundamental processes of cognitive development: assimilation and accommodation. Assimilation is fitting new information into your existing mental frameworks — you encounter a new fact and file it under an existing category. Accommodation is restructuring the frameworks themselves — when the new information doesn't fit, you reorganize how you think, not just what you think.
Most note-taking is assimilation. You read something, you add it to an existing note, you move on. The framework stays the same. Refactoring is accommodation. You take what you already have and restructure the framework itself.
Vosniadou and Brewer's 1992 research on conceptual change showed that genuine learning — the kind that corrects misconceptions rather than papering over them — requires exactly this kind of restructuring. They studied how children's mental models of the Earth changed over time. The shift from a flat-earth model to a spherical model wasn't additive (just adding the fact "the Earth is round"). It required the child to reorganize their entire spatial framework — gravity, horizons, the concept of "down." Twelve of twenty children achieved this restructuring by fifth grade, but only through a process that dismantled and rebuilt their existing model, not one that merely added to it.
The same principle applies to your notes and ideas. When you split a compound note apart and rewrite the connections, you're performing accommodation. You're not adding new information — you're restructuring how your existing information relates. And that restructuring changes your understanding, just as it did for Vosniadou and Brewer's subjects.
Sonke Ahrens captures this in How to Take Smart Notes, his operationalization of Luhmann's Zettelkasten method. Ahrens describes a workflow where fleeting notes progress through stages — literature notes, then permanent notes — with each stage requiring the writer to restructure the idea into a more precise, self-contained form. Luhmann himself wrote each Zettel "carefully, as if for publication." The rigor wasn't in the capturing. It was in the restructuring. And the result was seventy books and over four hundred academic papers built from a system of 90,000+ atomic notes that could be recombined endlessly because each one had been individually refined.
The KonMari parallel: reorganizing changes your relationship
Marie Kondo's KonMari method offers a surprisingly useful physical analogy. Kondo doesn't just tell you to organize your closet. She tells you to take everything out, hold each item individually, and ask: "Does this spark joy?" The magic isn't in the sorting. It's in the handling — the forced attention to each individual object.
Research published in the Journal of Sustainability Research found that participants who completed the KonMari process reported "a more reflective and restrained approach with regard to the acquisition of new things" and "a reinterpretation of the meanings of possession." The process of physically reorganizing their belongings changed their psychological relationship to ownership itself.
Your notes work the same way. When you pull a compound note apart, hold each idea individually, and decide where it belongs and what it connects to, you're forced into the same kind of deliberate attention. You discover which ideas still resonate and which were filler. You find connections you missed when everything was tangled together. You identify the gaps — the places where you thought you had an idea but actually had a vague gesture toward one.
The value isn't the tidier note system. The value is the sharper thinking that the tidying process demands.
AI as your refactoring partner
Software engineers don't refactor alone anymore. Modern IDEs suggest extractions, identify duplicates, and flag overly complex methods. AI-powered code tools go further — detecting structural patterns, recommending decompositions, and automating the mechanical parts of restructuring so the engineer can focus on the design decisions.
The same capability is arriving for knowledge work. AI tools can now scan a corpus of notes and surface structural problems: notes that cover multiple topics and should be split, near-duplicate notes that should be merged into a single sharper formulation, orphan notes that aren't connected to anything, and weak links that should be made explicit. Mem's AI-powered refactoring, for example, treats the problem exactly like code refactoring — identifying "zombie collections" and "orphan notes" that represent accumulated cognitive debt.
But here's the critical nuance: AI can identify structural problems and suggest changes, but the cognitive benefit comes from you making the decisions. When AI flags that your "Leadership Thoughts" note covers three separate topics, it's doing the detection work. When you decide which idea is the core claim, how the pieces relate, and what the connections mean — that's where the thinking happens. The restructuring is the thinking. Outsource the detection, but own the decisions.
This is the productive pattern: use AI to audit your knowledge base for structural debt, then do the refactoring yourself. The AI finds the compound notes, the duplicates, the broken connections. You do the splitting, merging, and reconnecting — and your understanding improves in the process.
Refactoring is a practice, not an event
The biggest mistake people make with refactoring — in code and in notes — is treating it as a one-time cleanup project. "I'll spend this weekend reorganizing my notes." That's like saying "I'll spend this weekend paying off all my technical debt." It doesn't work because the debt accumulates continuously, and the value of refactoring comes from doing it regularly.
Effective engineering teams allocate ongoing time for refactoring — not as a separate project, but woven into their daily work. The same principle applies to your knowledge system. A weekly twenty-minute refactoring session — pick one note that feels wrong, split it, rewrite the connections, notice what you learn — compounds over months into a fundamentally sharper body of knowledge and a fundamentally sharper mind.
Each refactoring session teaches you something. Not new information from outside, but new understanding of what you already know. That's why restructuring your notes restructures your understanding. The act of changing the structure forces you to re-examine the content, and re-examination produces insight that passive storage never will.
In L-0038, you learned that sequences are built by linking atomic ideas together. Refactoring is how you keep those atoms clean and those links honest. Without regular refactoring, atoms bloat into compounds, links decay into assumptions, and your knowledge graph slowly becomes unusable.
The next lesson, L-0040: Atomicity is a practice, not a rule, takes this further. The goal was never perfect decomposition from the start. It's the ongoing discipline of improving your decompositions over time — and refactoring is the mechanism that makes that improvement possible.