Physical vs Conceptual File Organization

Physical ≠ Conceptual: A Mental Model for File Chaos

Hook

Your files are scattered across iCloud, Git repos, Zotero, Downloads. You’ve tried to unify them. You’ve failed. Here’s why that’s okay — and what to do instead.

The Problem

As a knowledge worker, I have:

• PDFs and books (need cloud sync, read anywhere)
• Code repos (need Git, can’t use iCloud)
• Academic papers (Zotero manages metadata)
• Notes and knowledge (Obsidian vault)
• Course materials, work docs, personal projects…

The instinct: Put everything in one place. The reality: Technically impossible. Git + iCloud = corruption. Zotero needs its database. Different tools, different needs.

The anxiety: If files are scattered, how do I find anything? And if I use my Zettelkasten to link to files… am I polluting my knowledge base?

The Failed Attempts

1. One mega-folder: Tried putting everything in ~/Documents. Git repos corrupted. Zotero confused.

2. Abandon ZK purity: Used Obsidian as a “life dashboard” linking to everything. Felt wrong. Cards linking to PDFs isn’t knowledge connection.

3. Separate everything: Different app for each thing. Context switching killed productivity.

The Insight

Physical organization ≠ Conceptual organization

CONCEPTUAL (unified)          PHYSICAL (scattered)
────────────────────          ────────────────────
     Obsidian                 ~/Documents/Life/
        │                     ~/Developer/
        │ links to            ~/Zotero/
        ▼                     ~/Downloads/
   MOCs & Cards          →    (files wherever they need to be)

Stop fighting the scatter. Accept physical fragmentation. Achieve conceptual unity.

The file system is just storage backend. Your PKM tool is the unified interface.

The Resolution: ZK Core + Practical Scaffolding

The key insight: My Zettelkasten vault already had non-ZK elements:

• 00-dashboard.md — Dataview queries
• 0-inbox/ — Capture inbox
• 3-drafts/ — Output production

Only 1-cards/ is pure Zettelkasten. Everything else is scaffolding.

Layer	Purpose	Pure ZK?
1-cards/	Atomic knowledge	Yes
2-moc/	Navigation	Scaffolding
_references/	External file access	Scaffolding
Dashboard, inbox, drafts	Workflow	Scaffolding

The rule: Cards link to cards only. MOCs can link anywhere — they’re maps, not territory.

This preserves ZK where it matters (idea-to-idea connections) while being practical where it helps (file navigation).

The Implementation

Physical Layer (Accept Fragmentation)

~/Documents/                    # iCloud synced
├── Obsidian/Note/             # Knowledge
└── Life/
    ├── Resources/             # PDFs, books, courses
    ├── Writing/               # Non-code outputs
    └── Archive/               # Completed

~/Developer/                    # Local, Git-managed
├── personal/
├── work/
└── courses/

~/Zotero/                       # App-managed papers

~/Downloads/                    # Transient inbox ONLY

Conceptual Layer (Unified in Obsidian)

Each project gets an MOC — the “one door” to scattered files:

# moc-project-x
 
## Knowledge (cards)
- [[concept-a]]
- [[concept-b]]
 
## Resources
- [Design Doc](_references/Projects/x/design.pdf)
- [Zotero Collection](zotero://select/...)
 
## Code
- Local: `~/Developer/project-x/`
- GitHub: https://github.com/...

The Symlink Bridge

Note/_references → ~/Documents/Life/Resources/

One symlink. If Resources/ moves, update one pointer. All MOC links stay valid.

The Habits

What changes:

1. Adding files: Put in right physical location + update relevant MOC
2. Finding files: Go through MOC, not Finder browsing
3. Downloads: Treat as inbox — process weekly, never permanent

The overhead is real but small. And with AI assistants, MOC maintenance becomes trivial.

Why Not DEVONthink?

DEVONthink solves the same problem differently — proprietary database, AI classification, smart groups.

	This Approach	DEVONthink
Lock-in	None (plain files)	Proprietary DB
Portability	High	Lower
Cost	Free	$99-199
Philosophy	Unix (composable)	Monolith

DEVONthink is powerful. But I prefer owning my files and knowledge in plain formats.

Key Takeaways

1. Physical ≠ Conceptual — stop trying to unify files physically
2. Accept fragmentation — it’s technically necessary
3. Unify conceptually — MOCs are the “one door”
4. Keep ZK pure — cards link to cards; everything else is scaffolding
5. Symlinks bridge locations — one update if paths change

---

Meta

• Source: Conversation designing my own file system
• Related: 2026-01-17-file-organization-plan
• Potential outlets: Personal blog, dev.to, Medium