I have always called this the “one true taxonomy” problem, because whenever you sit with multiple stakeholders in a room talking about a taxonomy, you can never get to agreement, because there is no such thing as the “one true taxonomy”.

Any hierarchical taxonomy classifies on one dimension at each taxonomic level. Invariably someone wants to classify on one criteria when someone else wants to classify on another. Taxonomies that humans use aren’t multi-dimensional. So if there is a disagreement, someone wins and someone(s) has to lose.

No one is wrong; they just have different priorities or preferences or goals.

So now as an architect I never argue (and seldom discuss) taxonomies. I make two points and then bow out:

1. Whatever your taxonomy is, you need a rubric for each level. You need a procedure or set of questions that unambiguously map any $THING you encounter into exactly one bucket. Validate that competent people with no specific domain knowledge can properly classify things with your rubric; it must be repeatable by amateurs, not just experts (software is dumb).

2. Existence trumps theory. If there exists a taxonomy and rubric for what you’re classifying, you need to provide a $DARN_GOOD_REASON why this wheel needs reinventing. Personal preference and your 1% edge case probably don’t justify all the work to reinvent everything.

Then, I go back to the implementers and tell them to design in a tagging system, which is a DIY taxonomy, and except in ridiculous use cases, I can make indexes make it fast enough to let everyone overlay their own classification system.

The problem with trees is that the are a dimensional reduction, an aggregation; taking a problem without directionality and applying a useful/functional hierarchy.

And that's a problem because Aggregability is NP-Hard: https://dl.acm.org/doi/abs/10.1145/1165555.1165556

So a tree is a way to take a high dimensionality graph and make it usefully lower dimensionality, but, given the aforementioned proof, that reduction is going to go from being a lossless compression to a heuristic. So any interesting problem (at least, any problem interesting to me) is only going to be aided (read: not solved exhaustively) by that hierarchy.

I'm okay with this. Being okay with this has been one of the most freeing things over the last 20 years of my career. Accept inaccuracy, and find usefulness in your data structures.

This is good diagnosis of the problem. I found that often the right solution is to ditch the hierarchy and use flat structure. I wrote about this some time ago: https://yoyo-code.com/embrace-flatness/

Big insight in that article is also from https://matklad.github.io/2021/08/22/large-rust-workspaces.h... about structuring large rust workspaces as a flat list.

This is an independent riff on an argument Ted Nelson wrote down 50 years ago (and the reason why he coined the term "hypertext").

<https://en.wikipedia.org/wiki/Computer_Lib/Dream_Machines>

<http://link.springer.com/10.1007/978-3-319-16925-5>

There are only two hard problems in computer programming:

1. Naming things 2. Cache invalidation 3. off-by-one errors

  There are only three hard problems in computer science:

  1. Naming things
  2. Cache invalidation
  3. Off-by4. Multi-threading
  -one errors.

I think all three problems are really one problem under the hood:

Are these two things actually the same thing, or they separate?

One nice tool for analyzing maps as a tree is as a dominator trees. I wrote a bit about it here: https://neugierig.org/software/blog/2023/07/dominator.html

I have a deep distrust of hierarchies, because they keep you trapped into a single model that keeps extending its authority, usuall without anyone explicitly deciding that it should do so. For example, the file system: once it was deemed hierarchy is the main metaphor for navigation, the structure persisted and was reused for organisation, ownership, access control and governance. And it became infrastructure we cannot easily remove before we could even question if it was right or not. And once it dominated, non-hierarchical things were retrofitted as glue, e.g.: symlinks, aliases, shortcuts... also, when's the last time you've used a tag?

The webs are so much more malleable, but they're also not free. All the 'good enough's you were that a hierarchy that was taking care of implicitly are now your responsibility to model precisely and make sure they're performant as well. Look at ReBAC, for example. It gives you expressive power, but it also forces you to reason precisely about relationships, graph traversal, consistency, and cost. Strikingly similar is GraphQL.

Interestingly, source code is hierarchical, but compiles almost immediately to a graph IR and most analysis and optimisations happen there. But almost nobody looks at a CFG/SSA graph directly. You author in a hierarchical manner, yet the operational substrate is a malleable graph.

I thought the two hard problems were naming things, cache invalidation, and off-by-one errors?

John Ousterhout has also written about this in A Philosophy of Software Design:

The most fundamental problem in computer science is problem decomposition: how to take a complex problem and divide it up into pieces that can be solved independently.

Well elucidated. This problem has irked me for years in the form of multiple inheritance. When it's disallowed (like Java, unfortunately), trying to reduce a directed graph structure to a single dominant hierarchy is quite the bothersome choice.

I doubt there would exist a perfect taxonomy for everything. Taxonomies are subjective to individuals but somehow can be (ahem! AI) mapped relative to someone else’s preference taxonomy. What efficiency and meaning each individual (or organization or community) yields would be completely different.

I thought it was timezones.

Is there an OS whose primary FS is a taggedFS? It'd be interesting to hear from the users if this is nice to use or not..

I think I've always called this "Ontology is hard". It's genuinely useful when it's used as a tool for clarification. It's constraining when it's used as a tool for modeling.

For me, the canonical example is organising images in folders vs tags.

Every few years I watch, with amusement, our management restructuring the organizational hierarchy, allegedly because the old one didn't work.

Putting object into trees is basically a caching problem.

I wonder whether the author deliberately avoided ontology? That's what comes to mind when I read this. The age-old debate between taxonomy and ontology.

The article veers from saying computers are different, to saying they should be different but maybe aren't, back to how special they are:

> The next time you sit down to an empty design doc and don’t know where to start, be kind to yourself. You’re solving a hard problem.

This supposed hard problem in computing has always been with us, in real life. Which he admits multiple times, e.g.:

> Yet Victorian-era gentlemen might have pondered the same questions while sorting letters as we do while sorting virtual paper.

He appears to claim that the sole organizing principle in real life is the hierarchy, but, of course, that computers and ideas are different:

> Hierarchies are so natural to us that they ... [work] for physical objects that can be in only one place at a time. Ideas and information, however, resist taxonomies. They form intricate webs that penetrate rigid boundaries.

This distinction of physical vs. virtual requirements doesn't hold up under any sort of rigorous analysis. As he admits, hierarchies are not always ideal in physical space -- do we organize parts and supplies separate from tools, or place them next to their probable job sites?

And of course, the "in only one place at a time" is certainly true for any given group of atoms, but we have become adept at making fungible copies of atoms for many things. I might have drywall screws or 33 ohm resistors in multiple cached locations, and I have soldering irons and screwdrivers and pliers on more than one workbench.

One thing that is true is that we can usually add non-hierarchical groupings to information more easily than we can to groupings of atoms.

Another thing that is true is that we already often do so whenever the convenience outweighs the various costs.

And the third thing that is true is that this, also, is not much different than the physical world, where we routinely both break our hierarchies and create copies of things when needed.

This an issue of growing ontologies and taxonomies.

I have found that the best answer I have is:

1) Gossip and use the existing ontology and add new items only if genuinely needed

2) Combine synonyms, sometimes using vector embedding and cosine similarity during search

The insight is that trees are not a storage constraint but a traversal consequence — any walk through a graph starting from a given node produces a tree as a byproduct, and different starting points or orderings produce different trees from the same underlying structure. Rather than forcing a choice of canonical hierarchy at write time (the dentist-bill-goes-in-which-folder problem), you store the graph and let the tree emerge lazily from context: whoever is querying, from wherever they enter, gets the tree that is relevant to them, and no connections are sacrificed to produce it.

In general, federated systems have this quality emerge. For example, in OpenStreetMap, one group can label Nagorno Karabakh, the other Artsakh, and no one has to fight Google etc.

Use multiple trees.

The first chapter of this waves away the fact that hierarchical filesystems are now useless, but it is still a fact. There is no more reason to organize your files than there is to drive around in a chariot. It is hard to map one domain to the other, but it is also not necessary. With AI indexing and recall it's less necessary than it has ever been.

This is more true as stated than people want to give credit for, usually.

> before we could even question if it was right or not

But we could. Early filesystems didn't have heirachy. They'd sometimes support a single level of organization by treating a prefix of the filename as directory, but nothing below that. We looked at that and considered heirarchy better.

What you lament is that we stopped with heirarchy. You wish for something more general, and that you have received. With hardlinks and ACL the filesystem is freed from its shackles of heirarchy. Most people don't need that most of the the time.

The strict heirarchy sits as the third step of a complexity ladder. The reason we stopped there, in most cases, is that it's enough complexity.

Here is my take using the city as a metaphor.

All physical things have to be arranged in a linear fashion, this is pauli exclusion principle writ large.

A type of mereological nihilism is true, so hierarchy is real but in a weak emergence sense.

When I am standing on a street corner in a city, I can walk into a building and then navigate into a room inside that building and pick up a piece of paper inside.

Or I can walk down the street and as I pass landmarks, I will pass things in order, this is also a perceived hierarchy, because my starting position and movement are bound by time, I will always have a fixed order of experiences from any x,y coordinate.

So everything bounded by time and space acts as an emergent hierarchy via movement for a specific loci.

The paper can be moved however, and that same piece of paper sitting in the drawer at an attorneys office means something very different than when its sitting in the approved licenses cabinet in an offical government building.

Semantic meaning is first class but its an entirely different dimension than other types of meaning and due to pointers it isn't bound by pauli exclusion.

When people start thinking about the semantics of objects in computer programs they often become confused, because the semantic representation of the object follows semantic ontology laws not physical object ontology.

People can fuck this up in either direction and think physical laws apply to semantic meaning or physical meaning applies to semantics.

IMO hard links are underused in filesystems. You can have the same file / dir appear in different places under different names. Once linked, app doesn't have to care and runtime cost is zero.