You've seen test-rot, specification rot, and documentation rot; we now introduce; prompt rot!

Cluttering the repo with out-dated, very wordy and quickly outdated prompts will just confuse any agent tasked with looking at the repo in the future. Keeping context windows down is a real limitation to good LLM output, and this workflow may work completely against it.

- A plan.md describing the project, main abstraction idea, end costumer, and so on is great; but it should be kept minimal and up-to-date with the repo.

- Block comments on top of source-files and functions are great, and already very useful to coding agents. I don't see a value to anything more than what is already typical best practice.

My favourite projects typically have documentation in comments.

One example is SpiderMonkey, which uses these beautiful, long expository comments explaining not only what, but why design choices have been made. https://searchfox.org/firefox-main/source/js/public/RootingA...

If the goal is "locality", you can't get much closer than as a comment.

As far as markdown becoming "source code for agents" under the agentic paradigm, per-directory `AGENTS.md` seems more consistent, at least visually. If agent managed markdown is going to be high-churn, I'd rather it be confined to a single file. Constraints, especially for agents, are good.

If we go that route, can we have rich syntax highlighting, "go to definition"/"show usage sites", debuggers etc for the markdown docs as well? :)

But I don't really like the "LLMs as compiler" metaphor. If you followed that logic to the end, you'd have to "rebuild" your entire project from the spec every time the spec changes. Not just would the token cost be insane, but you'd also get a completely different implementation each time, maybe with different UI and design decisions where the spec left things open.

The alternative is to see the code as the source of truth and LLMs as (extremely sophisticated) editing or refactoring tools. Then by all means, still check in your prompts, but now they are documentation on how a feature was implemented, not the source of truth themselves.

I generally put markdown in /docs. I don't uppercase filenames. Instead I make a documentation generator consume the files so I get a decent navigation in HTML/PDF builds.

We did put non-code into /src for a very long time: It was heredocs, multiline docs, etc. Actually my preference is to put texts close to code and only fallback to /docs/something.md at a conceptual level. Which is probably what the author proposes, given that he sees markdown as primary interface to code.

We are close to inventing something like deep modules [1] for markdown and a whole methodology of managing docs abstraction and layers. And I'm somewhat serious. It's hard to manage one random, interconnected bag of (spaghetti) markdown. Abstract is the new interface.

1. https://softengbook.org/articles/deep-modules

I realize I've been doing this as part of working with agents heavily the last few weeks. The issue is remembering to have it write and keep them up to date. One thing I've been considering is using a Claude Hook[1] when the session ends to basically "update readme and todo from this session. only change them if needed" or something similar

I wrote something similar a few months ago [1], though admittedly I haven't been following my own advice terribly well.

The interesting part of any program source is what it took to make that program. I view AI-generated code in the same category that I see a binary.

[1] https://blog.tombert.com/Posts/Technical/2026/04-April/Stop-...

Developer documentation in /src, yes. Anything else, no way.

IME developers have low tolerance for interrupting flow to track down the docu that is aimed at them, so keep it near and obvious.

I have found a lot of value in the approach the post describes. I store my markdown as GitHub issues, regardless of how I come up with a detailed feature description (usually a chat session).

Before implementation, context is always cleared to ensure that the model is working only from known context (skills, AGENT.md, etc).

A major benefit of this is that agents can look up prior prompt instructions as needed or when mentioned in the current prompt it's working on.

I recently described my workflow here https://jaisenmathai.com/articles/sojourn-for-ios-was-45-one...

Docs in VCS, yes. Docs in /src, no.

> Markdown is becoming source code, not documentation

> That Markdown should be checked in to /src

I've made a similar argument last June, although I made the point with a sample project rather than manifesto style

https://github.com/TZubiri/keyboard-transpositions-checker

> A Proof of Concept for LLM as source code. I am of the position that the "code" is now target code and not source code. My strongest source for this claim is Stallman's classical definition of Source Code which is the "preferred way to modify the program".

> Upload the conversation with ChatGPT as source code

Although this was pre-agents/markdown, the main way to generate code was just with user-interface conversations with the LLM.

And my position differs in which I argue against uploading the target code, just the source code. Which is an issue if the LLM is not deterministic, but it's workable.

That said I apparently did foreshadow solutions to these issues

> Since we are using a consumer interface, and not an api, (first we have no guarantees that the code will not be used for training, so there's no IP protection, but also), we don't have much reproducibility, robust publishing should use API access and publish exact model with revision as well as seed (and even then we are not guaranteed reproducibility.

I think in general we'll end up rewinding so much, the sloppers are recursing and building a ton of harnessing tools that will need to be trashed because they made a fundamental mistake at the very first steps. Those of us who are a bit more careful will probably only get back to agentic engineering once the slopper activity dies down, it's pretty much career suicide at this point to get into it. Anyone who is barely careful is just waiting it out.

I still like the idea of source code as documentation and unit tests as documentation. While revising code written by an LLM to make it easier for humans to understand is now a controversial practice, I believe it's worthwhile in a lot of case.

Let’s keep the Codex session JSONL there too, why the hell not. And the debug build logs, since they’re easily greppable text useful for diagnosing recurring problems. And logs/reports from every test run - a ton of useful info there, lets you track regressions over time; would be a shame to throw it away. We could also store screenshots of every app run to have a LLM-compatible historical record of how each component changed visually. And the token provider billing documents, since we’re gonna have a lot of those once we’ll start maintaining all that.

So

1. he's describing a manual version of Spec-Kit / OpenSpec / BMAD?

2. Thinks Markdown is... somehow different from normal text or other markup languages?

3. Doesn't seem to understand that LLMs are not deterministic?

This sounds a lot like a low tech version of Delta from Zed. All your agent transcripts live in the same place as code.

src/md doesn’t seem all that different from docs. Maybe it changes how people search the filesystem, though?

If you split code up into multiple packages, moving the docs closer to the code might make sense. The docs for package foo could be in packages/foo/docs.