This repository is the canonical working tree behind Rooted Layers. Most tracked content lives under publications/: essay packages, umbrella publication packages, supporting artifacts, and local research surfaces.
The root is meant to stay navigable. Root docs orient you. Package README.md files explain local structure. Tracked workflow docs explain repeatable processes. Tracked repo-local skills live under workflows/skills/ and are mirrored into local .agents/skills/ for Codex discovery.
The repo is organized around one main lifecycle:
- intake papers and convert them into usable markdown
- research and shortlist sources
- draft and iterate essays with review artifacts
- generate NotebookLM artifacts
- polish the article with images, transcript insights, and references
- publish to Substack
- sync the public archive and mirror
That lifecycle does not force one rigid folder shape on every package. The repo uses three package classes:
- Single-publication package: one live essay surface plus local
archive/ - Umbrella package: several related publications or a course/series sharing papers, artifacts, or source layers
- Workflow/framework package: tracked operational infrastructure, not forced into the essay-package layout
| Surface | Role | Start Here |
|---|---|---|
publications/ |
Canonical essay and publication packages | publications/README.md |
workflows/ |
Canonical tracked playbooks | workflows/README.md |
scripts/ |
Tracked repo automation | scripts/README.md |
publication_strategy_and_archive/ |
Substack archive, mirror, publication map, and editorial atlas | publication_strategy_and_archive/README.md |
reviewable-runs/ |
Reviewable execution framework and examples | reviewable-runs/README.md |
publications/security-research/ |
Research bucket, not yet normalized into publication packages | publications/security-research/README.md |
Use these layers in order:
- root README
publications/README.mdor the relevant workflow/support README- the specific package
README.md - the matching workflow doc in
workflows/ - tracked scripts and tracked skills if execution help is needed
Across content packages, use these terms consistently:
- live draft
- companion
- blueprint / plan
- claims / review artifacts
- artifacts
- archive
- papers
- distribution / socials
For single-publication packages, the default paper-intake convention is:
papers/papers/markdown/papers/index.md
Umbrella packages may preserve stronger established variants when those structures already carry more meaning than the generic layout.
Essay and publication packages now live under publications/. That directory is the canonical package index and the right place to understand:
- which folders are single-publication packages vs umbrellas
- which publication packages map to published Substack essays
- where live drafts, companions, papers, artifacts, and archives live for each package
- which packages are still transitional or structurally uneven
Root keeps only the cross-package orientation. Package-level detail belongs in publications/README.md and the local package READMEs.
The published archive is tracked centrally in publication_strategy_and_archive/substack_archive/. The generated table below maps published Substack posts to their canonical package or umbrella package in this repo.
| Substack Publication | Repository Folder |
|---|---|
| The Binding Gap | publications/binding-gap/ |
| The Illusion of the Swarm | publications/illusion-of-swarm/ |
| The Moltbook Phenomenon | publications/moltbook-phenomenon/ |
| The Autonomy Tax | publications/autonomy-tax/ |
| The Transformer Attractor | publications/neural-architectures/ |
| When the LLM Programs Its Own Thinking | publications/programmable-thinking/ |
| The Orchestration Paradigm: Issue 4 - The Reality | publications/orchestration-paradigm/ |
| The Orchestration Paradigm: Issue 3 - The Behavior | publications/orchestration-paradigm/ |
| The Orchestration Paradigm: Issue 2 - The Factory | publications/orchestration-paradigm/ |
| The Orchestration Paradigm Series | publications/orchestration-paradigm/ |
| The Hardware Friction Map | publications/hardware-friction/ |
| What Actually Works: The Hardware Compatibility Filter in Neural Architecture (2023–2025) | publications/hardware-friction/ |
| Autonomous AI Agents: Core Foundations and Recent Breakthroughs | publications/autonomous-agents/ |
| Neural Architecture Design as a Compositional Language | publications/neural-architectures/ |
| Operating Agents: Preface | publications/autonomous-agents/essays/launch-note/ |
| Operating Agents I: Action Systems and Tool Use | publications/autonomous-agents/essays/action/ |
| Operating Agents II: Memory Systems and Authority | publications/autonomous-agents/essays/memory/ |
| Operating Agents III: Reasoning Scaffolds and Planning | publications/autonomous-agents/essays/reasoning/ |
| Operating Agents IV: Multi-Agent Boundaries and Handoffs | publications/autonomous-agents/essays/multi-agent/ |
| Operating Agents V: Trust Boundaries and Agent Safety | publications/autonomous-agents/essays/safety/ |
| Operating Agents Bonus: Workflow Optimization and Evaluation | publications/autonomous-agents/essays/optimization/ |
| Welcome | (N/A / Root) |
Published posts may map to umbrella packages or nested subpackages rather than one folder per post. That is intentional.
Tracked workflow docs live in workflows/. The current article-development canon is:
workflows/paper-intake/README.mdworkflows/alphaxiv-research/README.mdworkflows/essay-iteration/README.mdworkflows/notebooklm-artifacts/README.mdworkflows/article-polish/README.mdworkflows/substack-publishing/README.mdworkflows/substack-archive-sync/README.md
Adjacent YouTube and channel operations live in the same tracked layer:
workflows/youtube-production/README.mdworkflows/youtube-channel-ops/README.mdworkflows/youtube-series-operating-agents/README.md
The canonical root toolchain is tracked in requirements.txt and explained operationally in local AGENTS.md.
Core tools:
markitdown[pdf]alphaxiv-pynotebooklm-py[browser]python-substack
Adjacent publishing automation:
- tracked scripts under
scripts/ - tracked skill bundles under
workflows/skills/
Tracked repo-local skills live under workflows/skills/. The local .agents/skills/ tree is a discovery mirror for Codex, not the canonical documentation layer.
Use workflow docs to understand the process. Use skill bundles to execute that process efficiently.