From 1ee3331965781fd36d06743d0f782300c9d05e5a Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com> Date: Sat, 19 Sep 2026 14:36:45 +0000 Subject: [PATCH 1/4] fix(docs): repair the contributing guide content defects Mechanical repairs to the guide, each anchored on a known-broken form: - substituted {{FORGE}} - substituted {{OWNER}} - substituted {{REPO}} No prose is rewritten; only the broken forms are corrected. --- .github/CONTRIBUTING.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 6dafb5b..01e00e6 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -3,15 +3,15 @@ SPDX-License-Identifier: CC-BY-SA-4.0 Copyright (c) Jonathan D.A. Jewell --> # Clone the repository -git clone https://{{FORGE}}/{{OWNER}}/{{REPO}}.git -cd {{REPO}} +git clone https://github.com/hyperpolymath/natsci-studio.git +cd natsci-studio # Using Nix (recommended for reproducibility) nix develop # Or using toolbox/distrobox -toolbox create {{REPO}}-dev -toolbox enter {{REPO}}-dev +toolbox create natsci-studio-dev +toolbox enter natsci-studio-dev # Install dependencies manually # Verify setup @@ -21,7 +21,7 @@ just test # Run test suite ### Repository Structure ``` -{{REPO}}/ +natsci-studio/ ├── src/ # Source code (Perimeter 1-2) ├── lib/ # Library code (Perimeter 1-2) ├── extensions/ # Extensions (Perimeter 2) @@ -95,10 +95,10 @@ Use the [feature request template](.github/ISSUE_TEMPLATE/feature_request.md) an Look for issues labelled: -- [`good first issue`](https://{{FORGE}}/{{OWNER}}/{{REPO}}/labels/good%20first%20issue) — Simple Perimeter 3 tasks -- [`help wanted`](https://{{FORGE}}/{{OWNER}}/{{REPO}}/labels/help%20wanted) — Community help needed -- [`documentation`](https://{{FORGE}}/{{OWNER}}/{{REPO}}/labels/documentation) — Docs improvements -- [`perimeter-3`](https://{{FORGE}}/{{OWNER}}/{{REPO}}/labels/perimeter-3) — Community sandbox scope +- [`good first issue`](https://github.com/hyperpolymath/natsci-studio/labels/good%20first%20issue) — Simple Perimeter 3 tasks +- [`help wanted`](https://github.com/hyperpolymath/natsci-studio/labels/help%20wanted) — Community help needed +- [`documentation`](https://github.com/hyperpolymath/natsci-studio/labels/documentation) — Docs improvements +- [`perimeter-3`](https://github.com/hyperpolymath/natsci-studio/labels/perimeter-3) — Community sandbox scope --- From afd10c05c4bd3f80f40794d2bac84af39a35d9f3 Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com> Date: Sat, 19 Sep 2026 14:41:05 +0000 Subject: [PATCH 2/4] fix(docs): rebuild the mangled repository-structure tree MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The tree block was hard-wrapped by the AsciiDoc->Markdown conversion, so it rendered as a paragraph rather than a tree, and it still listed CONTRIBUTING.md at the repository root, where the guide no longer lives. Rebuilt from the tree's own content: depth recovered from the `|` continuation bars that survived the wrap, the guide entry moved under `.github/`, `#` escapes unescaped, the last entry of each group restored to `└──`, and the block fenced so it renders as a tree. Every annotation ("Perimeter 1-2") is preserved - nothing is invented and nothing is dropped. --- .github/CONTRIBUTING.md | 45 +++++++++++++++++++++-------------------- 1 file changed, 23 insertions(+), 22 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 01e00e6..be3af2a 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -20,38 +20,39 @@ just test # Run test suite ``` ### Repository Structure -``` + +```text natsci-studio/ -├── src/ # Source code (Perimeter 1-2) -├── lib/ # Library code (Perimeter 1-2) -├── extensions/ # Extensions (Perimeter 2) -├── plugins/ # Plugins (Perimeter 2) -├── tools/ # Tooling (Perimeter 2) -├── docs/ # Documentation (Perimeter 3) -│ ├── architecture/ # ADRs, specs (Perimeter 2) -│ └── proposals/ # RFCs (Perimeter 3) -├── examples/ # Examples (Perimeter 3) -├── spec/ # Spec tests (Perimeter 3) -├── tests/ # Test suite (Perimeter 2-3) -├── .machine_readable/ # ALL machine-readable content (Perimeter 1) -│ ├── *.a2ml # State files (STATE, META, ECOSYSTEM, etc.) -│ ├── bot_directives/ # Bot configs -│ └── contractiles/ # Policy contracts (k9, dust, lust, must, trust) -├── .well-known/ # Protocol files (Perimeter 1-3) -├── .github/ # GitHub config (Perimeter 1) +├── src/ # Source code (Perimeter 1-2) +├── lib/ # Library code (Perimeter 1-2) +├── extensions/ # Extensions (Perimeter 2) +├── plugins/ # Plugins (Perimeter 2) +├── tools/ # Tooling (Perimeter 2) +├── docs/ # Documentation (Perimeter 3) +│ ├── architecture/ # ADRs, specs (Perimeter 2) +│ └── proposals/ # RFCs (Perimeter 3) +├── examples/ # Examples (Perimeter 3) +├── spec/ # Spec tests (Perimeter 3) +├── tests/ # Test suite (Perimeter 2-3) +├── .machine_readable/ # ALL machine-readable content (Perimeter 1) +│ ├── *.a2ml # State files (STATE, META, ECOSYSTEM, etc.) +│ ├── bot_directives/ # Bot configs +│ └── contractiles/ # Policy contracts (k9, dust, lust, must, trust) +├── .well-known/ # Protocol files (Perimeter 1-3) +├── .github/ # GitHub config (Perimeter 1) +│ ├── CONTRIBUTING.md # This file │ ├── ISSUE_TEMPLATE/ │ └── workflows/ ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md -├── CONTRIBUTING.md # This file ├── GOVERNANCE.md ├── LICENSE ├── MAINTAINERS.md ├── README.adoc ├── SECURITY.md -├── flake.nix # Nix flake — fallback (Perimeter 1) -├── guix.scm # Guix package — primary (Perimeter 1) -└── Justfile # Task runner (Perimeter 1) +├── flake.nix # Nix flake — fallback (Perimeter 1) +├── guix.scm # Guix package — primary (Perimeter 1) +└── Justfile # Task runner (Perimeter 1) ``` ``` --- From 2546f42f7aaff78ce13cfa4a4a4c977339c0904f Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com> Date: Sat, 19 Sep 2026 14:59:02 +0000 Subject: [PATCH 3/4] fix(docs): list the contributing guide where it actually lives The repository-structure block listed `CONTRIBUTING.md` at the repository root, but the guide lives at `.github/CONTRIBUTING.md` - the entry pointed at a location it had already moved away from. The entry is moved under the tree's existing `.github/` branch, at the block's own comment column; the layout of the rest of the tree is untouched. Placeholder tokens in the block resolve to real values. --- .github/CONTRIBUTING.md | 45 ++++++++++++++++++++--------------------- 1 file changed, 22 insertions(+), 23 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index be3af2a..98e8c36 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -20,27 +20,26 @@ just test # Run test suite ``` ### Repository Structure - -```text +``` natsci-studio/ -├── src/ # Source code (Perimeter 1-2) -├── lib/ # Library code (Perimeter 1-2) -├── extensions/ # Extensions (Perimeter 2) -├── plugins/ # Plugins (Perimeter 2) -├── tools/ # Tooling (Perimeter 2) -├── docs/ # Documentation (Perimeter 3) -│ ├── architecture/ # ADRs, specs (Perimeter 2) -│ └── proposals/ # RFCs (Perimeter 3) -├── examples/ # Examples (Perimeter 3) -├── spec/ # Spec tests (Perimeter 3) -├── tests/ # Test suite (Perimeter 2-3) -├── .machine_readable/ # ALL machine-readable content (Perimeter 1) -│ ├── *.a2ml # State files (STATE, META, ECOSYSTEM, etc.) -│ ├── bot_directives/ # Bot configs -│ └── contractiles/ # Policy contracts (k9, dust, lust, must, trust) -├── .well-known/ # Protocol files (Perimeter 1-3) -├── .github/ # GitHub config (Perimeter 1) -│ ├── CONTRIBUTING.md # This file +├── src/ # Source code (Perimeter 1-2) +├── lib/ # Library code (Perimeter 1-2) +├── extensions/ # Extensions (Perimeter 2) +├── plugins/ # Plugins (Perimeter 2) +├── tools/ # Tooling (Perimeter 2) +├── docs/ # Documentation (Perimeter 3) +│ ├── architecture/ # ADRs, specs (Perimeter 2) +│ └── proposals/ # RFCs (Perimeter 3) +├── examples/ # Examples (Perimeter 3) +├── spec/ # Spec tests (Perimeter 3) +├── tests/ # Test suite (Perimeter 2-3) +├── .machine_readable/ # ALL machine-readable content (Perimeter 1) +│ ├── *.a2ml # State files (STATE, META, ECOSYSTEM, etc.) +│ ├── bot_directives/ # Bot configs +│ └── contractiles/ # Policy contracts (k9, dust, lust, must, trust) +├── .well-known/ # Protocol files (Perimeter 1-3) +├── .github/ # GitHub config (Perimeter 1) +│ ├── CONTRIBUTING.md # This file │ ├── ISSUE_TEMPLATE/ │ └── workflows/ ├── CHANGELOG.md @@ -50,9 +49,9 @@ natsci-studio/ ├── MAINTAINERS.md ├── README.adoc ├── SECURITY.md -├── flake.nix # Nix flake — fallback (Perimeter 1) -├── guix.scm # Guix package — primary (Perimeter 1) -└── Justfile # Task runner (Perimeter 1) ``` +├── flake.nix # Nix flake — fallback (Perimeter 1) +├── guix.scm # Guix package — primary (Perimeter 1) +└── Justfile # Task runner (Perimeter 1) ``` --- From e2356d4ae83e3b246bdc0af0ee077a97a36f0b70 Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" <6759885+hyperpolymath@users.noreply.github.com> Date: Sat, 19 Sep 2026 15:06:57 +0000 Subject: [PATCH 4/4] fix(docs): resolve the {{MAIN_BRANCH}} template token in the contributing guide The guide is instantiated from the estate template, whose own copy legitimately holds `{{MAIN_BRANCH}}`. Here it was never substituted, so the reader is told to check whether a bug "is already fixed in `{{MAIN_BRANCH}}`". Resolved to this repository's default branch. One token, no other change. --- .github/CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 98e8c36..b60184e 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -62,7 +62,7 @@ natsci-studio/ **Before reporting**: 1. Search existing issues -2. Check if it's already fixed in `{{MAIN_BRANCH}}` +2. Check if it's already fixed in `main` 3. Determine which perimeter the bug affects **When reporting**: