repo-nexus 0.3.0 → 0.3.3

package/README.md

@@ -7,7 +7,7 @@
 [![Platform](https://img.shields.io/badge/Platform-macOS%20%7C%20Linux-lightgrey)](#)
 [![FAQ](https://img.shields.io/badge/docs-FAQ-blue.svg)](docs/FAQ.md)
 
-A **simple, lightweight companion tool** for multi-repo workflows. It links multiple independent repositories and shares universal AI instructions (like `AGENTS.md`) using standard Unix symlinks — **without Git submodules, monorepo migrations, or complex setup**.
+A **simple, lightweight companion tool** for multi-repo workflows. It links multiple independent repositories and shares universal AI instructions (like `AGENTS.md`) using standard Unix symlinks **without Git submodules, monorepo migrations, or complex setup**.
 
 - **No Git Submodules or Nested Git Friction**: Keep your repositories completely independent. No detached HEADs, no `.gitmodules`, and no merge conflicts between repos.
 - **A Lean Companion, Not a Workspace Replacer**: It does not replace your editor, terminal, build tools, or package manager. It is a tiny (~20 KB) helper that seamlessly complements your existing workflow.
@@ -93,22 +93,25 @@ A **simple, lightweight companion tool** for multi-repo workflows. It links mult
 
 ## Installation
 
-Install `rnex` via npm, GitHub Packages, or the zero-dependency native installer:
+Install `rnex` via npm, standalone one-liner (`curl` / `wget`), or from source:
 
-### Option 1: Via npm (Recommended)
+### Option 1: Via npm (Global)
 
 ```bash
 npm install -g repo-nexus
 ```
-*(Installs both `repo-nexus` and `rnex` commands globally, or run via `npx repo-nexus init`)*
+*(Installs both `repo-nexus` and `rnex` commands globally, or run without installing via `npx repo-nexus init`)*
 
-### Option 2: Via GitHub Packages
+### Option 2: Standalone One-Liner (curl / wget — Zero Dependencies, No Node.js)
 
 ```bash
-npm install -g @nu-nenoi/repo-nexus --registry=https://npm.pkg.github.com
+curl -fsSL https://raw.githubusercontent.com/nu-nenoi/repo-nexus/main/scripts/install.sh | sh
+# or
+wget -qO- https://raw.githubusercontent.com/nu-nenoi/repo-nexus/main/scripts/install.sh | sh
 ```
+*(Downloads and links `rnex` and `repo-nexus` into `~/.local/bin` without requiring Node.js or npm)*
 
-### Option 3: Native Installer (Zero Dependencies)
+### Option 3: Native Installer (Clone & Install)
 
 Clone the repository and run the built-in installer:
 
@@ -144,7 +147,7 @@ rnex add frontend ../web-app          # relative paths work too
 rnex status
 ```
 
-During `rnex init`, the CLI automatically scans for existing AI configuration files (like `CLAUDE.md`, `.cursorrules`, `.github/copilot-instructions.md`) and adds them to your config.
+During `rnex init`, the CLI creates `rnex.yaml` if none exists for the directory, and merges Repo Nexus workspace instructions with any existing AI instructions (such as `AGENTS.md`, `CLAUDE.md`, `.cursorrules`).
 
 ---
 

package/docs/AGENTS.sample.md

@@ -4,8 +4,10 @@ This workspace operates as a **Repo Nexus** linking multiple independent reposit
 
 ## Rules for AI Coding Assistants
 
-1. **Symlink Write-Through**: Files edited under `repos/<name>/` directly modify the target repository.
-2. **Repo Boundaries**: Each repository is isolated. Do not introduce cross-repo imports unless explicitly architected.
-3. **Shared Context**: This file governs AI assistant behavior across all member repositories. Keep instructions universal. Use local instructions for repo-specific rules.
-4. **Member Repo RNEX Context**: Member repositories may contain an `.rnex/` directory (accessible via `repos/<name>/.rnex/`) containing repository-specific documents, instructions, rules, workflows, and scripts managed by Repo Nexus. AI assistants operating at the workspace level MUST inspect `repos/<name>/.rnex/` for member-specific context, guidelines, and commands.
-5. **Git Operations**: Commit and push changes directly within the respective member repository root.
+1. **Workspace Structure & Settings**: AI coding assistants MUST inspect and read `rnex.yaml` at the workspace root to understand the workspace structure (such as `repos_dir`), registered member repositories, and active configuration settings.
+2. **Symlink Write-Through**: Files edited under `repos/<name>/` directly modify the target repository.
+3. **Repo Boundaries**: Each repository is isolated. Do not introduce cross-repo imports unless explicitly architected.
+4. **Shared Context**: This file governs AI assistant behavior across all member repositories. Keep instructions universal. Use local instructions for repo-specific rules.
+5. **Member Repo RNEX Context**: Member repositories may contain an `.rnex/` directory (accessible via `repos/<name>/.rnex/`) containing repository-specific documents, instructions, rules, workflows, and scripts managed by Repo Nexus. AI assistants operating at the workspace level MUST inspect `repos/<name>/.rnex/` for member-specific context, guidelines, and commands.
+6. **Plugin Instructions**: If plugins are enabled in `rnex.yaml` (under `plugins:`), AI coding assistants MUST read instructions for each enabled plugin from its separate instruction files (located in `.rnex/instructions/` or `.rnex/rules/`).
+7. **Git Operations**: Commit and push changes directly within the respective member repository root.

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.3.0",
+  "version": "0.3.3",
   "description": "Lightweight, zero-dependency companion tool for multi-repo workspaces and shared AI context via symlinks (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",

package/rnex

@@ -559,12 +559,13 @@ plugin_list_rules() {
   _pdir="$1"
   [ -f "$_pdir/plugin.yaml" ] || return 0
   awk '
-    /^rules:/ || /^ai_files:/ { r=1; next }
-    r && /^[^ #]/ { exit }
-    r && /^[ ]*-[ ]*/ {
-      sub(/^[ ]*-[ ]*/, "");
-      sub(/[ ]*#.*/, "");
-      if (length($0) > 0) print $0
+    /^(rules|instructions|ai_files):[ ]*(#.*)?$/ { in_sec = 1; next }
+    in_sec && /^[^ #]/ { in_sec = 0 }
+    in_sec && /^[ ]*-[ ]*/ {
+      line = $0
+      sub(/^[ ]*-[ ]*/, "", line)
+      sub(/[ ]*#.*/, "", line)
+      if (length(line) > 0) print line
     }
   ' "$_pdir/plugin.yaml"
 }
@@ -641,53 +642,113 @@ sync_plugins() {
   done
 }
 
-# ============================================================================
-# Commands
-# ============================================================================
-
-cmd_init() {
-  _target_dir="${1:-$PWD}"
-  _target_dir="$(resolve_path "$_target_dir")"
-  mkdir -p "$_target_dir"
-
-  _target_yaml="$_target_dir/$RNEX_CONFIG_FILE"
+# ---- AI Instructions Management -------------------------------------------
 
-  if [ -f "$_target_yaml" ]; then
-    log_warn "Workspace already initialized at $_target_dir ($RNEX_CONFIG_FILE exists)"
-    log_dim "To reconcile symlinks and plugins, run:"
-    log_dim "  rnex sync"
-    return 0
-  fi
+AI_MARKER_START="<!-- REPO-NEXUS:START -->"
+AI_MARKER_END="<!-- REPO-NEXUS:END -->"
 
-  # ---- Create AGENTS.md from sample if not present -------------------------
-  _target_agents="$_target_dir/AGENTS.md"
-  if [ ! -f "$_target_agents" ]; then
-    _script_dir="$(dirname "$SCRIPT_LOCATION")"
-    _sample="$_script_dir/docs/AGENTS.sample.md"
-    if [ -f "$_sample" ]; then
-      cp "$_sample" "$_target_agents"
-      log_ok "Created AGENTS.md from sample template"
-    else
-      cat <<'AGENTS_EOF' > "$_target_agents"
+get_rnex_instructions() {
+  cat <<'AGENTS_EOF'
 # Multi-Repo AI Workspace Context
 
 This workspace operates as a **Repo Nexus** linking multiple independent repositories via symlinks.
 
 ## Rules for AI Coding Assistants
 
-1. **Symlink Write-Through**: Files edited under `repos/<name>/` directly modify the target repository.
-2. **Repo Boundaries**: Each repository is isolated. Do not introduce cross-repo imports unless explicitly architected.
-3. **Shared Context**: This file provides root workspace guidelines across all member repositories. Keep instructions universal. Use local instructions for repo-specific rules.
-4. **Git Operations**: Commit and push changes directly within the respective member repository root.
+1. **Workspace Structure & Settings**: AI coding assistants MUST inspect and read `rnex.yaml` at the workspace root to understand the workspace structure (such as `repos_dir`), registered member repositories, and active configuration settings.
+2. **Symlink Write-Through**: Files edited under `repos/<name>/` directly modify the target repository.
+3. **Repo Boundaries**: Each repository is isolated. Do not introduce cross-repo imports unless explicitly architected.
+4. **Shared Context**: This file governs AI assistant behavior across all member repositories. Keep instructions universal. Use local instructions for repo-specific rules.
+5. **Member Repo RNEX Context**: Member repositories may contain an `.rnex/` directory (accessible via `repos/<name>/.rnex/`) containing repository-specific documents, instructions, rules, workflows, and scripts managed by Repo Nexus. AI assistants operating at the workspace level MUST inspect `repos/<name>/.rnex/` for member-specific context, guidelines, and commands.
+6. **Plugin Instructions**: If plugins are enabled in `rnex.yaml` (under `plugins:`), AI coding assistants MUST read instructions for each enabled plugin from its separate instruction files (located in `.rnex/instructions/` or `.rnex/rules/`).
+7. **Git Operations**: Commit and push changes directly within the respective member repository root.
 AGENTS_EOF
-      log_ok "Created AGENTS.md with default template"
-    fi
+}
+
+merge_rnex_instructions() {
+  _dst="$1"
+  _body_tmp="$(mktemp)"
+  get_rnex_instructions > "$_body_tmp"
+
+  if [ ! -f "$_dst" ]; then
+    mkdir -p "$(dirname "$_dst")"
+    printf '%s\n' "$AI_MARKER_START" > "$_dst"
+    cat "$_body_tmp" >> "$_dst"
+    printf '\n%s\n' "$AI_MARKER_END" >> "$_dst"
+    rm -f "$_body_tmp"
+    log_ok "Created $(basename "$_dst") with Repo Nexus instructions"
+    return 0
+  fi
+
+  # If delimiters already exist, update the block in-place
+  if grep -qF "$AI_MARKER_START" "$_dst" 2>/dev/null; then
+    _tmp="$(mktemp)"
+    awk -v s="$AI_MARKER_START" -v e="$AI_MARKER_END" -v src="$_body_tmp" '
+      $0 == s {
+        in_b = 1
+        print s
+        while ((getline line < src) > 0) print line
+        close(src)
+        next
+      }
+      $0 == e {
+        in_b = 0
+        print e
+        next
+      }
+      !in_b { print }
+    ' "$_dst" > "$_tmp" && mv "$_tmp" "$_dst"
+    rm -f "$_body_tmp"
+    log_ok "Updated Repo Nexus instructions in $(basename "$_dst")"
+    return 0
+  fi
+
+  # If no delimiters, check if file already has up-to-date rnex instructions
+  if grep -q "rnex.yaml" "$_dst" 2>/dev/null && grep -qi "Plugin Instructions" "$_dst" 2>/dev/null; then
+    rm -f "$_body_tmp"
+    log_info "$(basename "$_dst") already contains Repo Nexus instructions"
+    return 0
+  fi
+
+  # Append rnex instructions block to existing instructions
+  _tmp="$(mktemp)"
+  cp "$_dst" "$_tmp"
+  if [ -s "$_tmp" ] && [ -n "$(tail -c 1 "$_tmp" 2>/dev/null)" ]; then
+    printf '\n' >> "$_tmp"
+  fi
+  {
+    printf '\n%s\n' "$AI_MARKER_START"
+    cat "$_body_tmp"
+    printf '\n%s\n' "$AI_MARKER_END"
+  } >> "$_tmp"
+  mv "$_tmp" "$_dst"
+  rm -f "$_body_tmp"
+  log_ok "Merged Repo Nexus instructions with existing $(basename "$_dst")"
+}
+
+# ============================================================================
+# Commands
+# ============================================================================
+
+cmd_init() {
+  if [ -n "$CUSTOM_CONFIG" ]; then
+    _target_yaml="$(resolve_path "$CUSTOM_CONFIG")"
+    _target_dir="$(dirname "$_target_yaml")"
   else
-    log_info "AGENTS.md already exists, skipping creation"
+    _target_dir="${1:-$PWD}"
+    _target_dir="$(resolve_path "$_target_dir")"
+    _target_yaml="$_target_dir/$RNEX_CONFIG_FILE"
   fi
+  mkdir -p "$_target_dir"
 
-  # ---- Generate config file ------------------------------------------------
-  cat > "$_target_yaml" <<YAML_EOF
+  # ---- 1. Create config file if no one is existing for specified or current dir ----
+  _config_created=0
+  if [ -f "$_target_yaml" ]; then
+    log_warn "Workspace configuration already exists at $_target_dir ($RNEX_CONFIG_FILE exists)"
+    log_dim "To reconcile symlinks and plugins, run:"
+    log_dim "  rnex sync"
+  else
+    cat > "$_target_yaml" <<YAML_EOF
 # Repo Nexus workspace configuration
 # See docs/rnex.example.yaml for a comprehensive example with all options.
 
@@ -700,6 +761,26 @@ plugins:
 # Member repositories managed by Repo Nexus
 repos:
 YAML_EOF
+    _config_created=1
+    log_ok "Created $RNEX_CONFIG_FILE"
+  fi
+
+  # ---- 2. Merge rnex instructions with existing instructions if they exist --------
+  _target_agents="$_target_dir/AGENTS.md"
+  _existing_inst_found=0
+
+  for _cand in "AGENTS.md" "CLAUDE.md" ".cursorrules" ".github/copilot-instructions.md" "GEMINI.md" ".windsurfrules"; do
+    _c_path="$_target_dir/$_cand"
+    if [ -f "$_c_path" ]; then
+      _existing_inst_found=1
+      merge_rnex_instructions "$_c_path"
+    fi
+  done
+
+  # If AGENTS.md was not among existing files, ensure AGENTS.md is created
+  if [ ! -f "$_target_agents" ]; then
+    merge_rnex_instructions "$_target_agents"
+  fi
 
   # ---- Create repos directory -----------------------------------------------
   _repos_dir="$_target_dir/repos"
@@ -707,14 +788,18 @@ YAML_EOF
 
   # ---- Create internal .rnex directory --------------------------------------
   mkdir -p "$_target_dir/.rnex"
-
-  printf '\n'
-  log_ok "Initialized Repo Nexus workspace at ${_BOLD}$_target_dir${_NC}"
-  log_dim "Created $RNEX_CONFIG_FILE, AGENTS.md, .rnex/, and repos/"
-  printf '\n'
-  log_info "Next steps:"
-  log_dim "1. Add repositories with: rnex add <name> <path>"
-  log_dim "2. See docs/rnex.example.yaml for a full configuration reference"
+  mkdir -p "$_target_dir/.rnex/rules"
+  mkdir -p "$_target_dir/.rnex/instructions"
+
+  if [ "$_config_created" -eq 1 ]; then
+    printf '\n'
+    log_ok "Initialized Repo Nexus workspace at ${_BOLD}$_target_dir${_NC}"
+    log_dim "Created $RNEX_CONFIG_FILE, AGENTS.md, .rnex/, and repos/"
+    printf '\n'
+    log_info "Next steps:"
+    log_dim "1. Add repositories with: rnex add <name> <path>"
+    log_dim "2. See docs/rnex.example.yaml for a full configuration reference"
+  fi
 }
 
 cmd_add() {
@@ -1101,7 +1186,13 @@ cmd_plugin_disable() {
         if [ -L "$_rpath/.rnex/$_rel_sub" ]; then
           rm -f "$_rpath/.rnex/$_rel_sub"
         fi
+        rmdir "$_rpath/.rnex/instructions" 2>/dev/null || true
+        rmdir "$_rpath/.rnex/rules" 2>/dev/null || true
+        rmdir "$_rpath/.rnex/workflows" 2>/dev/null || true
       done
+      rmdir "$NEXUS_DIR/.rnex/instructions" 2>/dev/null || true
+      rmdir "$NEXUS_DIR/.rnex/rules" 2>/dev/null || true
+      rmdir "$NEXUS_DIR/.rnex/workflows" 2>/dev/null || true
     done
   fi
 

package/toolkit/plugins/karpathy-llm/README.md

@@ -42,15 +42,16 @@ Reference specification: [setup-karpathy-wiki.md](https://github.com/nu-nenoi/ai
 When an AI agent or developer sets up the Karpathy LLM Wiki in a repository or workspace, consult the Step 0 configuration questions:
 
 1. **[Q1] Which AI agent instruction file should the wiki rules be written to?**
-   - `AGENTS.md` (universal, works across most harnesses)
-   - `CLAUDE.md` (Claude Code / Anthropic)
-   - `.cursor/rules/wiki.mdc` (Cursor)
-   - `.github/copilot-instructions.md` (GitHub Copilot)
-   - `GEMINI.md` (Google Gemini / Antigravity)
-   - `.windsurfrules` (Windsurf)
-   - Other — specify path
-
-   *Append the `## Karpathy Wiki Rules` section to that file while preserving all existing content.*
+   - In a **Repo Nexus workspace**: Instructions are maintained in separate instructions files (`.rnex/instructions/karpathy-llm.md` and `.rnex/rules/KARPATHY_RULES.md`). Agents read `rnex.yaml` to detect enabled plugins and read their dedicated instructions files automatically.
+   - In a **standalone setup** (outside Repo Nexus):
+     - `AGENTS.md` (universal, works across most harnesses)
+     - `CLAUDE.md` (Claude Code / Anthropic)
+     - `.cursor/rules/wiki.mdc` (Cursor)
+     - `.github/copilot-instructions.md` (GitHub Copilot)
+     - `GEMINI.md` (Google Gemini / Antigravity)
+     - `.windsurfrules` (Windsurf)
+     - Other — specify path
+     *Append the `## Karpathy Wiki Rules` section to that file while preserving all existing content.*
 
 2. **[Q2] What is this wiki for?**
    - Research / reading list — articles, papers, PDFs on a topic
@@ -87,6 +88,8 @@ my-workspace/
 │   ├── hot.md                       # Rolling ~500-word quick-orient context
 │   └── _log.md                      # Ingestion & lint audit history
 ├── .rnex/
+│   ├── instructions/
+│   │   └── karpathy-llm.md          # Dedicated plugin instructions (auto-symlinked)
 │   ├── rules/
 │   │   └── KARPATHY_RULES.md        # Cardinal principles & wiki rules (auto-symlinked)
 │   ├── workflows/

package/toolkit/plugins/karpathy-llm/instructions/karpathy-llm.md

@@ -0,0 +1,85 @@
+# Karpathy LLM Agent Guidelines & Behavioral Principles
+
+> "The delicate art and science of context engineering: filling the context window with just the right information for the next step." — Andrej Karpathy
+
+These guidelines provide standing operational instructions for AI coding assistants (Cursor, Claude Code, GitHub Copilot, Antigravity, Windsurf) working within multi-repository environments and managing Karpathy LLM Wiki knowledge bases.
+
+---
+
+## 1. The Four Cardinal Principles
+
+### Principle 1: Think Before Coding
+* **State Assumptions Explicitly:** Before implementing any non-trivial change, state your understanding of the problem, assumptions made, and proposed solution.
+* **Surface Trade-Offs:** If multiple approaches exist, outline the alternatives with their trade-offs before generating code.
+* **Verify Repository Boundaries:** In multi-repo workspaces, determine which member repositories are affected. Never make silent architectural assumptions that span across repo boundaries.
+
+### Principle 2: Simplicity First
+* **Favor Readable Over Clever:** Write the simplest code that solves the immediate problem. Avoid unnecessary abstractions, speculative generics, and premature optimizations.
+* **Zero Boilerplate Bloat:** Do not introduce extra wrapper layers, helper classes, or framework-heavy patterns unless explicitly requested or required by existing codebase conventions.
+* **Less Code is Better Code:** If an existing utility, POSIX primitive, or library function does the job, reuse it.
+
+### Principle 3: Surgical Changes
+* **Minimal Blast Radius:** Touch *only* the lines and files required to achieve the goal.
+* **Preserve Documentation & Comments:** Never delete or overwrite existing comments, documentation, or code structure unrelated to your changes.
+* **Zero Unintended Reformatting:** Avoid running blanket code formatters across entire files that create massive, unreadable git diffs. Keep diffs tight, focused, and reviewable.
+
+### Principle 4: Goal-Driven Execution & Verification
+* **Define Success Criteria Upfront:** Know how you will prove that your change works before you write the first line of code.
+* **Verify with Automated Checks:** Run linters, unit tests, and build commands before declaring a task complete.
+* **Inspect the Diff:** Review your own git diff before committing or presenting the solution to ensure no extraneous changes were introduced.
+
+---
+
+## 2. Multi-Repo Context Engineering
+
+In a Repo Nexus workspace, independent repositories are unified into a single active scope via Unix symlinks. Coding agents must follow these rules:
+
+1. **Symlink Write-Through:**
+   - Edits made to `repos/<name>/` write directly through to the underlying member repository on disk.
+   - Do not attempt to move or replace symlinks with regular directories.
+
+2. **Repository Autonomy & Member .rnex Directory:**
+   - Member repositories are independent projects. Do not introduce cross-repository source imports or shared runtime dependencies unless an explicit monorepo architecture is configured.
+   - Member repositories may contain an `.rnex/` directory (e.g. `repos/<name>/.rnex/`) containing repository-specific documents, instructions, rules, workflows, and scripts. Coding assistants must inspect this directory for member-specific instructions.
+   - Run git operations (commits, branches, pushes) within the respective member repository root.
+
+3. **Context Economy:**
+   - Do not redundantly read entire files or directory trees when targeted symbol lookups or line ranges suffice.
+   - Rely on active workspace context, indexing, and compiled documentation rather than re-scanning raw files repeatedly.
+
+---
+
+## 3. Karpathy Wiki Rules
+
+When working in a repository with an active Karpathy LLM Wiki (`/wiki/` and `/raw/` directories):
+
+- **Intake**: All source material (articles, transcripts, docs, notes) goes to `/raw/` unmodified. Never write directly to `/wiki/` without ingesting.
+- **Orientation**: Before answering domain questions, read `/wiki/index.md` to find relevant pages, then read only those pages. If `hot.md` exists, read it first as a quick-orient step.
+- **Ingestion**: When files appear in `/raw/`, run the `wiki-ingest` workflow (`.rnex/workflows/wiki-ingest.md`). One source document typically produces many atomic pages (commonly 5–25 pages) — do not collapse a source into a single file.
+- **Cadence**: After any session where repository files were created, edited, or deleted, run `.rnex/scripts/wiki-lint-trigger.sh`. If it outputs `[WIKI MAINTENANCE DUE]`, run the `wiki-lint` workflow (`.rnex/workflows/wiki-lint.md`) before stopping.
+- **No-op sessions**: Do not run the trigger after read-only or purely conversational sessions where no files changed.
+- **Enable/disable**: Wiki automation is controlled by `lint_trigger_enabled: true|false` in `rnex.yaml` (and `lint_trigger: enabled|disabled` in `/wiki/index.md` frontmatter). Edit either field to toggle.
+
+---
+
+## 4. Typed Frontmatter Relation Schema
+
+Every page in `/wiki/` must maintain typed frontmatter relations:
+
+```yaml
+---
+title: ""
+tags: []
+last_updated: YYYY-MM-DD
+# Typed relation fields — paths relative to /wiki/
+sources: []          # /raw/ files this page was derived from
+related: []          # thematically related wiki pages
+extends: []          # pages this one builds upon or specialises
+contradicts: []      # pages with conflicting information
+mentioned_in: []     # pages that link to this one (maintained by lint)
+---
+```
+
+**Body:** concise summary, key facts or insights, and inline standard Markdown links (`[Label](./path.md)`) where contextually useful in prose.
+
+The relation graph lives in frontmatter, not in prose links. Agents traverse the graph by reading frontmatter fields, not by scanning body text.

package/toolkit/plugins/karpathy-llm/plugin.yaml

@@ -7,6 +7,8 @@ rules:
   - rules/KARPATHY_RULES.md: .rnex/rules/KARPATHY_RULES.md
   - workflows/wiki-ingest.md: .rnex/workflows/wiki-ingest.md
   - workflows/wiki-lint.md: .rnex/workflows/wiki-lint.md
+instructions:
+  - instructions/karpathy-llm.md: .rnex/instructions/karpathy-llm.md
 templates:
   - templates/index.md: wiki/index.md
   - templates/_log.md: wiki/_log.md

package/toolkit/prompts/setup-karpathy-wiki.md

@@ -17,15 +17,16 @@ Do not hard-code any specific AI tool or harness into the wiki structure itself.
 Ask ALL of the following questions and wait for answers:
 
 [Q1] Which AI agent instruction file should the wiki rules be written to?
-  - `AGENTS.md` (universal, works across most harnesses)
-  - `CLAUDE.md` (Claude Code / Anthropic)
-  - `.cursor/rules/wiki.mdc` (Cursor)
-  - `.github/copilot-instructions.md` (GitHub Copilot)
-  - `GEMINI.md` (Google Gemini / Antigravity)
-  - `.windsurfrules` (Windsurf)
-  - Other — specify path
-
-  Append a `## Karpathy Wiki Rules` section to that file. Preserve all existing content.
+  - In a Repo Nexus workspace: plugin instructions are maintained in separate instructions files (`.rnex/instructions/karpathy-llm.md` and `.rnex/rules/KARPATHY_RULES.md`). Agents read `rnex.yaml` to detect enabled plugins and read their separate instructions files.
+  - In a standalone setup (outside Repo Nexus):
+    - `AGENTS.md` (universal, works across most harnesses)
+    - `CLAUDE.md` (Claude Code / Anthropic)
+    - `.cursor/rules/wiki.mdc` (Cursor)
+    - `.github/copilot-instructions.md` (GitHub Copilot)
+    - `GEMINI.md` (Google Gemini / Antigravity)
+    - `.windsurfrules` (Windsurf)
+    - Other — specify path
+    Append a `## Karpathy Wiki Rules` section to that file. Preserve all existing content.
 
 [Q2] What is this wiki for?
   - Research / reading list — articles, papers, PDFs on a topic