repo-nexus 0.7.0 → 0.7.2

package/docs/plugins/index.md

@@ -109,7 +109,7 @@ plugins:
 
   # Functional / Knowledge Plugins
   karpathy-llm:
-    lint_trigger: git-post-merge
+    lint_trigger: manual
     notify_on_changes: true
 ```
 

package/docs/plugins/karpathy-llm.md

@@ -97,7 +97,7 @@ plugins:
 
     # Automated Git hook trigger for wiki verification
     # Options: git-post-merge, git-post-commit, git-pre-commit, git-pre-push, manual
-    lint_trigger: git-post-merge
+    lint_trigger: manual
 
     # Notify developer when changes are committed to ./docs/ or .rnex/wiki/
     notify_on_changes: true
@@ -110,7 +110,7 @@ plugins:
 |:---|:---|:---|:---|
 | `wiki_dir` | string | `.rnex/wiki` | Directory containing curated atomic markdown pages. |
 | `raw_dir` | string | `./docs` | Append-only directory for unmodified source intake documents. |
-| `lint_trigger` | string | `git-post-merge` | Git hook event that triggers wiki change detection (`git-post-merge`, `git-post-commit`, `git-pre-commit`, `git-pre-push`, `manual`). |
+| `lint_trigger` | string | `manual` | Git hook event that triggers wiki change detection (`git-post-merge`, `git-post-commit`, `git-pre-commit`, `git-pre-push`, `manual`). |
 | `notify_on_changes` | boolean | `true` | Show notification banner when changes are committed to `./docs/` or `.rnex/wiki/`. |
 | `enabled` | boolean | `true` | Enable or disable the plugin. Overridable in `.local.rnex.yaml`. |
 

package/docs/rnex.example.yaml

@@ -113,9 +113,9 @@ plugins:
   #   prompts: true        # mirror prompts to .windsurf/prompts/*.md (default: true)
   #   workflows: true      # mirror workflows as prompts (default: true)
   # karpathy-llm:
-  #   wiki_dir: .rnex/wiki        # Directory for curated atomic markdown pages (default: .rnex/wiki)
-  #   raw_dir: ./docs             # Append-only directory for unmodified intake documents (default: ./docs)
-  #   lint_trigger: git-post-merge # Git hook event: git-post-merge, git-post-commit, git-pre-commit, git-pre-push, manual
+  #   raw_dir: "./docs"           # Append-only directory for unmodified intake documents (default: ./docs)
+  #   wiki_dir: ".rnex/wiki"      # Directory for curated atomic markdown pages (default: .rnex/wiki)
+  #   lint_trigger: "manual"      # Runs manually via 'rnex sync' or validation checklists (git-post-merge, git-post-commit, git-pre-commit, git-pre-push, manual)
   #   notify_on_changes: true     # Show notification when changes are committed to ./docs or .rnex/wiki
 
 # ------------------------------------------------------------------------------

package/lib/commands/init.sh

@@ -15,6 +15,7 @@ cmd_init() {
   _cli_gemini=""
   _cli_cursor=""
   _cli_windsurf=""
+  _cli_karpathy=""
 
   while [ $# -gt 0 ]; do
     case "$1" in
@@ -31,6 +32,8 @@ cmd_init() {
       --no-cursor) _cli_cursor="false" ;;
       --windsurf) _cli_windsurf="true" ;;
       --no-windsurf) _cli_windsurf="false" ;;
+      --karpathy|--karpathy-llm) _cli_karpathy="true" ;;
+      --no-karpathy|--no-karpathy-llm) _cli_karpathy="false" ;;
       --ai|--instructions|--ai-instructions)
         shift
         # Legacy flag ignored in favor of plugins
@@ -116,6 +119,9 @@ cmd_init() {
     if [ "$_cli_windsurf" = "true" ]; then
       _init_plugins="${_init_plugins}  windsurf:\n    instructions: true\n    prompts: true\n    workflows: true\n"
     fi
+    if [ "$_cli_karpathy" = "true" ]; then
+      _init_plugins="${_init_plugins}  karpathy-llm:\n    raw_dir: \"./docs\"\n    wiki_dir: \".rnex/wiki\"\n    lint_trigger: \"manual\"\n"
+    fi
 
     cat > "$_target_yaml" <<YAML_EOF
 # Repo Nexus workspace configuration

package/lib/commands/plugin.sh

@@ -87,7 +87,7 @@ cmd_plugin_info() {
     printf '\n%bConfigurable Options (in rnex.yaml or .local.rnex.yaml):%b\n' "$_BOLD" "$_NC"
     printf '  - wiki_dir: <dir>  (directory for curated markdown pages; current: %s)\n' "$(karpathy_wiki_dir)"
     printf '  - raw_dir: <dir>   (directory for unmodified intake documents; current: %s)\n' "$(karpathy_raw_dir)"
-    printf '  - lint_trigger: git-post-merge|git-post-commit|git-pre-commit|git-pre-push|manual  (current: %s)\n' "${_cur_lt:-git-post-merge}"
+    printf '  - lint_trigger: git-post-merge|git-post-commit|git-pre-commit|git-pre-push|manual  (current: %s)\n' "${_cur_lt:-manual}"
     printf '  - notify_on_changes: true|false  (show notification when raw/wiki changes are committed; current: %s)\n' "${_cur_nc:-true}"
   fi
 

package/lib/commands/sync.sh

@@ -108,6 +108,9 @@ cmd_sync() {
     [ "$_sync_quiet" -eq 0 ] && log_ok "Upgraded workspace configuration and routing instructions to v$RNEX_VERSION"
   fi
 
+  # Dispatch before_sync plugin lifecycle hook
+  run_hook "before_sync" "$@"
+
   # 1. Ensure .gitignore ignores repos/, local configs; ensure .ignore has !repos/*
   reconcile_gitignore "$NEXUS_DIR"
 
@@ -184,6 +187,9 @@ cmd_sync() {
   # 10. Update sync stamp
   update_sync_stamp "$NEXUS_DIR"
 
+  # Dispatch after_sync plugin lifecycle hook
+  run_hook "after_sync" "$@"
+
   if [ "$_sync_quiet" -eq 0 ]; then
     log_ok "Sync complete — workspace, plugins, prompts, and member .rnex directories reconciled"
   fi

package/lib/yaml.sh

@@ -309,6 +309,22 @@ yaml_enable_plugin() {
           }
         ' "$_target_file" > "$_tmp" && mv "$_tmp" "$_target_file"
         ;;
+      karpathy-llm)
+        awk -v name="$_name" '
+          /^plugins:[ ]*$/ || /^plugins:[ ]*#/ {
+            print
+            printf "  %s:\n    raw_dir: \"./docs\"\n    wiki_dir: \".rnex/wiki\"\n    lint_trigger: \"manual\"\n", name
+            added=1
+            next
+          }
+          { print }
+          END {
+            if (!added) {
+              printf "plugins:\n  %s:\n    raw_dir: \"./docs\"\n    wiki_dir: \".rnex/wiki\"\n    lint_trigger: \"manual\"\n", name
+            }
+          }
+        ' "$_target_file" > "$_tmp" && mv "$_tmp" "$_target_file"
+        ;;
       *)
         awk -v name="$_name" '
           /^plugins:[ ]*$/ || /^plugins:[ ]*#/ {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.7.0",
+  "version": "0.7.2",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",
@@ -68,4 +68,4 @@
   "devDependencies": {
     "vitepress": "^1.6.0"
   }
-}
+}

package/templates/rnex.example.yaml

@@ -113,9 +113,9 @@ plugins:
   #   prompts: true        # mirror prompts to .windsurf/prompts/*.md (default: true)
   #   workflows: true      # mirror workflows as prompts (default: true)
   # karpathy-llm:
-  #   wiki_dir: .rnex/wiki        # Directory for curated atomic markdown pages (default: .rnex/wiki)
-  #   raw_dir: ./docs             # Append-only directory for unmodified intake documents (default: ./docs)
-  #   lint_trigger: git-post-merge # Git hook event: git-post-merge, git-post-commit, git-pre-commit, git-pre-push, manual
+  #   raw_dir: "./docs"           # Append-only directory for unmodified intake documents (default: ./docs)
+  #   wiki_dir: ".rnex/wiki"      # Directory for curated atomic markdown pages (default: .rnex/wiki)
+  #   lint_trigger: "manual"      # Runs manually via 'rnex sync' or validation checklists (git-post-merge, git-post-commit, git-pre-commit, git-pre-push, manual)
   #   notify_on_changes: true     # Show notification when changes are committed to ./docs or .rnex/wiki
 
 # ------------------------------------------------------------------------------

package/toolkit/plugins/karpathy-llm/hooks/after_sync.sh

@@ -1,8 +1,15 @@
 #!/bin/sh
 set -e
 
+# Exit early if rnex utilities aren't available 
+[ -z "$RNEX_ROOT" ] && { echo "Error: RNEX_ROOT not set"; exit 1; }
+
 # Resolve root workspace
-_root="${RNEX_ROOT:-$PWD}"
+_root="$RNEX_ROOT"
+
+# Target directory inside .rnex/ (the internal wiki's Raw intake state)
+WIKI_RAW_DIR="$RNEX_ROOT/.rnex/wiki/raw"
+mkdir -p "$WIKI_RAW_DIR"
 
 # Helper to read plugin config
 get_cfg() {
@@ -74,3 +81,73 @@ mkdir -p "$_pdir/templates"
 if [ -f "$_tmpl_dir/rnex-wiki-page.sample.md" ] && [ ! -f "$_pdir/templates/rnex-wiki-page.template.md" ]; then
   cp "$_tmpl_dir/rnex-wiki-page.sample.md" "$_pdir/templates/rnex-wiki-page.template.md"
 fi
+
+# 1. Parse 'raw_dir' configuration from rnex.yaml/.local.rnex.yaml (Defaults to './docs')
+# We check if parsed in RNEX_CONFIG_MERGED (YAML) using a standard grep/sed lookup
+RAW_DIR_VAL=$(grep -h -E '^\s*raw_dir:' "$RNEX_ROOT/rnex.yaml" "$RNEX_ROOT/.local.rnex.yaml" 2>/dev/null | tail -n1 | awk -F: '{print $NF}' | awk '{print $1}' | tr -d '"'\''')
+[ -z "$RAW_DIR_VAL" ] && RAW_DIR_VAL="$(get_cfg "raw_dir" "./docs")"
+RAW_DIR="${RAW_DIR_VAL:-./docs}"
+
+# Clear and sync custom local raw folder files to raw intake (skip if RAW_DIR is a documentation site)
+if [ -d "$RNEX_ROOT/$RAW_DIR" ] && [ ! -d "$RNEX_ROOT/$RAW_DIR/.vitepress" ]; then
+  _raw_abs="$(cd "$RNEX_ROOT/$RAW_DIR" 2>/dev/null && pwd -P || true)"
+  _wiki_raw_abs="$(cd "$WIKI_RAW_DIR" 2>/dev/null && pwd -P || true)"
+  if [ -n "$_raw_abs" ] && [ "$_raw_abs" != "$_wiki_raw_abs" ]; then
+    find "$RNEX_ROOT/$RAW_DIR" -type f \( -name "*.md" -o -name "*.txt" -o -name "*.json" \) 2>/dev/null | while read -r filepath; do
+      filename=$(basename "$filepath")
+      # Prevent overwriting standard operational files
+      if [ "$filename" != "index.md" ] && [ "$filename" != "hot.md" ] && [ "$filename" != "_log.md" ]; then
+        cp "$filepath" "$WIKI_RAW_DIR/$filename"
+      fi
+    done
+  fi
+fi
+
+# 2. Automatically sync README.md from all enabled/cloned member repositories
+# Get list of enabled repositories using a secure cross-repo read or `rnex list`
+REPOS_DIR_VAL=$(grep -h -E '^\s*repos_dir:' "$RNEX_ROOT/rnex.yaml" "$RNEX_ROOT/.local.rnex.yaml" 2>/dev/null | tail -n1 | awk -F: '{print $NF}' | awk '{print $1}' | tr -d '"'\''')
+REPOS_DIR="${REPOS_DIR_VAL:-./repos}"
+
+if [ -d "$RNEX_ROOT/$REPOS_DIR" ]; then
+  for repo_path in "$RNEX_ROOT/$REPOS_DIR"/*; do
+    [ ! -d "$repo_path" ] && continue
+    repo_name=$(basename "$repo_path")
+    
+    # Check if this repository is explicitly disabled in .local.rnex.yaml or rnex.yaml (block-scoped)
+    _is_disabled=""
+    for _cfg_file in "$RNEX_ROOT/.local.rnex.yaml" "$RNEX_ROOT/rnex.yaml"; do
+      [ -f "$_cfg_file" ] || continue
+      _en="$(awk -v repo="$repo_name" '
+        /^repos:[ ]*$/ || /^repos:[ ]*#/ { r=1; next }
+        r && /^[^ #]/ { r=0 }
+        r && match($0, "^  " repo ":[ ]*(#.*)?$") { in_target=1; next }
+        in_target && /^  [^ #]/ { in_target=0 }
+        in_target && match($0, "^    enabled:[ ]*") {
+          line = $0
+          sub("^    enabled:[ ]*", "", line)
+          sub(/[ ]*#.*$/, "", line)
+          gsub(/^["\x27]|["\x27]$/, "", line)
+          print line
+          exit
+        }
+      ' "$_cfg_file")"
+      if [ -n "$_en" ]; then
+        case "$(printf '%s' "$_en" | tr '[:upper:]' '[:lower:]')" in
+          false|no|0|disabled|off) _is_disabled=1 ;;
+          *) _is_disabled=0 ;;
+        esac
+        break
+      fi
+    done
+    [ "$_is_disabled" = "1" ] && continue
+
+    # Read and sync any README file with case-insensitive check
+    for readme_name in README.md readme.md README.markdown README; do
+      if [ -f "$repo_path/$readme_name" ]; then
+        # Namespace the copied file with its repo name to prevent conflicts
+        cp "$repo_path/$readme_name" "$WIKI_RAW_DIR/README_${repo_name}.md"
+        break
+      fi
+    done
+  done
+fi

package/toolkit/plugins/karpathy-llm/hooks/git_post-commit.sh

@@ -40,7 +40,7 @@ _raw="$(get_cfg "raw_dir" "./docs")"
 _wiki="$(printf '%s' "$_wiki" | sed -e 's#^/##' -e 's#/$##')"
 _raw="$(printf '%s' "$_raw" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
-_trigger="$(get_cfg "lint_trigger" "git-post-merge")"
+_trigger="$(get_cfg "lint_trigger" "manual")"
 if [ "$_trigger" = "git-post-commit" ] || [ "$_trigger" = "post-commit" ]; then
   if git -C "$_root" diff-tree -r --name-only HEAD 2>/dev/null | grep -qE "(^|/)($_raw|$_wiki)/"; then
     _notify="$(get_cfg "notify_on_changes" "true")"

package/toolkit/plugins/karpathy-llm/hooks/git_post-merge.sh

@@ -40,7 +40,7 @@ _raw="$(get_cfg "raw_dir" "./docs")"
 _wiki="$(printf '%s' "$_wiki" | sed -e 's#^/##' -e 's#/$##')"
 _raw="$(printf '%s' "$_raw" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
-_trigger="$(get_cfg "lint_trigger" "git-post-merge")"
+_trigger="$(get_cfg "lint_trigger" "manual")"
 if [ "$_trigger" = "git-post-merge" ] || [ "$_trigger" = "post-merge" ]; then
   if git -C "$_root" diff-tree -r --name-only ORIG_HEAD HEAD 2>/dev/null | grep -qE "(^|/)($_raw|$_wiki)/"; then
     _notify="$(get_cfg "notify_on_changes" "true")"

package/toolkit/plugins/karpathy-llm/hooks/git_pre-commit.sh

@@ -40,7 +40,7 @@ _raw="$(get_cfg "raw_dir" "./docs")"
 _wiki="$(printf '%s' "$_wiki" | sed -e 's#^/##' -e 's#/$##')"
 _raw="$(printf '%s' "$_raw" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
-_trigger="$(get_cfg "lint_trigger" "git-post-merge")"
+_trigger="$(get_cfg "lint_trigger" "manual")"
 if [ "$_trigger" = "git-pre-commit" ] || [ "$_trigger" = "pre-commit" ]; then
   if git -C "$_root" diff --cached --name-only 2>/dev/null | grep -qE "(^|/)($_raw|$_wiki)/"; then
     _notify="$(get_cfg "notify_on_changes" "true")"

package/toolkit/plugins/karpathy-llm/hooks/git_pre-push.sh

@@ -40,7 +40,7 @@ _raw="$(get_cfg "raw_dir" "./docs")"
 _wiki="$(printf '%s' "$_wiki" | sed -e 's#^/##' -e 's#/$##')"
 _raw="$(printf '%s' "$_raw" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
-_trigger="$(get_cfg "lint_trigger" "git-post-merge")"
+_trigger="$(get_cfg "lint_trigger" "manual")"
 if [ "$_trigger" = "git-pre-push" ] || [ "$_trigger" = "pre-push" ]; then
   _notify="$(get_cfg "notify_on_changes" "true")"
   if [ "$_notify" != "false" ]; then

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

@@ -1,17 +1,28 @@
 name: karpathy-llm
-version: 0.5.1
-description: Andrej Karpathy's agent behavioral principles, context engineering guidelines, and autonomous LLM Wiki knowledge architecture
+version: 1.0.0
+description: Andréj Karpathy's verification frameworks & wiki patterns for AI coding agents.
 author: unoxen
 homepage: https://github.com/unoxen/repo-nexus
+
+config_defaults:
+  raw_dir: "./docs"
+  wiki_dir: ".rnex/wiki"
+  lint_trigger: "manual" # Default changed to manual to avoid unsolicited background trigger tasks
+  notify_on_changes: true
+
 config:
-  wiki_dir: .rnex/wiki
-  raw_dir: ./docs
-  lint_trigger: git-post-merge
+  raw_dir: "./docs"
+  wiki_dir: ".rnex/wiki"
+  lint_trigger: "manual"
   notify_on_changes: true
+
 rules:
   - rules/rnex-behavioral.md: .rnex/plugins/karpathy-llm/rules/rnex-behavioral.md
+  - rules/behavioral.md: .rnex/plugins/karpathy-llm/rules/behavioral.md
   - workflows/rnex-wiki-ingest.md: .rnex/plugins/karpathy-llm/workflows/rnex-wiki-ingest.md
+  - workflows/wiki-ingest.md: .rnex/plugins/karpathy-llm/workflows/wiki-ingest.md
   - workflows/rnex-wiki-lint.md: .rnex/plugins/karpathy-llm/workflows/rnex-wiki-lint.md
+  - workflows/wiki-lint.md: .rnex/plugins/karpathy-llm/workflows/wiki-lint.md
 instructions:
   - instructions/rnex-wiki-architecture.md: .rnex/plugins/karpathy-llm/instructions/rnex-wiki-architecture.md
 templates:

package/toolkit/prompts/index.md

@@ -20,3 +20,4 @@ When an AI assistant is assigned a cross-repo or workspace-wide task, consult th
 4. **[`rnex-wiki-lint.md`](./rnex-wiki-lint.md)**
    - **Purpose**: Deterministic graph audit, dead link validation, `mentioned_in` backlink reconciliation, and index rebuild.
    - **When to use**: Routine wiki maintenance, pre-commit validation, or after adding/renaming wiki pages.
+

package/toolkit/prompts/rnex-cross-repo-feature.md

@@ -1,35 +1,16 @@
-# Cross-Repository Feature Implementation Workflow
+# Operational Task: Cross-Repository Feature Implementation
 
-Use this prompt to guide the planning, execution, and verification of features spanning multiple member repositories in a Repo Nexus workspace.
+You are tasked with planning, coordinating, and executing a feature spanning multiple member repositories in this Repo Nexus workspace.
 
----
+## Context & Inputs
+- Target Scope: `repos/<name>/` directory trees
+- Workspace Manifest: `rnex.yaml` and `.local.rnex.yaml`
+- AI Instructions: `.rnex/ai-instructions.md`
 
-## 1. Discovery & Scope Analysis
-1. Inspect `.local.rnex.yaml` (if present) and `rnex.yaml` to identify active member repositories in `repos/<name>/`.
-2. Inspect `repos/<name>/.rnex/` in each target repository for repo-specific architectural rules or constraints.
-3. If `wiki/` is present, read `wiki/hot.md` and `wiki/index.md` to orient on existing domain contracts and data models.
-4. Clearly define the interface contract or boundary change between repositories (e.g. API payload, shared type definitions, database schema).
+## Skill & Workflow Router
+1. Read the operational skill requirements in `.rnex/skills/rnex-cross-repo-feature/SKILL.md`.
+2. Follow the staged execution protocol strictly in `.rnex/workflows/rnex-cross-repo-feature.md`.
+3. Adhere to mandatory session startup, routing protocols, and member repo boundary rules in `.rnex/ai-instructions.md`.
+4. Do NOT execute uncompiled heuristics or perform unguided exploratory codebase scans.
 
-## 2. Staged Implementation Plan
-1. Order repository changes by dependency hierarchy (e.g. backend / shared models first, frontend / consumers second).
-2. For each member repository:
-   - Identify specific files to modify.
-   - Check member repo test suite requirements.
-
-## 3. Execution
-1. Perform file modifications directly in the target `repos/<name>/` directory trees.
-2. Maintain documentation and type integrity across boundary contracts.
-3. Verify changes locally within each modified repository using `rnex exec` or targeted test runners:
-   ```sh
-   rnex exec npm test
-   # or targeted:
-   cd repos/<name> && npm test
-   ```
-
-## 4. Git & Commit Hygiene
-1. Member repositories are autonomous Git repositories:
-   - Commit changes independently within each member repository root:
-     ```sh
-     cd repos/<name> && git add -A && git commit -m "feat: <description>"
-     ```
-   - Never commit member repository source code directly to the Repo Nexus workspace root.
+Execute the referenced workflow across affected member repositories. Maintain boundary contracts, run targeted test suites, and commit changes independently within each member repository root.

package/toolkit/prompts/rnex-wiki-ingest.md

@@ -0,0 +1,18 @@
+# Operational Task: Karpathy LLM Wiki Ingestion
+
+You are tasked with executing the knowledge ingestion and atomic decomposition workflow for the Karpathy LLM Wiki.
+
+## Context & Inputs
+- Target Scope: Curated wiki directory (`wiki_dir`, default: `.rnex/wiki/`)
+- Intake Sources: Configured raw intake directory (`raw_dir`, default: `./docs`) and synchronized member repository READMEs
+- Workspace Manifest: `rnex.yaml` and `.local.rnex.yaml`
+- AI Instructions: `.rnex/ai-instructions.md`
+
+## Skill & Workflow Router
+1. Read the operational skill requirements in `.rnex/plugins/karpathy-llm/skills/rnex-wiki-ingest/SKILL.md`.
+2. Follow the atomic decomposition and ingestion protocol strictly in `.rnex/plugins/karpathy-llm/workflows/rnex-wiki-ingest.md`.
+3. Follow architectural and behavioral constraints in `.rnex/plugins/karpathy-llm/rules/rnex-behavioral.md`.
+4. Adhere to mandatory session startup, routing protocols, and global rules in `.rnex/ai-instructions.md`.
+5. Do NOT invent new frontmatter schemas, skip atomic decomposition, or alter source materials directly.
+
+Decompose intake documents into atomic, interlinked wiki pages with typed frontmatter relations. Update the master index and append a timestamped entry to the operation log.

package/toolkit/prompts/rnex-wiki-lint.md

@@ -0,0 +1,17 @@
+# Operational Task: Karpathy LLM Wiki Lint & Graph Audit
+
+You are tasked with auditing graph integrity, validating bidirectional relations, and repairing links for the Karpathy LLM Wiki.
+
+## Context & Inputs
+- Target Scope: Curated wiki directory (`wiki_dir`, default: `.rnex/wiki/`)
+- Workspace Manifest: `rnex.yaml` and `.local.rnex.yaml`
+- AI Instructions: `.rnex/ai-instructions.md`
+
+## Skill & Workflow Router
+1. Read the operational skill requirements in `.rnex/plugins/karpathy-llm/skills/rnex-wiki-lint/SKILL.md`.
+2. Follow the multi-step audit and graph reconciliation protocol in `.rnex/plugins/karpathy-llm/workflows/rnex-wiki-lint.md`.
+3. Follow architectural and behavioral constraints in `.rnex/plugins/karpathy-llm/rules/rnex-behavioral.md`.
+4. Adhere to mandatory session startup, routing protocols, and global rules in `.rnex/ai-instructions.md`.
+5. Do NOT invent new lint checks or execute uncompiled heuristic instructions.
+
+Execute the referenced lint workflow across all wiki pages. Validate frontmatter relation filepaths, recompute `mentioned_in` backlinks, identify orphan pages, reconcile the master index, and record findings in the operation log.

package/toolkit/prompts/rnex-workspace-audit.md

@@ -1,34 +1,16 @@
-# Repo Nexus Workspace Audit Workflow
+# Operational Task: Workspace Configuration & Health Audit
 
-Use this prompt to audit workspace configuration integrity, member repository git statuses, and active plugin states.
+You are tasked with executing a comprehensive audit of the Repo Nexus workspace configuration, member repository git statuses, and active plugin states.
 
----
+## Context & Inputs
+- Target Scope: Root workspace configuration, `.rnex/`, and active member repositories in `repos/<name>/`
+- Workspace Manifest: `rnex.yaml` and `.local.rnex.yaml`
+- AI Instructions: `.rnex/ai-instructions.md`
 
-## 1. Configuration & Health Audit
-1. Run `rnex status` to inspect:
-   - Configuration files (`rnex.yaml` and `.local.rnex.yaml`).
-   - Main AI instructions file existence and routing markers.
-   - VS Code / Cursor `.code-workspace` synchronization.
-   - Git ignore status for `repos/`, `.rnex/`, and local overrides.
-   - Active plugins and member repository registry.
+## Skill & Workflow Router
+1. Read the operational skill requirements in `.rnex/skills/rnex-workspace-audit/SKILL.md`.
+2. Follow the multi-step audit and remediation protocol in `.rnex/workflows/rnex-workspace-audit.md`.
+3. Adhere to mandatory session startup, routing protocols, and member repo boundary rules in `.rnex/ai-instructions.md`.
+4. Do NOT execute uncompiled heuristics or alter workspace configuration outside the referenced workflow.
 
-## 2. Multi-Repository Git Status Audit
-1. Check working tree cleanliness across all active member repositories:
-   ```sh
-   rnex exec git status -s
-   ```
-2. Check branch tracking and unpushed/unpulled commits:
-   ```sh
-   rnex exec git status -uno
-   ```
-3. Report any detached HEADs, uncommitted modifications, or untracked changes.
-
-## 3. Reconciliation & Remediation
-1. If any configuration issues, missing directories, or unlinked plugin assets are detected, run:
-   ```sh
-   rnex status --fix
-   ```
-2. If member repositories declared in `rnex.yaml` are missing on disk, run:
-   ```sh
-   rnex clone
-   ```
+Execute the audit according to the referenced workflow and report configuration integrity, working tree cleanliness, and active plugin health.