repo-nexus 0.7.8 → 0.7.11

package/docs/plugins/claude.md

@@ -7,7 +7,7 @@ description: Integrate Anthropic Claude Code with Repo Nexus, generating zero-lo
 
 The **`claude`** plugin integrates Anthropic Claude Code CLI (`claude`) and Claude Desktop into a Repo Nexus Virtual Meta-Repo.
 
-All AI assistants in Repo Nexus share [`AGENTS.md`](file:///Users/admin/Projects/ai/repo-nexus/AGENTS.md) at the workspace root as the single universal source of truth for routing. When enabled, the `claude` plugin generates zero-logic User Skill pointers into `.claude/skills/` (e.g. `rnex-clone-sync.md`, `rnex-batch-exec.md`, `rnex-wiki-ingest.md`).
+All AI assistants in Repo Nexus share [`AGENTS.md`](file:///Users/admin/Projects/ai/repo-nexus/AGENTS.md) at the workspace root as the single universal source of truth for routing. When enabled, the `claude` plugin generates zero-logic User Skill pointers into `.claude/skills/` (e.g. `rnex-clone-sync.md`, `rnex-batch-exec.md`, `rnex-karpathy-llm-wiki-ingest`).
 
 Operational skills, rules, and subagents remain cleanly encapsulated within `.rnex/skills/` and active plugin directories (`.rnex/plugins/<plugin-name>/`).
 
@@ -84,8 +84,8 @@ my-workspace/
 │       ├── rnex-clone-sync.md
 │       ├── rnex-batch-exec.md
 │       ├── rnex-workspace-status.md
-│       ├── rnex-wiki-ingest.md
-│       └── rnex-wiki-lint.md
+│       ├── rnex-karpathy-llm-wiki-ingest/
+│       └── rnex-karpathy-llm-wiki-lint/
 ├── .rnex/
 │   ├── skills/                        # Core workspace agentic skills
 │   └── plugins/

package/docs/plugins/cursor.md

@@ -83,8 +83,8 @@ my-workspace/
 │       ├── rnex-clone-sync.md
 │       ├── rnex-batch-exec.md
 │       ├── rnex-workspace-status.md
-│       ├── rnex-wiki-ingest.md
-│       └── rnex-wiki-lint.md
+│       ├── rnex-karpathy-llm-wiki-ingest.md
+│       └── rnex-karpathy-llm-wiki-lint.md
 ├── .rnex/
 │   ├── skills/                        # Core workspace agentic skills
 │   └── plugins/

package/docs/plugins/gemini.md

@@ -7,7 +7,7 @@ description: Integrate Google Gemini and Antigravity IDE with Repo Nexus, genera
 
 The **`gemini`** plugin integrates Google Gemini CLI and Google Antigravity IDE into a Repo Nexus Virtual Meta-Repo.
 
-All AI assistants in Repo Nexus share [`AGENTS.md`](file:///Users/admin/Projects/ai/repo-nexus/AGENTS.md) at the workspace root as the single universal source of truth for routing. When enabled, the `gemini` plugin generates zero-logic User Skill pointers into `.gemini/skills/` (e.g. `rnex-clone-sync.md`, `rnex-batch-exec.md`, `rnex-wiki-ingest.md`).
+All AI assistants in Repo Nexus share [`AGENTS.md`](file:///Users/admin/Projects/ai/repo-nexus/AGENTS.md) at the workspace root as the single universal source of truth for routing. When enabled, the `gemini` plugin generates zero-logic User Skill pointers into `.gemini/skills/` (e.g. `rnex-clone-sync.md`, `rnex-batch-exec.md`, `rnex-karpathy-llm-wiki-ingest`).
 
 Operational skills, rules, and subagents remain cleanly encapsulated within `.rnex/skills/` and active plugin directories (`.rnex/plugins/<plugin-name>/`).
 
@@ -83,8 +83,8 @@ my-workspace/
 │       ├── rnex-clone-sync.md
 │       ├── rnex-batch-exec.md
 │       ├── rnex-workspace-status.md
-│       ├── rnex-wiki-ingest.md
-│       └── rnex-wiki-lint.md
+│       ├── rnex-karpathy-llm-wiki-ingest/
+│       └── rnex-karpathy-llm-wiki-lint/
 ├── .rnex/
 │   ├── skills/                        # Core workspace agentic skills
 │   └── plugins/

package/docs/plugins/karpathy-llm.md

@@ -169,7 +169,7 @@ The `karpathy-llm` plugin encapsulates its agentic skills in `.rnex/plugins/karp
 - `wiki-ingest.md`
 - `wiki-lint.md`
 
-During `rnex sync`, its `after_sync.sh` lifecycle hook automatically registers zero-logic User Skill pointers (`rnex-wiki-ingest.md` and `rnex-wiki-lint.md`) across all enabled AI provider directories (`.cursor/rules/`, `.claude/skills/`, `.gemini/skills/`, `.windsurf/rules/`).
+During `rnex sync`, its `after_sync.sh` lifecycle hook automatically registers zero-logic User Skill pointers (`rnex-karpathy-llm-wiki-ingest` and `rnex-karpathy-llm-wiki-lint`) across all enabled AI provider directories (`.cursor/rules/`, `.claude/skills/`, `.gemini/skills/`, `.windsurf/rules/`).
 
 When running `rnex plugin disable karpathy-llm`, its `before_plugin_disable.sh` lifecycle hook automatically unregisters the User Skills from all provider directories, while keeping core workspace skills intact.
 

package/docs/plugins/windsurf.md

@@ -7,7 +7,7 @@ description: Integrate Windsurf IDE and Cascade with Repo Nexus, generating zero
 
 The **`windsurf`** plugin integrates Codeium's Windsurf IDE and Cascade into a Repo Nexus Virtual Meta-Repo.
 
-All AI assistants in Repo Nexus share [`AGENTS.md`](file:///Users/admin/Projects/ai/repo-nexus/AGENTS.md) at the workspace root as the single universal source of truth for routing. When enabled, the `windsurf` plugin generates zero-logic User Skill pointers into `.windsurf/rules/` (e.g. `rnex-clone-sync.md`, `rnex-batch-exec.md`, `rnex-wiki-ingest.md`).
+All AI assistants in Repo Nexus share [`AGENTS.md`](file:///Users/admin/Projects/ai/repo-nexus/AGENTS.md) at the workspace root as the single universal source of truth for routing. When enabled, the `windsurf` plugin generates zero-logic User Skill pointers into `.windsurf/rules/` (e.g. `rnex-clone-sync.md`, `rnex-batch-exec.md`, `rnex-karpathy-llm-wiki-ingest.md`).
 
 Operational skills, rules, and subagents remain cleanly encapsulated within `.rnex/skills/` and active plugin directories (`.rnex/plugins/<plugin-name>/`).
 
@@ -83,8 +83,8 @@ my-workspace/
 │       ├── rnex-clone-sync.md
 │       ├── rnex-batch-exec.md
 │       ├── rnex-workspace-status.md
-│       ├── rnex-wiki-ingest.md
-│       └── rnex-wiki-lint.md
+│       ├── rnex-karpathy-llm-wiki-ingest.md
+│       └── rnex-karpathy-llm-wiki-lint.md
 ├── .rnex/
 │   ├── skills/                        # Core workspace agentic skills
 │   └── plugins/

package/docs/rnex.example.yaml

@@ -107,6 +107,8 @@ plugins:
   #   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
+  #   ingest_member_readmes: true # Automatically ingest member repository READMEs into atomic wiki pages (default: true)
+
 
 # ------------------------------------------------------------------------------
 # repos — Member repositories managed by Repo Nexus

package/lib/ai.sh

@@ -367,9 +367,16 @@ if [ -z "$RNEX_PROVIDER_SKILL_DIRS" ]; then
   export RNEX_PROVIDER_SKILL_DIRS="$_dirs"
 fi
 
-rnex_register_user_skill() {
+rnex_generate_user_skill() {
   skill_name="$1"
   target_path="$2"
+  plugin_name="${3:-}"
+
+  if [ -n "$plugin_name" ]; then
+    full_name="rnex-${plugin_name}-${skill_name}"
+  else
+    full_name="rnex-${skill_name}"
+  fi
   _dirs="${RNEX_PROVIDER_SKILL_DIRS:-}"
   _r="${RNEX_ROOT:-.}"
 
@@ -385,7 +392,7 @@ rnex_register_user_skill() {
     _skill_desc="$(awk 'NF && !/^#/ { print; exit }' "$_target_file" 2>/dev/null)"
   fi
   if [ -z "$_skill_desc" ]; then
-    _skill_desc="Repo Nexus agentic skill protocol for ${skill_name}."
+    _skill_desc="Repo Nexus agentic skill protocol for ${full_name}."
   fi
   _skill_desc="$(printf '%s' "$_skill_desc" | tr '\n\r' '  ' | sed 's/^[[:space:]]*//;s/[[:space:]]*$//;s/"/\\"/g')"
 
@@ -393,24 +400,24 @@ rnex_register_user_skill() {
     case "$provider_dir" in
       *rules*)
         mkdir -p "$_r/$provider_dir"
-        rm -rf "$_r/$provider_dir/rnex-${skill_name}" 2>/dev/null || true
-        cat << EOF > "$_r/$provider_dir/rnex-${skill_name}.md"
-# User Skill: rnex-${skill_name}
+        rm -rf "${_r:?}/${provider_dir:?}/${full_name:?}" 2>/dev/null || true
+        cat << EOF > "$_r/$provider_dir/${full_name}.md"
+# User Skill: ${full_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
 EOF
         ;;
       *)
-        mkdir -p "$_r/$provider_dir/rnex-${skill_name}"
-        rm -f "$_r/$provider_dir/rnex-${skill_name}.md" 2>/dev/null || true
-        cat << EOF > "$_r/$provider_dir/rnex-${skill_name}/SKILL.md"
+        mkdir -p "$_r/$provider_dir/${full_name}"
+        rm -f "$_r/$provider_dir/${full_name}.md" 2>/dev/null || true
+        cat << EOF > "$_r/$provider_dir/${full_name}/SKILL.md"
 ---
-name: rnex-${skill_name}
+name: ${full_name}
 description: "${_skill_desc}"
 ---
 
-# User Skill: rnex-${skill_name}
+# User Skill: ${full_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
@@ -420,13 +427,30 @@ EOF
   done
 }
 
+rnex_register_user_skill() {
+  rnex_generate_user_skill "$@"
+}
+
 rnex_unregister_user_skill() {
   skill_name="$1"
+  plugin_name="${2:-}"
+  if [ -n "$plugin_name" ]; then
+    full_name="rnex-${plugin_name}-${skill_name}"
+  else
+    case "$skill_name" in
+      rnex-*) full_name="$skill_name" ;;
+      *)      full_name="rnex-${skill_name}" ;;
+    esac
+  fi
   _dirs="${RNEX_PROVIDER_SKILL_DIRS:-}"
   _r="${RNEX_ROOT:-.}"
   for provider_dir in $_dirs; do
-    rm -f "$_r/$provider_dir/rnex-${skill_name}.md"
-    rm -rf "$_r/$provider_dir/rnex-${skill_name}"
+    rm -f "$_r/$provider_dir/${full_name}.md"
+    rm -rf "${_r:?}/${provider_dir:?}/${full_name:?}"
+    if [ -n "$plugin_name" ]; then
+      rm -f "$_r/$provider_dir/rnex-${skill_name}.md"
+      rm -rf "${_r:?}/${provider_dir:?}/rnex-${skill_name:?}"
+    fi
   done
 }
 ENV_EOF
@@ -453,10 +477,18 @@ get_active_provider_skill_dirs() {
   printf '%s' "$_dirs"
 }
 
-# Usage: rnex_register_user_skill <skill_name> <target_path_in_rnex>
-rnex_register_user_skill() {
+# Usage: rnex_generate_user_skill <skill_name> <target_path_in_rnex> [plugin_name]
+rnex_generate_user_skill() {
   skill_name="$1"
   target_path="$2"
+  plugin_name="${3:-}"
+
+  if [ -n "$plugin_name" ]; then
+    full_name="rnex-${plugin_name}-${skill_name}"
+  else
+    full_name="rnex-${skill_name}"
+  fi
+
   _dirs="${RNEX_PROVIDER_SKILL_DIRS:-$(get_active_provider_skill_dirs)}"
   _r="${NEXUS_DIR:-${RNEX_ROOT:-.}}"
 
@@ -472,7 +504,7 @@ rnex_register_user_skill() {
     _skill_desc="$(awk 'NF && !/^#/ { print; exit }' "$_target_file" 2>/dev/null)"
   fi
   if [ -z "$_skill_desc" ]; then
-    _skill_desc="Repo Nexus agentic skill protocol for ${skill_name}."
+    _skill_desc="Repo Nexus agentic skill protocol for ${full_name}."
   fi
   _skill_desc="$(printf '%s' "$_skill_desc" | tr '\n\r' '  ' | sed 's/^[[:space:]]*//;s/[[:space:]]*$//;s/"/\\"/g')"
 
@@ -480,24 +512,24 @@ rnex_register_user_skill() {
     case "$provider_dir" in
       *rules*)
         mkdir -p "$_r/$provider_dir"
-        rm -rf "$_r/$provider_dir/rnex-${skill_name}" 2>/dev/null || true
-        cat << EOF > "$_r/$provider_dir/rnex-${skill_name}.md"
-# User Skill: rnex-${skill_name}
+        rm -rf "${_r:?}/${provider_dir:?}/${full_name:?}" 2>/dev/null || true
+        cat << EOF > "$_r/$provider_dir/${full_name}.md"
+# User Skill: ${full_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
 EOF
         ;;
       *)
-        mkdir -p "$_r/$provider_dir/rnex-${skill_name}"
-        rm -f "$_r/$provider_dir/rnex-${skill_name}.md" 2>/dev/null || true
-        cat << EOF > "$_r/$provider_dir/rnex-${skill_name}/SKILL.md"
+        mkdir -p "$_r/$provider_dir/${full_name}"
+        rm -f "$_r/$provider_dir/${full_name}.md" 2>/dev/null || true
+        cat << EOF > "$_r/$provider_dir/${full_name}/SKILL.md"
 ---
-name: rnex-${skill_name}
+name: ${full_name}
 description: "${_skill_desc}"
 ---
 
-# User Skill: rnex-${skill_name}
+# User Skill: ${full_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
@@ -507,14 +539,33 @@ EOF
   done
 }
 
-# Usage: rnex_unregister_user_skill <skill_name>
+# Usage: rnex_register_user_skill <skill_name> <target_path_in_rnex> [plugin_name]
+rnex_register_user_skill() {
+  rnex_generate_user_skill "$@"
+}
+
+# Usage: rnex_unregister_user_skill <skill_name> [plugin_name]
 rnex_unregister_user_skill() {
   skill_name="$1"
+  plugin_name="${2:-}"
+  if [ -n "$plugin_name" ]; then
+    full_name="rnex-${plugin_name}-${skill_name}"
+  else
+    case "$skill_name" in
+      rnex-*) full_name="$skill_name" ;;
+      *)      full_name="rnex-${skill_name}" ;;
+    esac
+  fi
+
   _dirs="${RNEX_PROVIDER_SKILL_DIRS:-$(get_active_provider_skill_dirs)}"
   _r="${NEXUS_DIR:-${RNEX_ROOT:-.}}"
   for provider_dir in $_dirs; do
-    rm -f "$_r/$provider_dir/rnex-${skill_name}.md"
-    rm -rf "$_r/$provider_dir/rnex-${skill_name}"
+    rm -f "$_r/$provider_dir/${full_name}.md"
+    rm -rf "${_r:?}/${provider_dir:?}/${full_name:?}"
+    if [ -n "$plugin_name" ]; then
+      rm -f "$_r/$provider_dir/rnex-${skill_name}.md"
+      rm -rf "${_r:?}/${provider_dir:?}/rnex-${skill_name:?}"
+    fi
   done
 }
 
@@ -536,10 +587,12 @@ clean_provider_skills() {
 clean_plugin_user_skills() {
   _pdir="$1"
   [ -d "$_pdir" ] || return 0
+  _pname="$(basename "$_pdir")"
   if [ -d "$_pdir/skills" ]; then
     for _sk_file in "$_pdir/skills"/*.md; do
       [ -f "$_sk_file" ] || continue
       _sk_name="$(basename "$_sk_file" .md)"
+      rnex_unregister_user_skill "$_sk_name" "$_pname"
       rnex_unregister_user_skill "$_sk_name"
     done
   fi
@@ -634,6 +687,12 @@ sync_rnex_base_assets() {
   rm -f "$NEXUS_DIR/.rnex/skills/wiki-ingest.md" "$NEXUS_DIR/.rnex/skills/wiki-lint.md" \
         "$NEXUS_DIR/.rnex/skills/rnex-wiki-ingest.md" "$NEXUS_DIR/.rnex/skills/rnex-wiki-lint.md" 2>/dev/null || true
 
+  # Purge stale unprefixed wiki user skills across provider directories
+  for _p_dir in $(get_active_provider_skill_dirs 2>/dev/null || true); do
+    rm -f "$NEXUS_DIR/$_p_dir/rnex-wiki-ingest.md" "$NEXUS_DIR/$_p_dir/rnex-wiki-lint.md" 2>/dev/null || true
+    rm -rf "$NEXUS_DIR/$_p_dir/rnex-wiki-ingest" "$NEXUS_DIR/$_p_dir/rnex-wiki-lint" 2>/dev/null || true
+  done
+
   # Register core User Skills across active provider directories
   for _sk_file in "$NEXUS_DIR/.rnex/skills"/*.md; do
     [ -f "$_sk_file" ] || continue

package/lib/commands/init.sh

@@ -119,7 +119,7 @@ cmd_init() {
       _init_plugins="${_init_plugins}  windsurf:\n    instructions: true\n    skills: true\n"
     fi
     if [ "$_cli_karpathy" = "true" ]; then
-      _init_plugins="${_init_plugins}  karpathy-llm:\n    raw_dir: \"./docs\"\n    wiki_dir: \".rnex/wiki\"\n    lint_trigger: \"manual\"\n"
+      _init_plugins="${_init_plugins}  karpathy-llm:\n    raw_dir: \"./docs\"\n    wiki_dir: \".rnex/wiki\"\n    lint_trigger: \"manual\"\n    ingest_member_readmes: true\n"
     fi
 
     cat > "$_target_yaml" <<YAML_EOF

package/lib/commands/plugin.sh

@@ -83,11 +83,13 @@ cmd_plugin_info() {
   if [ "$_name" = "karpathy-llm" ]; then
     _cur_lt="$(yaml_plugin_get "karpathy-llm" "lint_trigger" 2>/dev/null || true)"
     _cur_nc="$(yaml_plugin_get "karpathy-llm" "notify_on_changes" 2>/dev/null || true)"
+    _cur_imr="$(yaml_plugin_get "karpathy-llm" "ingest_member_readmes" 2>/dev/null || true)"
     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' "${_cur_lt:-manual}"
     printf '  - notify_on_changes: true|false  (show notification when raw/wiki changes are committed; current: %s)\n' "${_cur_nc:-true}"
+    printf '  - ingest_member_readmes: true|false  (automatically track member repository READMEs in wiki; current: %s)\n' "${_cur_imr:-true}"
   fi
 
   printf '\n%bScoped Directory:%b .rnex/plugins/%s\n' "$_BOLD" "$_NC" "$_name"

package/lib/hooks.sh

@@ -59,9 +59,16 @@ run_hook() {
         RNEX_PROVIDER_SKILL_DIRS="$_skill_dirs"
         export RNEX_ROOT RNEX_CONFIG_MERGED RNEX_PLUGIN_DIR RNEX_CMD RNEX_ARGS RNEX_QUIET RNEX_PROVIDER_SKILL_DIRS
         # shellcheck disable=SC2329
-        rnex_register_user_skill() {
+        rnex_generate_user_skill() {
           skill_name="$1"
           target_path="$2"
+          plugin_name="${3:-}"
+
+          if [ -n "$plugin_name" ]; then
+            full_name="rnex-${plugin_name}-${skill_name}"
+          else
+            full_name="rnex-${skill_name}"
+          fi
           _target_file=""
           if [ -f "$RNEX_ROOT/$target_path" ]; then
             _target_file="$RNEX_ROOT/$target_path"
@@ -73,7 +80,7 @@ run_hook() {
             _skill_desc="$(awk 'NF && !/^#/ { print; exit }' "$_target_file" 2>/dev/null)"
           fi
           if [ -z "$_skill_desc" ]; then
-            _skill_desc="Repo Nexus agentic skill protocol for ${skill_name}."
+            _skill_desc="Repo Nexus agentic skill protocol for ${full_name}."
           fi
           _skill_desc="$(printf '%s' "$_skill_desc" | tr '\n\r' '  ' | sed 's/^[[:space:]]*//;s/[[:space:]]*$//;s/"/\\"/g')"
 
@@ -81,24 +88,24 @@ run_hook() {
             case "$provider_dir" in
               *rules*)
                 mkdir -p "$RNEX_ROOT/$provider_dir"
-                rm -rf "$RNEX_ROOT/$provider_dir/rnex-${skill_name}" 2>/dev/null || true
-                cat << EOF > "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md"
-# User Skill: rnex-${skill_name}
+                rm -rf "${RNEX_ROOT:?}/${provider_dir:?}/${full_name:?}" 2>/dev/null || true
+                cat << EOF > "$RNEX_ROOT/$provider_dir/${full_name}.md"
+# User Skill: ${full_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
 EOF
                 ;;
               *)
-                mkdir -p "$RNEX_ROOT/$provider_dir/rnex-${skill_name}"
-                rm -f "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md" 2>/dev/null || true
-                cat << EOF > "$RNEX_ROOT/$provider_dir/rnex-${skill_name}/SKILL.md"
+                mkdir -p "$RNEX_ROOT/$provider_dir/${full_name}"
+                rm -f "$RNEX_ROOT/$provider_dir/${full_name}.md" 2>/dev/null || true
+                cat << EOF > "$RNEX_ROOT/$provider_dir/${full_name}/SKILL.md"
 ---
-name: rnex-${skill_name}
+name: ${full_name}
 description: "${_skill_desc}"
 ---
 
-# User Skill: rnex-${skill_name}
+# User Skill: ${full_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
@@ -108,12 +115,30 @@ EOF
           done
         }
 
+        # shellcheck disable=SC2329
+        rnex_register_user_skill() {
+          rnex_generate_user_skill "$@"
+        }
+
         # shellcheck disable=SC2329
         rnex_unregister_user_skill() {
           skill_name="$1"
+          plugin_name="${2:-}"
+          if [ -n "$plugin_name" ]; then
+            full_name="rnex-${plugin_name}-${skill_name}"
+          else
+            case "$skill_name" in
+              rnex-*) full_name="$skill_name" ;;
+              *)      full_name="rnex-${skill_name}" ;;
+            esac
+          fi
           for provider_dir in $RNEX_PROVIDER_SKILL_DIRS; do
-            rm -f "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md"
-            rm -rf "$RNEX_ROOT/$provider_dir/rnex-${skill_name}"
+            rm -f "$RNEX_ROOT/$provider_dir/${full_name}.md"
+            rm -rf "${RNEX_ROOT:?}/${provider_dir:?}/${full_name:?}"
+            if [ -n "$plugin_name" ]; then
+              rm -f "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md"
+              rm -rf "${RNEX_ROOT:?}/${provider_dir:?}/rnex-${skill_name:?}"
+            fi
           done
         }
         set -- "$@"
@@ -174,9 +199,16 @@ run_plugin_hook() {
       RNEX_PROVIDER_SKILL_DIRS="$_skill_dirs"
       export RNEX_ROOT RNEX_CONFIG_MERGED RNEX_PLUGIN_DIR RNEX_CMD RNEX_ARGS RNEX_QUIET RNEX_PROVIDER_SKILL_DIRS
       # shellcheck disable=SC2329
-      rnex_register_user_skill() {
+      rnex_generate_user_skill() {
         skill_name="$1"
         target_path="$2"
+        plugin_name="${3:-}"
+
+        if [ -n "$plugin_name" ]; then
+          full_name="rnex-${plugin_name}-${skill_name}"
+        else
+          full_name="rnex-${skill_name}"
+        fi
         _target_file=""
         if [ -f "$RNEX_ROOT/$target_path" ]; then
           _target_file="$RNEX_ROOT/$target_path"
@@ -188,7 +220,7 @@ run_plugin_hook() {
           _skill_desc="$(awk 'NF && !/^#/ { print; exit }' "$_target_file" 2>/dev/null)"
         fi
         if [ -z "$_skill_desc" ]; then
-          _skill_desc="Repo Nexus agentic skill protocol for ${skill_name}."
+          _skill_desc="Repo Nexus agentic skill protocol for ${full_name}."
         fi
         _skill_desc="$(printf '%s' "$_skill_desc" | tr '\n\r' '  ' | sed 's/^[[:space:]]*//;s/[[:space:]]*$//;s/"/\\"/g')"
 
@@ -196,24 +228,24 @@ run_plugin_hook() {
           case "$provider_dir" in
             *rules*)
               mkdir -p "$RNEX_ROOT/$provider_dir"
-              rm -rf "$RNEX_ROOT/$provider_dir/rnex-${skill_name}" 2>/dev/null || true
-              cat << EOF > "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md"
-# User Skill: rnex-${skill_name}
+              rm -rf "${RNEX_ROOT:?}/${provider_dir:?}/${full_name:?}" 2>/dev/null || true
+              cat << EOF > "$RNEX_ROOT/$provider_dir/${full_name}.md"
+# User Skill: ${full_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
 EOF
               ;;
             *)
-              mkdir -p "$RNEX_ROOT/$provider_dir/rnex-${skill_name}"
-              rm -f "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md" 2>/dev/null || true
-              cat << EOF > "$RNEX_ROOT/$provider_dir/rnex-${skill_name}/SKILL.md"
+              mkdir -p "$RNEX_ROOT/$provider_dir/${full_name}"
+              rm -f "$RNEX_ROOT/$provider_dir/${full_name}.md" 2>/dev/null || true
+              cat << EOF > "$RNEX_ROOT/$provider_dir/${full_name}/SKILL.md"
 ---
-name: rnex-${skill_name}
+name: ${full_name}
 description: "${_skill_desc}"
 ---
 
-# User Skill: rnex-${skill_name}
+# User Skill: ${full_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
@@ -223,12 +255,30 @@ EOF
         done
       }
 
+      # shellcheck disable=SC2329
+      rnex_register_user_skill() {
+        rnex_generate_user_skill "$@"
+      }
+
       # shellcheck disable=SC2329
       rnex_unregister_user_skill() {
         skill_name="$1"
+        plugin_name="${2:-}"
+        if [ -n "$plugin_name" ]; then
+          full_name="rnex-${plugin_name}-${skill_name}"
+        else
+          case "$skill_name" in
+            rnex-*) full_name="$skill_name" ;;
+            *)      full_name="rnex-${skill_name}" ;;
+          esac
+        fi
         for provider_dir in $RNEX_PROVIDER_SKILL_DIRS; do
-          rm -f "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md"
-          rm -rf "$RNEX_ROOT/$provider_dir/rnex-${skill_name}"
+          rm -f "$RNEX_ROOT/$provider_dir/${full_name}.md"
+          rm -rf "${RNEX_ROOT:?}/${provider_dir:?}/${full_name:?}"
+          if [ -n "$plugin_name" ]; then
+            rm -f "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md"
+            rm -rf "${RNEX_ROOT:?}/${provider_dir:?}/rnex-${skill_name:?}"
+          fi
         done
       }
       set -- "$@"

package/lib/yaml.sh

@@ -281,14 +281,14 @@ yaml_enable_plugin() {
         awk -v name="$_name" '
           /^plugins:[ ]*$/ || /^plugins:[ ]*#/ {
             print
-            printf "  %s:\n    raw_dir: \"./docs\"\n    wiki_dir: \".rnex/wiki\"\n    lint_trigger: \"manual\"\n", name
+            printf "  %s:\n    raw_dir: \"./docs\"\n    wiki_dir: \".rnex/wiki\"\n    lint_trigger: \"manual\"\n    ingest_member_readmes: true\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
+              printf "plugins:\n  %s:\n    raw_dir: \"./docs\"\n    wiki_dir: \".rnex/wiki\"\n    lint_trigger: \"manual\"\n    ingest_member_readmes: true\n", name
             }
           }
         ' "$_target_file" > "$_tmp" && mv "$_tmp" "$_target_file"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.7.8",
+  "version": "0.7.11",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",

package/templates/rnex.example.yaml

@@ -107,6 +107,8 @@ plugins:
   #   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
+  #   ingest_member_readmes: true # Automatically ingest member repository READMEs into atomic wiki pages (default: true)
+
 
 # ------------------------------------------------------------------------------
 # repos — Member repositories managed by Repo Nexus

package/toolkit/plugins/copilot/README.md

@@ -5,7 +5,7 @@ A built-in Repo Nexus plugin providing instructions and skill integration for Gi
 ## Capabilities
 
 1. **Instructions Integration**: Generates and maintains `.github/copilot-instructions.md` with Repo Nexus routing instructions while preserving custom instructions outside delimiters.
-2. **User Skills Generation**: Standardized Repo Nexus core skills and active plugins' skills are mirrored as zero-logic User Skill pointers (`rnex-<name>.md`) in `.github/skills/`.
+2. **User Skills Generation**: Standardized Repo Nexus core skills and active plugins' skills are mirrored as zero-logic User Skill pointers (`rnex-<name>/SKILL.md`) in `.github/skills/`.
 
 ## Usage
 

package/toolkit/plugins/copilot/instructions/rnex-copilot-integration.md

@@ -4,7 +4,7 @@ This workspace has the Repo Nexus `copilot` plugin enabled.
 
 ## Operating Principles
 - **Instructions Integration**: GitHub Copilot natively reads `.github/copilot-instructions.md` and root `AGENTS.md` for workspace routing and active plugin guidelines between `<!-- REPO-NEXUS:START -->` and `<!-- REPO-NEXUS:END -->`. Custom instructions outside these markers are strictly preserved.
-- **User Skills**: Standardized Repo Nexus core skills and active plugin skills can be accessed via `.github/skills/rnex-*.md` when `skills: true`.
+- **User Skills**: Standardized Repo Nexus core skills and active plugin skills can be accessed via `.github/skills/rnex-*/SKILL.md` when `skills: true`.
 
 ## Configuration
 Configure plugin options in `rnex.yaml` or override them per developer in `.local.rnex.yaml`:

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

@@ -10,13 +10,13 @@ Reference specification: [setup-karpathy-wiki.md](https://github.com/unoxen/ai-t
 
 ## What It Provides
 
-### 1. The 4 Cardinal Principles for Coding Agents (`rules/rnex-behavioral.md`)
+### 1. The 4 Cardinal Principles for Coding Agents (`rules/behavioral.md`)
 * **Think Before Coding:** Explicit assumptions, problem formulation, and trade-off evaluation before writing code.
 * **Simplicity First:** Minimal abstractions, readable implementations, and zero boilerplate bloat.
 * **Surgical Changes:** Minimal blast radius, preserved comments/docstrings, and tightly focused diffs.
 * **Goal-Driven Execution:** Upfront verification criteria, automated tests, and rigorous diff review.
 
-### 2. Multi-Repo Context Engineering & Autonomy (`rules/rnex-behavioral.md`)
+### 2. Multi-Repo Context Engineering & Autonomy (`rules/behavioral.md`)
 * Guidelines tailored for Repo Nexus workspaces respecting member repository autonomy and physical repository boundaries.
 
 ### 3. Complete Karpathy LLM Wiki Architecture (`instructions/rnex-wiki-architecture.md`)
@@ -26,9 +26,9 @@ Reference specification: [setup-karpathy-wiki.md](https://github.com/unoxen/ai-t
 * **Rolling Context Cache (`<wiki_dir>/hot.md`, default: `.rnex/wiki/hot.md`):** High-density ~500-word orientation summary for rapid agent onboarding without full wiki scans (especially for codebase knowledge and second-brain wikis).
 * **Audit Trail (`<wiki_dir>/_log.md`, default: `.rnex/wiki/_log.md`):** Append-only log recording every ingest and lint operation with timestamped details.
 
-### 4. Standardized Agent Workflows (`workflows/`)
-* **`rnex-wiki-ingest.md` (8 Steps):** Decomposes raw source documents into 5–25 atomic wiki pages with frontmatter relations.
-* **`rnex-wiki-lint.md` (10 Steps):** Integrity audit protocol to validate paths, recompute `mentioned_in`, eliminate orphans, merge duplicates, audit inconsistencies, identify gaps, suggest source candidates, and rebuild indexes.
+### 4. Standardized Agent Skills (`skills/`)
+* **`wiki-ingest.md` (User Skill: `rnex-karpathy-llm-wiki-ingest`):** Decomposes raw source documents into 5–25 atomic wiki pages with frontmatter relations.
+* **`wiki-lint.md` (User Skill: `rnex-karpathy-llm-wiki-lint`):** Integrity audit protocol to validate paths, recompute `mentioned_in`, eliminate orphans, merge duplicates, audit inconsistencies, identify gaps, suggest source candidates, and rebuild indexes.
 
 ---
 
@@ -45,9 +45,9 @@ Enabling the plugin (`rnex plugin enable karpathy-llm`) performs an exact, zero-
 
 ### Phase 2: Evolutionary Growth & Domain Specialization (Usage Phase)
 Once initialized, the workspace structure organically evolves according to actual domain needs and source materials:
-* **Source Ingestion (`rnex-wiki-ingest`)**: As raw source documents are deposited into `./docs` and ingested, atomic pages are generated. Users or agents can organize pages into categorical subfolders (e.g. `architecture/`, `decisions/`, `concepts/`, `projects/`) or keep them flat.
-* **Customizable Guidelines**: Teams can tailor `rules/rnex-behavioral.md` and `instructions/rnex-wiki-architecture.md` for their specific team conventions.
-* **Graph Maintenance (`rnex-wiki-lint`)**: The periodic lint workflow validates relation paths, updates `mentioned_in`, and rebuilds `index.md` and `hot.md` to match the evolved knowledge graph.
+* **Source Ingestion (`rnex-karpathy-llm-wiki-ingest`)**: As raw source documents are deposited into `./docs` and ingested, atomic pages are generated. Users or agents can organize pages into categorical subfolders (e.g. `architecture/`, `decisions/`, `concepts/`, `projects/`) or keep them flat.
+* **Customizable Guidelines**: Teams can tailor `rules/behavioral.md` and `instructions/rnex-wiki-architecture.md` for their specific team conventions.
+* **Graph Maintenance (`rnex-karpathy-llm-wiki-lint`)**: The periodic lint workflow validates relation paths, updates `mentioned_in`, and rebuilds `index.md` and `hot.md` to match the evolved knowledge graph.
 
 ---
 
@@ -70,10 +70,10 @@ my-workspace/
 │           ├── instructions/
 │           │   └── rnex-wiki-architecture.md# LLM Wiki architecture & relation schema
 │           ├── rules/
-│           │   └── rnex-behavioral.md    # Cardinal principles & context engineering
-│           ├── workflows/
-│           │   ├── rnex-wiki-ingest.md   # 8-step decomposition & ingestion workflow
-│           │   └── rnex-wiki-lint.md     # 10-step graph validation & maintenance workflow
+│           │   └── behavioral.md         # Cardinal principles & context engineering
+│           ├── skills/
+│           │   ├── wiki-ingest.md        # 8-step decomposition & ingestion workflow
+│           │   └── wiki-lint.md          # 10-step graph validation & maintenance workflow
 │           └── templates/
 │               ├── rnex-wiki-page.template.md# Atomic page template with typed relations
 │               └── rnex-llm-wiki.sample.md# Sample wiki walkthrough

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

@@ -7,9 +7,6 @@ set -e
 # Resolve root workspace
 _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() {
@@ -48,6 +45,7 @@ get_cfg() {
 
 _wiki="$(get_cfg "wiki_dir" ".rnex/wiki")"
 _raw="$(get_cfg "raw_dir" "./docs")"
+_ingest_readmes="$(get_cfg "ingest_member_readmes" "true")"
 
 # Clean relative paths
 _wiki="$(printf '%s' "$_wiki" | sed -e 's#^/##' -e 's#/$##')"
@@ -59,6 +57,9 @@ _raw_path="$_root/$_raw"
 mkdir -p "$_wiki_path" "$_raw_path"
 [ -f "$_raw_path/.gitkeep" ] || touch "$_raw_path/.gitkeep"
 
+# Ensure .rnex/wiki/ contains only agent-maintained wiki artifacts (no raw staging directory)
+rm -rf "$_wiki_path/raw" 2>/dev/null || true
+
 _pdir="${RNEX_PLUGIN_DIR:-$_root/.rnex/plugins/karpathy-llm}"
 if [ ! -d "$_pdir/templates" ] && [ -d "$_root/toolkit/plugins/karpathy-llm/templates" ]; then
   _tmpl_dir="$_root/toolkit/plugins/karpathy-llm/templates"
@@ -78,7 +79,7 @@ fi
 
 # Ensure template in .rnex/plugins/karpathy-llm/templates
 mkdir -p "$_pdir/templates"
-if [ -f "$_tmpl_dir/rnex-wiki-page.sample.md" ] && [ ! -f "$_pdir/templates/rnex-wiki-page.template.md" ]; then
+if [ -f "$_tmpl_dir/rnex-wiki-page.sample.md" ]; then
   cp "$_tmpl_dir/rnex-wiki-page.sample.md" "$_pdir/templates/rnex-wiki-page.template.md"
 fi
 
@@ -97,18 +98,31 @@ if [ -n "$_src_k_skills" ] && [ "$_src_k_skills" != "$RNEX_ROOT/.rnex/plugins/ka
   cp -R "$_src_k_skills"/. "$RNEX_ROOT/.rnex/plugins/karpathy-llm/skills"/ 2>/dev/null || true
 fi
 
-# 2. Register plugin User Skills via contract helper
-if ! command -v rnex_register_user_skill >/dev/null 2>&1; then
+# 2. Register plugin User Skills via contract helper (with plugin name prefix)
+if ! command -v rnex_register_user_skill >/dev/null 2>&1 && ! command -v rnex_generate_user_skill >/dev/null 2>&1; then
   if [ -f "$RNEX_ROOT/.rnex/bin/rnex-env.sh" ]; then
     . "$RNEX_ROOT/.rnex/bin/rnex-env.sh"
   fi
 fi
 
-if command -v rnex_register_user_skill >/dev/null 2>&1; then
+# Clean up stale unprefixed skills
+if command -v rnex_unregister_user_skill >/dev/null 2>&1; then
+  rnex_unregister_user_skill "wiki-ingest"
+  rnex_unregister_user_skill "wiki-lint"
+fi
+
+_reg_fn=""
+if command -v rnex_generate_user_skill >/dev/null 2>&1; then
+  _reg_fn="rnex_generate_user_skill"
+elif command -v rnex_register_user_skill >/dev/null 2>&1; then
+  _reg_fn="rnex_register_user_skill"
+fi
+
+if [ -n "$_reg_fn" ]; then
   for skill_file in "$RNEX_ROOT/.rnex/plugins/karpathy-llm/skills"/*.md; do
     [ -f "$skill_file" ] || continue
     skill_name=$(basename "$skill_file" .md)
-    rnex_register_user_skill "$skill_name" ".rnex/plugins/karpathy-llm/skills/${skill_name}.md"
+    "$_reg_fn" "$skill_name" ".rnex/plugins/karpathy-llm/skills/${skill_name}.md" "karpathy-llm"
   done
 fi
 
@@ -134,20 +148,6 @@ RAW_DIR_VAL=$(grep -h -E '^\s*raw_dir:' "$RNEX_ROOT/rnex.yaml" "$RNEX_ROOT/.loca
 [ -z "$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
 
 # Ingest member repository README into atomic wiki page, index, and hot cache
 ingest_member_readme() {
@@ -316,18 +316,24 @@ LOG_EOF
   fi
 }
 
-# 2. Automatically sync README.md from all enabled/cloned member repositories
+# 2. Automatically ingest README.md from all enabled/cloned member repositories in-place
 # Get list of enabled repositories using a secure cross-repo read or `rnex list`
+case "$(printf '%s' "$_ingest_readmes" | tr '[:upper:]' '[:lower:]')" in
+  false|no|0|disabled|off) _skip_all_readmes=1 ;;
+  *) _skip_all_readmes=0 ;;
+esac
+
 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
+if [ "$_skip_all_readmes" -ne 1 ] && [ -d "$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=""
+    _repo_ingest=""
     for _cfg_file in "$RNEX_ROOT/.local.rnex.yaml" "$RNEX_ROOT/rnex.yaml"; do
       [ -f "$_cfg_file" ] || continue
       _en="$(awk -v repo="$repo_name" '
@@ -344,21 +350,40 @@ if [ -d "$RNEX_ROOT/$REPOS_DIR" ]; then
           exit
         }
       ' "$_cfg_file")"
-      if [ -n "$_en" ]; then
+      if [ -n "$_en" ] && [ -z "$_is_disabled" ]; then
         case "$(printf '%s' "$_en" | tr '[:upper:]' '[:lower:]')" in
           false|no|0|disabled|off) _is_disabled=1 ;;
           *) _is_disabled=0 ;;
         esac
-        break
+      fi
+
+      _ingest_val="$(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, "^    ingest_member_readmes:[ ]*") {
+          line = $0
+          sub("^    ingest_member_readmes:[ ]*", "", line)
+          sub(/[ ]*#.*$/, "", line)
+          gsub(/^["\x27]|["\x27]$/, "", line)
+          print line
+          exit
+        }
+      ' "$_cfg_file")"
+      if [ -n "$_ingest_val" ] && [ -z "$_repo_ingest" ]; then
+        case "$(printf '%s' "$_ingest_val" | tr '[:upper:]' '[:lower:]')" in
+          false|no|0|disabled|off) _repo_ingest=0 ;;
+          *) _repo_ingest=1 ;;
+        esac
       fi
     done
     [ "$_is_disabled" = "1" ] && continue
+    [ "$_repo_ingest" = "0" ] && continue
 
-    # Read and sync any README file with case-insensitive check
+    # Read and ingest any README file directly in-place (no staging copy)
     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"
         # Ingest member repository README into atomic wiki page, index, and hot cache
         ingest_member_readme "$repo_name" "$repo_path" "$readme_name"
         break

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

@@ -11,11 +11,19 @@ if ! command -v rnex_unregister_user_skill >/dev/null 2>&1; then
 fi
 
 if command -v rnex_unregister_user_skill >/dev/null 2>&1; then
+  rnex_unregister_user_skill "wiki-ingest" "karpathy-llm"
+  rnex_unregister_user_skill "wiki-lint" "karpathy-llm"
   rnex_unregister_user_skill "wiki-ingest"
   rnex_unregister_user_skill "wiki-lint"
 else
   for _pdir in $RNEX_PROVIDER_SKILL_DIRS; do
+    rm -f "$RNEX_ROOT/$_pdir/rnex-karpathy-llm-wiki-ingest.md"
+    rm -f "$RNEX_ROOT/$_pdir/rnex-karpathy-llm-wiki-lint.md"
+    rm -rf "$RNEX_ROOT/$_pdir/rnex-karpathy-llm-wiki-ingest"
+    rm -rf "$RNEX_ROOT/$_pdir/rnex-karpathy-llm-wiki-lint"
     rm -f "$RNEX_ROOT/$_pdir/rnex-wiki-ingest.md"
     rm -f "$RNEX_ROOT/$_pdir/rnex-wiki-lint.md"
+    rm -rf "$RNEX_ROOT/$_pdir/rnex-wiki-ingest"
+    rm -rf "$RNEX_ROOT/$_pdir/rnex-wiki-lint"
   done
 fi

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

@@ -44,6 +44,10 @@ _trigger="$(get_cfg "lint_trigger" "manual")"
 if [ "$_trigger" = "git-pre-push" ] || [ "$_trigger" = "pre-push" ]; then
   _notify="$(get_cfg "notify_on_changes" "true")"
   if [ "$_notify" != "false" ]; then
-    printf '[WIKI] Pre-push trigger: verifying wiki changes in %s/.\n' "$_wiki"
+    _wiki_path="$_root/$_wiki"
+    if [ ! -f "$_wiki_path/index.md" ] || [ ! -f "$_wiki_path/hot.md" ]; then
+      printf '[WIKI] Warning: Required wiki files (index.md or hot.md) missing in %s/.\n' "$_wiki"
+    fi
+    printf '[WIKI] Reminder: Wiki files changed. Run the rnex-karpathy-llm-wiki-lint skill to verify.\n'
   fi
 fi

package/toolkit/plugins/karpathy-llm/instructions/rnex-scaffolding-meta-prompt.md

@@ -27,7 +27,7 @@ Do not create arbitrary or speculative subdirectories during initialization. Sca
 
 ### 2. Agent Rules & Routing
 
-- **Repo Nexus Workspaces**: Directories (`raw_dir`, default: `./docs`; `wiki_dir`, default: `.rnex/wiki`) are configured in `rnex.yaml` under `plugins.karpathy-llm`. Plugin assets are scoped under `.rnex/plugins/karpathy-llm/` (`rules/rnex-behavioral.md` and `instructions/rnex-wiki-architecture.md`). Agents resolve configuration dynamically.
+- **Repo Nexus Workspaces**: Directories (`raw_dir`, default: `./docs`; `wiki_dir`, default: `.rnex/wiki`) are configured in `rnex.yaml` under `plugins.karpathy-llm`. Plugin assets are scoped under `.rnex/plugins/karpathy-llm/` (`rules/behavioral.md` and `instructions/rnex-wiki-architecture.md`). Agents resolve configuration dynamically.
 - **Standalone Repositories**: Append the `## Karpathy Wiki Rules` section (see Section 4) to the primary AI instructions file (`AGENTS.md`, `CLAUDE.md`, `.cursorrules`, etc.), preserving all existing content.
 
 ---

package/toolkit/plugins/karpathy-llm/instructions/rnex-wiki-architecture.md

@@ -8,17 +8,33 @@ The curated wiki directory (`wiki_dir`, default: `.rnex/wiki`) and raw intake di
 
 ---
 
+## Mandatory Wiki-First Access Gate (Pre-Task Execution)
+
+Before inspecting, searching, or modifying code inside member repositories (`repos/`), AI assistants MUST execute this sequence:
+
+1. **Orientation Gate (`<wiki_dir>/hot.md`)**:
+   - Always read `<wiki_dir>/hot.md` (default: `.rnex/wiki/hot.md`) first to absorb architectural topology, member repo boundaries, and current focus.
+   - Do NOT access `repos/` until this high-level orientation is completed.
+2. **Catalog & Topic Lookup (`<wiki_dir>/index.md`)**:
+   - If the specific domain concept, API contract, or component required for the task is not resolved in `hot.md`, read `<wiki_dir>/index.md` (default: `.rnex/wiki/index.md`).
+   - Identify and read the specific atomic wiki page(s) (e.g. `<wiki_dir>/auth.md`) corresponding to the task.
+3. **Targeted Member Repository Access Only**:
+   - Only after acquiring domain context and contract specifications from the wiki should you inspect targeted files within `repos/<name>/`. Never execute blind repository-wide grep or unbounded directory scans across `repos/`.
+
+---
+
 ## 1. Operating Rules & Token Economy
 
 When working in a workspace with an active Karpathy LLM Wiki:
 
 - **Configuration Resolution**: Read `rnex.yaml` / `.local.rnex.yaml` to identify the active `raw_dir` (default: `./docs`) and `wiki_dir` (default: `.rnex/wiki`).
-- **Intake**: All source material (articles, transcripts, docs, notes) goes to `<raw_dir>/` (default: `./docs`) unmodified. Never write directly to `<wiki_dir>/` without ingesting.
+- **Read-Only Input Directives**: `raw_dir` (`./docs`) and `./repos/` are strictly read-only inputs during wiki operations. Never create, copy, or modify files inside `./docs`; write generated output exclusively inside `wiki_dir` (`.rnex/wiki/`).
+- **Intake**: All source material (articles, transcripts, docs, notes) goes to `<raw_dir>/` (default: `./docs`) unmodified, and member repository READMEs exist under `./repos/<name>/README.md`. Sources are read directly in-place without staging copies. Never write directly to `<wiki_dir>/` without ingesting.
 - **Orientation (Hot-Cache First)**: Read `<wiki_dir>/hot.md` (default: `.rnex/wiki/hot.md`) for quick ~500-word orientation. Consult `<wiki_dir>/index.md` (default: `.rnex/wiki/index.md`) on demand only if the specific topic or contract is not covered in `hot.md`.
 - **Bounded Hot Cache**: `<wiki_dir>/hot.md` enforces a strict ~500-word ceiling with 3 structured sections: 1. Architecture & Repo Map, 2. Current Focus & Recent Ingests, 3. Key Contracts. Ingest and lint workflows must condense older context to prevent bloat.
 - **Annotated Indexing**: `<wiki_dir>/index.md` entries must maintain a single 1-line summary next to each atomic page link (e.g. `- [Auth Flow](auth.md): JWT validation and token rotation`) so agents pinpoint target pages in a single read without trial-and-error scanning.
-- **Ingestion**: When files appear in `<raw_dir>/`, run the `rnex-wiki-ingest` workflow (`.rnex/plugins/karpathy-llm/workflows/rnex-wiki-ingest.md`). One source document produces 5–25 atomic pages — never collapse a source into a single file.
-- **Maintenance**: Run the `rnex-wiki-lint` workflow (`.rnex/plugins/karpathy-llm/workflows/rnex-wiki-lint.md`) to validate paths, update `mentioned_in`, and preserve graph integrity.
+- **Ingestion**: When files appear in `<raw_dir>/` or member repositories are added, execute the `wiki-ingest` agentic skill (`.rnex/plugins/karpathy-llm/skills/wiki-ingest.md`). One source document produces 5–25 atomic pages — never collapse a source into a single file.
+- **Maintenance**: Execute the `wiki-lint` agentic skill (`.rnex/plugins/karpathy-llm/skills/wiki-lint.md`) to validate paths, update `mentioned_in`, and preserve graph integrity.
 
 ---
 

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

@@ -8,16 +8,32 @@ The curated wiki directory (`wiki_dir`, default: `.rnex/wiki`) and raw intake di
 
 ---
 
+## Mandatory Wiki-First Access Gate (Pre-Task Execution)
+
+Before inspecting, searching, or modifying code inside member repositories (`repos/`), AI assistants MUST execute this sequence:
+
+1. **Orientation Gate (`<wiki_dir>/hot.md`)**:
+   - Always read `<wiki_dir>/hot.md` (default: `.rnex/wiki/hot.md`) first to absorb architectural topology, member repo boundaries, and current focus.
+   - Do NOT access `repos/` until this high-level orientation is completed.
+2. **Catalog & Topic Lookup (`<wiki_dir>/index.md`)**:
+   - If the specific domain concept, API contract, or component required for the task is not resolved in `hot.md`, read `<wiki_dir>/index.md` (default: `.rnex/wiki/index.md`).
+   - Identify and read the specific atomic wiki page(s) (e.g. `<wiki_dir>/auth.md`) corresponding to the task.
+3. **Targeted Member Repository Access Only**:
+   - Only after acquiring domain context and contract specifications from the wiki should you inspect targeted files within `repos/<name>/`. Never execute blind repository-wide grep or unbounded directory scans across `repos/`.
+
+---
+
 ## 1. Operating Rules & Token Economy
 
 When working in a workspace with an active Karpathy LLM Wiki:
 
 - **Configuration Resolution**: Read `rnex.yaml` / `.local.rnex.yaml` to identify the active `raw_dir` (default: `./docs`) and `wiki_dir` (default: `.rnex/wiki`).
-- **Intake**: All source material (articles, transcripts, docs, notes) goes to `<raw_dir>/` (default: `./docs`) unmodified. Never write directly to `<wiki_dir>/` without ingesting.
+- **Read-Only Input Directives**: `raw_dir` (`./docs`) and `./repos/` are strictly read-only inputs during wiki operations. Never create, copy, or modify files inside `./docs`; write generated output exclusively inside `wiki_dir` (`.rnex/wiki/`).
+- **Intake**: All source material (articles, transcripts, docs, notes) goes to `<raw_dir>/` (default: `./docs`) unmodified, and member repository READMEs exist under `./repos/<name>/README.md`. Sources are read directly in-place without staging copies. Never write directly to `<wiki_dir>/` without ingesting.
 - **Orientation (Hot-Cache First)**: Read `<wiki_dir>/hot.md` (default: `.rnex/wiki/hot.md`) for quick ~500-word orientation. Consult `<wiki_dir>/index.md` (default: `.rnex/wiki/index.md`) on demand only if the specific topic or contract is not covered in `hot.md`.
 - **Bounded Hot Cache**: `<wiki_dir>/hot.md` enforces a strict ~500-word ceiling with 3 structured sections: 1. Architecture & Repo Map, 2. Current Focus & Recent Ingests, 3. Key Contracts. Ingest and lint workflows must condense older context to prevent bloat.
 - **Behavioral Principles**: Strictly adhere to the coding agent principles defined at `.rnex/plugins/karpathy-llm/rules/behavioral.md`.
-- **Ingestion**: When files appear in `<raw_dir>/`, execute the `wiki-ingest` agentic skill protocol (`.rnex/plugins/karpathy-llm/skills/wiki-ingest.md`). One source document produces 5–25 atomic pages — never collapse a source into a single file.
+- **Ingestion**: When files appear in `<raw_dir>/` or when member repos are added, execute the `wiki-ingest` agentic skill protocol (`.rnex/plugins/karpathy-llm/skills/wiki-ingest.md`). One source document produces 5–25 atomic pages — never collapse a source into a single file.
 - **Maintenance**: Execute the `wiki-lint` agentic skill protocol (`.rnex/plugins/karpathy-llm/skills/wiki-lint.md`) to validate paths, update `mentioned_in`, and preserve graph integrity.
 
 ---

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

@@ -9,12 +9,14 @@ config_defaults:
   wiki_dir: ".rnex/wiki"
   lint_trigger: "manual" # Default changed to manual to avoid unsolicited background trigger tasks
   notify_on_changes: true
+  ingest_member_readmes: true
 
 config:
   raw_dir: "./docs"
   wiki_dir: ".rnex/wiki"
   lint_trigger: "manual"
   notify_on_changes: true
+  ingest_member_readmes: true
 
 rules:
   - rules/behavioral.md: .rnex/plugins/karpathy-llm/rules/behavioral.md

package/toolkit/plugins/karpathy-llm/rules/behavioral.md

@@ -45,3 +45,7 @@ In a Repo Nexus workspace, independent repositories are organized into `./repos/
 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.
+
+4. **Read-Only Intake & Source Directories:**
+   - `raw_dir` (`./docs`) and `./repos/` are strictly read-only inputs during wiki operations. Never create, copy, or modify files inside `./docs`; write generated output exclusively inside `wiki_dir` (`.rnex/wiki/`).
+

package/toolkit/plugins/karpathy-llm/skills/wiki-ingest.md

@@ -10,13 +10,17 @@ Use this skill when ingesting new reference materials, architecture documentatio
 
 ## Ingestion Protocol
 
-1. **Resolve Configuration & Scan Intake:**
+1. **Resolve Configuration & Direct Source Paths:**
    - Read `rnex.yaml` (and `.local.rnex.yaml` if present) to resolve the active `raw_dir` (default: `./docs`) and `wiki_dir` (default: `.rnex/wiki`) under `plugins.karpathy-llm`.
-   - Scan `<raw_dir>/` for source materials not yet recorded in `<wiki_dir>/_log.md`.
-   - All source material must reside in `<raw_dir>/` unmodified. Never write directly to `<wiki_dir>/` without ingesting.
+   - Direct input scope explicitly reads:
+     1. All files in `raw_dir` (`./docs`) (read-only).
+     2. `./repos/<name>/README.md` for every enabled member repository in `rnex.yaml` / `.local.rnex.yaml` (read-only).
+   - `raw_dir` (`./docs`) and `./repos/` are strictly read-only inputs during wiki operations. Never create, copy, or modify files inside `./docs`; write generated output exclusively inside `wiki_dir` (`.rnex/wiki/`).
+   - Scan direct source paths for source materials not yet recorded in `<wiki_dir>/_log.md`.
+   - All source material is read directly in-place without staging copies. Never write directly to `<wiki_dir>/` without ingesting.
 
 2. **Read & Clarify:**
-   - Read each source document thoroughly.
+   - Read each source document thoroughly in-place.
    - If scope, domain boundaries, or terminology are ambiguous, ask one round of clarifying questions before decomposing.
 
 3. **Atomic Decomposition:**
@@ -31,7 +35,7 @@ Use this skill when ingesting new reference materials, architecture documentatio
    title: ""
    tags: []
    last_updated: YYYY-MM-DD
-   sources: []          # <raw_dir>/ files this page was derived from
+   sources: []          # direct source files (<raw_dir>/... or repos/<name>/README.md) this page was derived from
    related: []          # thematically related wiki pages
    extends: []          # pages this one builds upon or specialises
    contradicts: []      # pages with conflicting information
@@ -56,4 +60,4 @@ Use this skill when ingesting new reference materials, architecture documentatio
    - Maintain the strict ~500-word ceiling. Condense or prune older focus items.
 
 8. **Append Operation Log:**
-   - Append a timestamped entry to `<wiki_dir>/_log.md` detailing date, raw source processed, generated atomic pages, and follow-ups.
+   - Append a timestamped entry to `<wiki_dir>/_log.md` detailing date, direct source path processed, generated atomic pages, and follow-ups.

package/toolkit/plugins/karpathy-llm/skills/wiki-lint.md

@@ -12,7 +12,11 @@ Use this skill to perform health checks and maintenance on the curated wiki know
 
 1. **Resolve Configuration & Verify Paths:**
    - Read `rnex.yaml` (and `.local.rnex.yaml` if present) to resolve `wiki_dir` (default: `.rnex/wiki`) and `raw_dir` (default: `./docs`) under `plugins.karpathy-llm`.
-   - For every page under `<wiki_dir>/`, verify that all paths in frontmatter relation fields (`related`, `extends`, `contradicts`, `sources`) resolve to existing files under `<wiki_dir>/` or `<raw_dir>/`.
+   - Direct input scope explicitly reads:
+     1. All files in `raw_dir` (`./docs`) (read-only).
+     2. `./repos/<name>/README.md` for every enabled member repository in `rnex.yaml` / `.local.rnex.yaml` (read-only).
+   - `raw_dir` (`./docs`) and `./repos/` are strictly read-only inputs during wiki operations. Never create, copy, or modify files inside `./docs`; write generated output exclusively inside `wiki_dir` (`.rnex/wiki/`).
+   - For every page under `<wiki_dir>/`, verify that all paths in frontmatter relation fields (`related`, `extends`, `contradicts`, `sources`) resolve to existing files under `<wiki_dir>/`, `<raw_dir>/`, or `./repos/<name>/README.md`.
    - Fix or flag broken paths.
 
 2. **Recompute `mentioned_in` Relations:**

package/toolkit/plugins/karpathy-llm/templates/hot.md

@@ -8,8 +8,8 @@
 
 ## 2. Current Focus & Recent Ingests
 * **Active Tasks:** Wiki initialization complete.
-* **Recent Ingests:** None yet. Deposit source documents into `/{raw_dir}/` and run `rnex-wiki-ingest`.
+* **Recent Ingests:** None yet. Deposit source documents into `{raw_dir}/` and run `rnex-karpathy-llm-wiki-ingest`.
 
 ## 3. Key Contracts & Boundaries
 * **Atomic Pages:** Concepts live in discrete files with frontmatter relations (`sources`, `related`, `extends`, `mentioned_in`).
-* **Deep Knowledge:** For detailed RFCs, data contracts, and secondary concepts, consult `/{wiki_dir}/index.md` on demand.
+* **Deep Knowledge:** For detailed RFCs, data contracts, and secondary concepts, consult `{wiki_dir}/index.md` on demand.

package/toolkit/plugins/karpathy-llm/templates/index.md

@@ -29,4 +29,4 @@ Master navigation index for the Karpathy LLM Wiki. Agents query this index on de
 * *(Key contributors, teams, organizations, and stakeholders)*
 
 ## Sources & Raw References
-* *(Catalog of ingested source materials from `/{raw_dir}/`)*
+* *(Catalog of ingested source materials from `{raw_dir}/`)*

package/toolkit/plugins/karpathy-llm/templates/rnex-llm-wiki.sample.md

@@ -37,7 +37,7 @@
 ### ADR-001: Independent Git Repositories over Monorepo
 * **Date:** YYYY-MM-DD
 * **Decision:** Keep repositories completely independent without Git submodules. Orchestrate via Repo Nexus Virtual Meta-Repo.
-* **Consequences:** Autonomous CI/CD per repo; AI assistants maintain shared context via `AGENTS.md` and `rnex-behavioral.md`.
+* **Consequences:** Autonomous CI/CD per repo; AI assistants maintain shared context via `AGENTS.md` and `behavioral.md`.
 
 ---
 

package/toolkit/plugins/karpathy-llm/templates/rnex-wiki-page.sample.md

@@ -2,8 +2,8 @@
 title: "Concept or Entity Name"
 tags: []
 last_updated: YYYY-MM-DD
-# Typed relation fields — paths relative to /{wiki_dir}/
-sources: []          # /{raw_dir}/ files this page was derived from
+# Typed relation fields — paths relative to <wiki_dir>/ (or workspace root for raw sources)
+sources: []          # <raw_dir>/ files this page was derived from
 related: []          # thematically related wiki pages
 extends: []          # pages this one builds upon or specialises
 contradicts: []      # pages with conflicting information
@@ -16,7 +16,7 @@ mentioned_in: []     # pages that link to this one (maintained by lint)
 A concise, 1-2 paragraph summary of the concept, entity, architecture decision, or contract.
 
 ## Key Facts & Insights
-* **Core Insight:** Grounded directly in source material from `/{raw_dir}/`.
+* **Core Insight:** Grounded directly in source material from `<raw_dir>/`.
 * **Scope & Boundaries:** Context of applicability and interfaces with other components.
 
 ## Contextual Links