repo-nexus 0.7.7 → 0.7.10

package/CHANGELOG.md

@@ -5,6 +5,19 @@ All notable changes to Repo Nexus (`rnex`) will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.7.7] - 2026-10-15
+
+### Added
+- **Native `SKILL.md` Bundle Support for User Skills**:
+  - Upgraded User Skill generator (`rnex_register_user_skill`) to emit dual formats tailored to each AI provider's discovery engine:
+    - **Skill-Based Providers (`.github/skills/`, `.claude/skills/`, `.gemini/skills/`)**: Generates native `rnex-<name>/SKILL.md` directory bundles containing YAML frontmatter (`name: rnex-<name>`, `description: "..."`) for automatic discoverability in VS Code, Copilot Chat, Antigravity, and Claude Code skill-pickers.
+    - **Rule-Based Providers (`.cursor/rules/`, `.windsurf/rules/`)**: Generates flat `rnex-<name>.md` pointer files aligning with Cursor and Windsurf rule conventions.
+  - Automatically extracts skill descriptions from target markdown headers to populate YAML frontmatter cleanly.
+- **GitHub Copilot Integration Plugin (`copilot`)**:
+  - Restored `copilot` as a first-class AI provider plugin in `toolkit/plugins/copilot/`.
+  - Supports `instructions: true` (managing `.github/copilot-instructions.md` within non-destructive delimiters) and `skills: true` (generating native User Skill bundles in `.github/skills/`).
+  - Added CLI flags `--copilot` and `--no-copilot` to `rnex init`.
+
 ## [0.7.5] - 2026-10-15
 
 ### Added

package/docs/CLI.md

@@ -87,8 +87,8 @@ Every lifecycle hook receives the following environment variables:
 | `RNEX_QUIET` | Set to `1` when `--quiet` was passed, `0` otherwise. |
 
 Hooks have access to POSIX helper functions for managing User Skill pointers:
-- `rnex_register_user_skill <skill_name> <target_path_in_rnex>`: Generates a zero-logic user skill pointer (`rnex-<skill_name>.md`) in active provider directories linking to the target skill protocol.
-- `rnex_unregister_user_skill <skill_name>`: Removes the `rnex-<skill_name>.md` user skill pointer from all active provider directories.
+- `rnex_register_user_skill <skill_name> <target_path_in_rnex>`: Generates a zero-logic user skill pointer (either a native `rnex-<name>/SKILL.md` bundle with YAML frontmatter for skill-based providers, or a flat `rnex-<name>.md` file for rule-based providers) linking to the target skill protocol.
+- `rnex_unregister_user_skill <skill_name>`: Removes the `rnex-<skill_name>` user skill pointer (bundle or flat file) from all active provider directories.
 
 ### Karpathy LLM Wiki Plugin
 The `karpathy-llm` plugin uses lifecycle hooks to manage its domain directories:

package/docs/ai-instructions.sample.md

@@ -23,3 +23,6 @@ When workspace configuration, routing blocks, plugin assets, or member repositor
 
 ## Git Operations
 Commit and push changes directly within the respective member repository root (`repos/<name>/`).
+
+## Wiki Operations
+`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/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>/`).
 
@@ -15,8 +15,8 @@ Operational skills, rules, and subagents remain cleanly encapsulated within `.rn
 
 ## Capabilities
 
-1. **Zero-Logic User Skills (`.claude/skills/rnex-*.md`)**:
-   - Generates lightweight user skill pointers prefixed with `rnex-` in `.claude/skills/`.
+1. **Zero-Logic User Skills (`.claude/skills/rnex-*/SKILL.md`)**:
+   - Generates native `SKILL.md` bundles prefixed with `rnex-` in `.claude/skills/` with YAML frontmatter for Claude Code skill discovery.
    - Contains zero inline heuristics—redirects Claude directly to the underlying agentic skill protocols inside `.rnex/`.
 
 2. **Native Instruction Support via `CLAUDE.md` & `AGENTS.md`**:
@@ -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/copilot.md

@@ -12,7 +12,7 @@ The `copilot` plugin integrates GitHub Copilot with Repo Nexus by projecting wor
 GitHub Copilot operates natively within VS Code, Visual Studio, JetBrains, and GitHub.com:
 - **Universal Routing (`AGENTS.md`)**: GitHub Copilot natively reads `AGENTS.md` at the workspace root.
 - **Custom Instructions (`.github/copilot-instructions.md`)**: When `instructions: true`, Repo Nexus injects its non-destructive routing block inside `<!-- REPO-NEXUS:START -->` and `<!-- REPO-NEXUS:END -->`. Custom developer rules outside these markers are strictly preserved.
-- **User Skills (`.github/skills/`)**: When `skills: true`, zero-logic User Skill pointers (`rnex-<name>.md`) redirect Copilot Chat to the underlying agentic skills under `.rnex/skills/` and active plugins.
+- **User Skills (`.github/skills/`)**: When `skills: true`, Repo Nexus generates native `SKILL.md` directory bundles (`.github/skills/rnex-<name>/SKILL.md`) with YAML frontmatter, making them automatically discoverable in VS Code and Copilot Chat skill-pickers while redirecting to the underlying agentic skills under `.rnex/skills/` and active plugins.
 
 ## Configuration
 

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>/`).
 
@@ -15,8 +15,8 @@ Operational skills, rules, and subagents remain cleanly encapsulated within `.rn
 
 ## Capabilities
 
-1. **Zero-Logic User Skills (`.gemini/skills/rnex-*.md`)**:
-   - Generates lightweight user skill pointers prefixed with `rnex-` in `.gemini/skills/`.
+1. **Zero-Logic User Skills (`.gemini/skills/rnex-*/SKILL.md`)**:
+   - Generates native `SKILL.md` bundles prefixed with `rnex-` in `.gemini/skills/` with YAML frontmatter for Gemini and Antigravity skill discovery.
    - Contains zero inline heuristics—redirects Gemini/Antigravity directly to the underlying agentic skill protocols inside `.rnex/`.
 
 2. **Native Instructions Support via `GEMINI.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/
+│       └── rnex-karpathy-llm-wiki-lint/
 ├── .rnex/
 │   ├── skills/                        # Core workspace agentic skills
 │   └── plugins/

package/docs/plugins/index.md

@@ -23,7 +23,7 @@ Active plugins are mirrored into each active member repository under `repos/<nam
 Repo Nexus decouples functional plugins from AI provider plugins:
 - **Core Skills (`toolkit/skills/` $\rightarrow$ `.rnex/skills/`)**: Workspace-level capabilities owned by Repo Nexus core.
 - **Plugin Skills (`toolkit/plugins/<plugin>/skills/` $\rightarrow$ `.rnex/plugins/<plugin>/skills/`)**: Scoped domain skills owned exclusively by individual plugins.
-- **User Skills (`rnex-<name>.md`)**: Provider plugins (`claude`, `gemini`, `cursor`, and `windsurf`) generate zero-logic user skill pointers in active provider directories (`.cursor/rules/`, `.claude/skills/`, `.gemini/skills/`, `.windsurf/rules/`) that redirect AI assistants directly to the underlying agentic skills in `.rnex/`.
+- **User Skills**: Provider plugins (`copilot`, `claude`, `gemini`, `cursor`, and `windsurf`) project zero-logic user skill pointers into active provider directories using native `SKILL.md` bundles with YAML frontmatter in skill directories (`.github/skills/`, `.claude/skills/`, `.gemini/skills/`) and flat files in rule directories (`.cursor/rules/`, `.windsurf/rules/`), redirecting AI assistants directly to the underlying agentic skills in `.rnex/`.
 
 ### 4. Non-Destructive Delimited Merging
 When plugins update root instruction files (`AGENTS.md`, `CLAUDE.md`, `GEMINI.md`, `.cursorrules`, `.windsurfrules`), Repo Nexus isolates auto-managed routing between explicit delimiters:

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

@@ -124,6 +124,9 @@ When workspace configuration, routing blocks, plugin assets, or member repositor
 
 ## Git Operations
 Commit and push changes directly within the respective member repository root (`repos/<name>/`).
+
+## Wiki Operations
+`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/`).
 BASE_AI_EOF
   fi
 
@@ -367,24 +370,90 @@ 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"
-  for provider_dir in $RNEX_PROVIDER_SKILL_DIRS; do
-    mkdir -p "$RNEX_ROOT/$provider_dir"
-    cat << EOF > "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md"
-# User Skill: rnex-${skill_name}
+  plugin_name="${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:-.}"
+
+  _target_file=""
+  if [ -f "$_r/$target_path" ]; then
+    _target_file="$_r/$target_path"
+  elif [ -f "$target_path" ]; then
+    _target_file="$target_path"
+  fi
+
+  _skill_desc=""
+  if [ -n "$_target_file" ]; then
+    _skill_desc="$(awk 'NF && !/^#/ { print; exit }' "$_target_file" 2>/dev/null)"
+  fi
+  if [ -z "$_skill_desc" ]; then
+    _skill_desc="Repo Nexus agentic skill protocol for ${full_name}."
+  fi
+  _skill_desc="$(printf '%s' "$_skill_desc" | tr '\n\r' '  ' | sed 's/^[[:space:]]*//;s/[[:space:]]*$//;s/"/\\"/g')"
+
+  for provider_dir in $_dirs; do
+    case "$provider_dir" in
+      *rules*)
+        mkdir -p "$_r/$provider_dir"
+        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/$provider_dir/${full_name}"
+        rm -f "$_r/$provider_dir/${full_name}.md" 2>/dev/null || true
+        cat << EOF > "$_r/$provider_dir/${full_name}/SKILL.md"
+---
+name: ${full_name}
+description: "${_skill_desc}"
+---
+
+# User Skill: ${full_name}
+
+CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
+\`${target_path}\`
+EOF
+        ;;
+    esac
   done
 }
 
+rnex_register_user_skill() {
+  rnex_generate_user_skill "$@"
+}
+
 rnex_unregister_user_skill() {
   skill_name="$1"
-  for provider_dir in $RNEX_PROVIDER_SKILL_DIRS; do
-    rm -f "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md"
+  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/$provider_dir/${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
@@ -411,30 +480,95 @@ 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:-.}}"
+
+  _target_file=""
+  if [ -f "$_r/$target_path" ]; then
+    _target_file="$_r/$target_path"
+  elif [ -f "$target_path" ]; then
+    _target_file="$target_path"
+  fi
+
+  _skill_desc=""
+  if [ -n "$_target_file" ]; then
+    _skill_desc="$(awk 'NF && !/^#/ { print; exit }' "$_target_file" 2>/dev/null)"
+  fi
+  if [ -z "$_skill_desc" ]; then
+    _skill_desc="Repo Nexus agentic skill protocol for ${full_name}."
+  fi
+  _skill_desc="$(printf '%s' "$_skill_desc" | tr '\n\r' '  ' | sed 's/^[[:space:]]*//;s/[[:space:]]*$//;s/"/\\"/g')"
+
   for provider_dir in $_dirs; do
-    mkdir -p "$_r/$provider_dir"
-    cat << EOF > "$_r/$provider_dir/rnex-${skill_name}.md"
-# User Skill: rnex-${skill_name}
+    case "$provider_dir" in
+      *rules*)
+        mkdir -p "$_r/$provider_dir"
+        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/$provider_dir/${full_name}"
+        rm -f "$_r/$provider_dir/${full_name}.md" 2>/dev/null || true
+        cat << EOF > "$_r/$provider_dir/${full_name}/SKILL.md"
+---
+name: ${full_name}
+description: "${_skill_desc}"
+---
+
+# User Skill: ${full_name}
+
+CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
+\`${target_path}\`
+EOF
+        ;;
+    esac
   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 -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
 }
 
@@ -444,8 +578,7 @@ clean_provider_user_skills() {
   rm -f "$_sk_dir"/rnex-*.md 2>/dev/null || true
   for _d in "$_sk_dir"/rnex-*; do
     [ -d "$_d" ] || continue
-    rm -f "$_d/SKILL.md" 2>/dev/null || true
-    rmdir "$_d" 2>/dev/null || true
+    rm -rf "$_d" 2>/dev/null || true
   done
   rmdir "$_sk_dir" 2>/dev/null || true
 }
@@ -457,10 +590,12 @@ 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
@@ -555,6 +690,12 @@ 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/commands/status.sh

@@ -165,15 +165,18 @@ cmd_status() {
   if [ -d "$NEXUS_DIR/.cursor/rules" ] && ls "$NEXUS_DIR/.cursor/rules"/rnex-*.md >/dev/null 2>&1; then
     printf '  %b✓%b %s %b(Cursor user skills)%b\n' "$_G" "$_NC" ".cursor/rules/" "$_DIM" "$_NC"
   fi
-  if [ -d "$NEXUS_DIR/.claude/skills" ] && ls "$NEXUS_DIR/.claude/skills"/rnex-*.md >/dev/null 2>&1; then
+  if [ -d "$NEXUS_DIR/.claude/skills" ] && { ls "$NEXUS_DIR/.claude/skills"/rnex-*.md >/dev/null 2>&1 || ls -d "$NEXUS_DIR/.claude/skills"/rnex-* >/dev/null 2>&1; }; then
     printf '  %b✓%b %s %b(Claude user skills)%b\n' "$_G" "$_NC" ".claude/skills/" "$_DIM" "$_NC"
   fi
   if [ -d "$NEXUS_DIR/.windsurf/rules" ] && ls "$NEXUS_DIR/.windsurf/rules"/rnex-*.md >/dev/null 2>&1; then
     printf '  %b✓%b %s %b(Windsurf user skills)%b\n' "$_G" "$_NC" ".windsurf/rules/" "$_DIM" "$_NC"
   fi
-  if [ -d "$NEXUS_DIR/.gemini/skills" ] && ls "$NEXUS_DIR/.gemini/skills"/rnex-*.md >/dev/null 2>&1; then
+  if [ -d "$NEXUS_DIR/.gemini/skills" ] && { ls "$NEXUS_DIR/.gemini/skills"/rnex-*.md >/dev/null 2>&1 || ls -d "$NEXUS_DIR/.gemini/skills"/rnex-* >/dev/null 2>&1; }; then
     printf '  %b✓%b %s %b(Gemini user skills)%b\n' "$_G" "$_NC" ".gemini/skills/" "$_DIM" "$_NC"
   fi
+  if [ -d "$NEXUS_DIR/.github/skills" ] && { ls "$NEXUS_DIR/.github/skills"/rnex-*.md >/dev/null 2>&1 || ls -d "$NEXUS_DIR/.github/skills"/rnex-* >/dev/null 2>&1; }; then
+    printf '  %b✓%b %s %b(Copilot user skills)%b\n' "$_G" "$_NC" ".github/skills/" "$_DIM" "$_NC"
+  fi
   printf '\n'
 
   printf '%bActive Plugins:%b\n' "$_BOLD" "$_NC"

package/lib/hooks.sh

@@ -59,25 +59,86 @@ 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"
+          elif [ -f "$target_path" ]; then
+            _target_file="$target_path"
+          fi
+          _skill_desc=""
+          if [ -n "$_target_file" ]; then
+            _skill_desc="$(awk 'NF && !/^#/ { print; exit }' "$_target_file" 2>/dev/null)"
+          fi
+          if [ -z "$_skill_desc" ]; then
+            _skill_desc="Repo Nexus agentic skill protocol for ${full_name}."
+          fi
+          _skill_desc="$(printf '%s' "$_skill_desc" | tr '\n\r' '  ' | sed 's/^[[:space:]]*//;s/[[:space:]]*$//;s/"/\\"/g')"
+
           for provider_dir in $RNEX_PROVIDER_SKILL_DIRS; do
-            mkdir -p "$RNEX_ROOT/$provider_dir"
-            cat << EOF > "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md"
-# User Skill: rnex-${skill_name}
+            case "$provider_dir" in
+              *rules*)
+                mkdir -p "$RNEX_ROOT/$provider_dir"
+                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/${full_name}"
+                rm -f "$RNEX_ROOT/$provider_dir/${full_name}.md" 2>/dev/null || true
+                cat << EOF > "$RNEX_ROOT/$provider_dir/${full_name}/SKILL.md"
+---
+name: ${full_name}
+description: "${_skill_desc}"
+---
+
+# User Skill: ${full_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
 EOF
+                ;;
+            esac
           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 -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-${skill_name:?}"
+            fi
           done
         }
         set -- "$@"
@@ -138,25 +199,86 @@ 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"
+        elif [ -f "$target_path" ]; then
+          _target_file="$target_path"
+        fi
+        _skill_desc=""
+        if [ -n "$_target_file" ]; then
+          _skill_desc="$(awk 'NF && !/^#/ { print; exit }' "$_target_file" 2>/dev/null)"
+        fi
+        if [ -z "$_skill_desc" ]; then
+          _skill_desc="Repo Nexus agentic skill protocol for ${full_name}."
+        fi
+        _skill_desc="$(printf '%s' "$_skill_desc" | tr '\n\r' '  ' | sed 's/^[[:space:]]*//;s/[[:space:]]*$//;s/"/\\"/g')"
+
         for provider_dir in $RNEX_PROVIDER_SKILL_DIRS; do
-          mkdir -p "$RNEX_ROOT/$provider_dir"
-          cat << EOF > "$RNEX_ROOT/$provider_dir/rnex-${skill_name}.md"
-# User Skill: rnex-${skill_name}
+          case "$provider_dir" in
+            *rules*)
+              mkdir -p "$RNEX_ROOT/$provider_dir"
+              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/$provider_dir/${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: ${full_name}
+description: "${_skill_desc}"
+---
+
+# User Skill: ${full_name}
+
+CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
+\`${target_path}\`
+EOF
+              ;;
+          esac
         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 -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": "0.7.7",
+  "version": "0.7.10",
   "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/ai-instructions.sample.md

@@ -23,3 +23,6 @@ When workspace configuration, routing blocks, plugin assets, or member repositor
 
 ## Git Operations
 Commit and push changes directly within the respective member repository root (`repos/<name>/`).
+
+## Wiki Operations
+`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/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/karpathy-llm/README.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.
+* **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/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.
+* **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.
 
 ---
 
@@ -71,9 +71,9 @@ my-workspace/
 │           │   └── 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
+│           ├── 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"
@@ -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/instructions/rnex-wiki-architecture.md

@@ -13,12 +13,13 @@ The curated wiki directory (`wiki_dir`, default: `.rnex/wiki`) and raw intake di
 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

@@ -13,11 +13,12 @@ The curated wiki directory (`wiki_dir`, default: `.rnex/wiki`) and raw intake di
 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

@@ -8,7 +8,7 @@
 
 ## 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`).