repo-nexus 0.7.7 → 0.7.8

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/plugins/claude.md

@@ -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`**:

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/gemini.md

@@ -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`**:

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/lib/ai.sh

@@ -370,21 +370,63 @@ fi
 rnex_register_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"
+  _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 ${skill_name}."
+  fi
+  _skill_desc="$(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/rnex-${skill_name}" 2>/dev/null || true
+        cat << EOF > "$_r/$provider_dir/rnex-${skill_name}.md"
 # User Skill: rnex-${skill_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"
+---
+name: rnex-${skill_name}
+description: "${_skill_desc}"
+---
+
+# User Skill: rnex-${skill_name}
+
+CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
+\`${target_path}\`
+EOF
+        ;;
+    esac
   done
 }
 
 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"
+  _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}"
   done
 }
 ENV_EOF
@@ -417,14 +459,51 @@ rnex_register_user_skill() {
   target_path="$2"
   _dirs="${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 ${skill_name}."
+  fi
+  _skill_desc="$(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"
+    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}
+
+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"
+---
+name: rnex-${skill_name}
+description: "${_skill_desc}"
+---
+
 # User Skill: rnex-${skill_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
 EOF
+        ;;
+    esac
   done
 }
 
@@ -435,6 +514,7 @@ rnex_unregister_user_skill() {
   _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}"
   done
 }
 
@@ -444,8 +524,7 @@ 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
 }

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

@@ -62,14 +62,49 @@ run_hook() {
         rnex_register_user_skill() {
           skill_name="$1"
           target_path="$2"
+          _target_file=""
+          if [ -f "$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 ${skill_name}."
+          fi
+          _skill_desc="$(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"
+            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}
+
+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"
+---
+name: rnex-${skill_name}
+description: "${_skill_desc}"
+---
+
 # User Skill: rnex-${skill_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
 EOF
+                ;;
+            esac
           done
         }
 
@@ -78,6 +113,7 @@ EOF
           skill_name="$1"
           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-${skill_name}"
           done
         }
         set -- "$@"
@@ -141,14 +177,49 @@ run_plugin_hook() {
       rnex_register_user_skill() {
         skill_name="$1"
         target_path="$2"
+        _target_file=""
+        if [ -f "$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 ${skill_name}."
+        fi
+        _skill_desc="$(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"
+          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}
+
+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"
+---
+name: rnex-${skill_name}
+description: "${_skill_desc}"
+---
+
 # User Skill: rnex-${skill_name}
 
 CRITICAL: Do not execute inline heuristics. Read and strictly follow the agentic skill protocol at:
 \`${target_path}\`
 EOF
+              ;;
+          esac
         done
       }
 
@@ -157,6 +228,7 @@ EOF
         skill_name="$1"
         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-${skill_name}"
         done
       }
       set -- "$@"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.7.7",
+  "version": "0.7.8",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",