repo-nexus 0.5.4 → 0.5.6

package/CHANGELOG.md

@@ -16,6 +16,19 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Interactive `rnex init` determines and records `git_hooks` preference upfront in new workspaces.
   - Workspace schema migration in `rnex update` and `rnex fix -y` non-destructively inserts `git_hooks` into older configurations.
   - `rnex status` and `rnex hooks status` display configuration state alongside runtime Git hooks status.
+- **Modular GitHub Copilot Plugin & Extensible Provider Sync (`plugins: copilot: ...`)**:
+  - Encapsulated GitHub Copilot integration as a built-in Repo Nexus plugin (`copilot`) located in `toolkit/plugins/copilot/`.
+  - Extensible configuration options per provider under `plugins:` in `rnex.yaml` and `.local.rnex.yaml`:
+    - `prompts: true|false`: Syncs operational prompts into `.github/prompts/*.prompt.md` with YAML frontmatter for VS Code Copilot Chat prompt picker & slash commands.
+    - `skills: true|false`: Syncs agent skills into `.github/skills/<name>/SKILL.md` for Copilot Agent mode & `gh skill`.
+    - `instructions: true|false`: Synthesizes workspace routing and active plugin guidelines into `.github/copilot-instructions.md`, preserving manual user instructions outside `<!-- REPO-NEXUS -->` markers.
+    - `agents: true|false`: Syncs active plugin custom agents into `.github/agents/*.agent.md` and Copilot skills.
+    - `enabled: false`: Allows local machine overrides in `.local.rnex.yaml` without altering team configuration.
+  - Decoupled cross-plugin asset discovery: `copilot` provider inspects all active plugins (e.g. `karpathy-llm`) and mirrors their prompts, workflows, skills, agents, and guidelines without introducing plugin dependencies.
+  - CLI management via `rnex plugin enable [--local] copilot`, `rnex plugin disable [--local] copilot`, and `rnex plugin info copilot`.
+  - Added `--copilot` initialization flag to `rnex init` enabling the plugin in newly generated workspaces.
+  - Clean reconciliation in `rnex fix`: safely removes `.github/prompts/`, `.github/skills/`, `.github/agents/`, and `.github/copilot-instructions.md` when disabled or when specific target options are toggled off.
+  - Diagnostics and configurable options reporting integrated into `rnex status`.
 
 ### Fixed
 - **Git Hooks Self-Rewrite & Wrapper Preservation**:
@@ -24,6 +37,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Preserved custom / repository-owned wrappers in `.rnex/hooks/` that are not auto-managed by `rnex`.
   - Added `cmp -s` check before writing hook files to eliminate unnecessary file churn and in-place overwrites.
   - Automatically chain to existing repository-owned `.githooks/` scripts if present.
+- **Track Workspace `.rnex/` in Version Control**:
+  - Removed `.rnex/` from `.gitignore` templates and generation.
+  - `reconcile_gitignore` and `rnex fix` actively strip legacy `.rnex/` ignore rules from `.gitignore` so that team prompts (`.rnex/prompts/`), plugins (`.rnex/plugins/`), and hooks (`.rnex/hooks/`) are tracked in git.
+  - Updated `rnex status` to expect `.rnex/` to remain tracked by git.
 
 ## [0.5.1] - 2026-10-08
 

package/README.md

@@ -215,7 +215,25 @@ rnex plugin enable karpathy-llm
 rnex plugin disable karpathy-llm
 ```
 
-### Built-in Plugin: `karpathy-llm`
+### Built-in Plugins
+
+#### 1. `copilot`
+The `copilot` plugin provides GitHub Copilot integration, automatically mirroring workspace and active plugin assets:
+* **Prompts (`.github/prompts/*.prompt.md`)**: Formatted with YAML frontmatter (`name`, `description`) for the VS Code Copilot Chat prompt picker and slash commands.
+* **Agent Skills (`.github/skills/<name>/SKILL.md`)**: Configured for GitHub Copilot Agent mode and `gh skill`.
+* **Custom Agents (`.github/agents/*.agent.md`)**: Active plugins' agent definitions mirrored for Copilot workspace custom agents.
+* **Instructions (`.github/copilot-instructions.md`)**: Synthesized workspace routing and active plugin guidelines, preserving manual user instructions.
+* **Configurable Options**:
+  ```yaml
+  plugins:
+    copilot:
+      prompts: true        # mirror prompts to .github/prompts/*.prompt.md (default: true)
+      skills: true         # mirror skills to .github/skills/<name>/SKILL.md (default: true)
+      instructions: true   # mirror guidelines to .github/copilot-instructions.md (default: true)
+      agents: true         # mirror custom agents to .github/agents/*.agent.md (default: true)
+  ```
+
+#### 2. `karpathy-llm`
 The `karpathy-llm` plugin packages Andrej Karpathy's verified LLM agent design patterns, context engineering principles, and the autonomous **Karpathy LLM Wiki** architecture:
 * **The 4 Cardinal Agent Rules** (`.rnex/plugins/karpathy-llm/rules/behavioral.md`):
   1. *Think Before Coding:* Formulate explicit assumptions, boundary checks, and trade-offs before writing code.
@@ -248,8 +266,13 @@ repos_dir: ./repos
 # Automated workspace Git hooks (default: true)
 git_hooks: true
 
-# Workspace plugins
+# Workspace plugins and tool integrations
 plugins:
+  copilot:
+    prompts: true
+    skills: true
+    instructions: true
+    agents: true
   karpathy-llm: {}
 
 # Member repositories (enabled by default)

package/docs/CLI.md

@@ -72,15 +72,18 @@ rnex init [options] [directory]
 - `--code-workspace [filename]`: Enable VS Code / Cursor multi-root workspace file generation. Defaults to `<directory-name>.code-workspace` if omitted.
 - `--hooks`: Force-enable automated Git hooks setup during initialization.
 - `--no-hooks`: Skip Git hooks configuration during initialization.
+- `--copilot`: Enable GitHub Copilot integration plugin (mirrors prompts, skills, agents, and instructions to `.github/`).
+- `--no-copilot`: Skip GitHub Copilot plugin (default).
 
 #### What it does:
 1. Creates `rnex.yaml` with schema versioning (`version: <version>`), `repos_dir: ./repos`, and configured defaults.
 2. Merges Repo Nexus routing instructions (`<!-- REPO-NEXUS:START -->` ... `<!-- REPO-NEXUS:END -->`) into the target AI instructions file.
 3. Creates `./repos/` directory with a tracked `.gitkeep`.
 4. Creates `.rnex/`, `.rnex/plugins/`, and copies standardized prompts to `.rnex/prompts/`.
-5. Reconciles `.gitignore` to ensure `repos/`, `.rnex/`, and `.local.rnex.yaml` are never tracked by the meta-repo.
+5. Reconciles `.gitignore` to ensure `repos/` and `.local.rnex.yaml` are never tracked by the meta-repo (while keeping `.rnex/` tracked).
 6. Generates a multi-root `.code-workspace` file if configured.
 7. Prompts to configure automated workspace Git hooks (`core.hooksPath = .rnex/hooks`) if inside a Git repository.
+8. Configures enabled plugins (including `copilot` if requested).
 
 #### Examples:
 ```sh
@@ -110,7 +113,7 @@ rnex status
 #### What it reports:
 - **Configuration & Versions**: Path, version tag, and load status of `rnex.yaml` and `.local.rnex.yaml`.
 - **Paths**: Clones directory (`repos_dir`) and primary AI instructions file.
-- **Git Integration**: Validation that `.gitignore` ignores `repos/`, `.rnex/`, and local files, and whether `core.hooksPath` points to `.rnex/hooks`.
+- **Git Integration**: Validation that `.gitignore` ignores `repos/` and local files (while keeping `.rnex/` tracked), and whether `core.hooksPath` points to `.rnex/hooks`.
 - **AI Routing Context**: Existence and routing block markers in `AGENTS.md`, `CLAUDE.md`, `.code-workspace`, and prompts catalog (`.rnex/prompts/index.md`).
 - **Active Plugins**: List of enabled plugins, scoped versions, and asset directories.
 - **Member Repositories**: Every registered repository, enabled/disabled state, clone health, and active Git branch.
@@ -353,14 +356,14 @@ Unsets `core.hooksPath` in Git configuration, removes `.rnex/hooks/`, and record
 Repo Nexus features a modular plugin architecture where plugin rules, instructions, and templates are scoped strictly under `.rnex/plugins/<plugin-name>/`.
 
 ```sh
-rnex plugin <list|info|enable|disable> [name]
+rnex plugin <list|info|enable|disable> [options] [name]
 ```
 
 ### Subcommands
 - **`rnex plugin list`**: Displays all available plugins distributed with `rnex` and highlights enabled plugins.
-- **`rnex plugin info <name>`**: Shows description, version, scoped directory, and external template paths for a plugin.
-- **`rnex plugin enable <name>`**: Enables a plugin in `rnex.yaml`, copies assets to `.rnex/plugins/<name>/`, and reconciles workspace files.
-- **`rnex plugin disable <name>`**: Removes plugin assets from `.rnex/plugins/<name>/` and disables the plugin in `rnex.yaml`.
+- **`rnex plugin info <name>`**: Shows description, version, configurable options, scoped directory, and external template paths for a plugin.
+- **`rnex plugin enable [--local] <name>`**: Enables a plugin in `rnex.yaml` (or `.local.rnex.yaml` with `--local`), copies assets to `.rnex/plugins/<name>/`, and reconciles workspace files.
+- **`rnex plugin disable [--local] <name>`**: Removes plugin assets from `.rnex/plugins/<name>/` and disables the plugin in `rnex.yaml` (or overrides with `enabled: false` in `.local.rnex.yaml` with `--local`).
 
 ---
 

package/docs/rnex.example.yaml

@@ -74,21 +74,29 @@ code_workspace: false
 git_hooks: true
 
 # ------------------------------------------------------------------------------
-# plugins — Workspace plugins and AI instruction packs
+# plugins — Workspace plugins, tool integrations, and AI instruction packs
 # ------------------------------------------------------------------------------
 # Plugins extend your workspace with curated AI guidelines, context rules,
-# and scaffolding templates scoped within `.rnex/plugins/<plugin-name>/`.
+# tool provider integrations (e.g. GitHub Copilot), and templates.
 #
 # Manage plugins with:
-#   rnex plugin list              # View available and active plugins
-#   rnex plugin enable <name>     # Enable plugin in workspace
-#   rnex plugin disable <name>    # Disable plugin from workspace
+#   rnex plugin list                 # View available and active plugins
+#   rnex plugin enable [--local] <name>  # Enable plugin (global or local override)
+#   rnex plugin disable [--local] <name> # Disable plugin from workspace
+#   rnex plugin info <name>          # View plugin details & configurable options
 #
 # Built-in plugins:
+#   copilot        — GitHub Copilot integration: mirrors operational prompts, skills,
+#                    agents, and synthesized instructions into .github/
 #   karpathy-llm   — Andrej Karpathy's agent behavioral principles,
 #                    context engineering guidelines, and LLM Wiki architecture
 
 plugins:
+  # copilot:
+  #   prompts: true        # mirror prompts to .github/prompts/*.prompt.md (default: true)
+  #   skills: true         # mirror skills to .github/skills/<name>/SKILL.md (default: true)
+  #   instructions: true   # mirror instructions to .github/copilot-instructions.md (default: true)
+  #   agents: true         # mirror custom agents to .github/agents/*.agent.md (default: true)
   # karpathy-llm: {}
 
 # ------------------------------------------------------------------------------

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.5.4",
+  "version": "0.5.6",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",

package/rnex

@@ -147,6 +147,7 @@ require_workspace() {
     _load_ai_instructions_file
     _load_code_workspace
     _load_git_hooks
+    _load_copilot
     log_info "Using workspace at ${_BOLD}$NEXUS_DIR${_NC} ${_DIM}(via config: $WORKSPACE_YAML)${_NC}"
     return 0
   fi
@@ -177,6 +178,7 @@ require_workspace() {
   _load_ai_instructions_file
   _load_code_workspace
   _load_git_hooks
+  _load_copilot
 
   log_info "Using workspace at ${_BOLD}$NEXUS_DIR${_NC} ${_DIM}($(basename "$WORKSPACE_YAML") found)${_NC}"
 }
@@ -268,6 +270,18 @@ _load_git_hooks() {
   GIT_HOOKS_CONFIG="$_gh"
 }
 
+_load_copilot() {
+  _cp=""
+  if [ -f "$WORKSPACE_LOCAL_YAML" ]; then
+    _cp="$(awk '/^(copilot|copilot_sync):/ { sub(/^[a-zA-Z0-9_]+:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$WORKSPACE_LOCAL_YAML")"
+  fi
+  if [ -z "$_cp" ] && [ -f "$WORKSPACE_YAML" ]; then
+    _cp="$(awk '/^(copilot|copilot_sync):/ { sub(/^[a-zA-Z0-9_]+:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$WORKSPACE_YAML")"
+  fi
+  _cp="$(echo "$_cp" | tr -d " \t\r\n'\"")"
+  COPILOT_CONFIG="$_cp"
+}
+
 # ---- YAML Parser / Manipulator (for rnex.yaml & .local.rnex.yaml) ----------
 
 _yaml_list_plugins_from_file() {
@@ -352,22 +366,211 @@ yaml_has_plugin() {
   yaml_list_plugins | grep -qx "$1" 2>/dev/null
 }
 
-yaml_enable_plugin() {
-  _name="$1"
-  if ! grep -q '^plugins:' "$WORKSPACE_YAML" 2>/dev/null; then
-    printf '\nplugins:\n' >> "$WORKSPACE_YAML"
+yaml_plugin_enabled() {
+  _plugin="$1"
+  yaml_has_plugin "$_plugin" || return 1
+  _val="$(yaml_plugin_get "$_plugin" "enabled")"
+  _val="$(printf '%s' "$_val" | tr '[:upper:]' '[:lower:]')"
+  case "$_val" in
+    false|no|0|disabled|off) return 1 ;;
+    *) return 0 ;;
+  esac
+}
+
+copilot_plugin_enabled() {
+  if yaml_plugin_enabled "copilot"; then
+    return 0
+  fi
+  case "$COPILOT_CONFIG" in
+    true|yes|1) return 0 ;;
+    *) return 1 ;;
+  esac
+}
+
+copilot_prompts_enabled() {
+  copilot_plugin_enabled || return 1
+  _val="$(yaml_plugin_get "copilot" "prompts")"
+  _val="$(printf '%s' "$_val" | tr '[:upper:]' '[:lower:]')"
+  case "$_val" in
+    false|no|0|disabled|off) return 1 ;;
+    *) return 0 ;;
+  esac
+}
+
+copilot_skills_enabled() {
+  copilot_plugin_enabled || return 1
+  _val="$(yaml_plugin_get "copilot" "skills")"
+  _val="$(printf '%s' "$_val" | tr '[:upper:]' '[:lower:]')"
+  case "$_val" in
+    false|no|0|disabled|off) return 1 ;;
+    *) return 0 ;;
+  esac
+}
+
+copilot_instructions_enabled() {
+  copilot_plugin_enabled || return 1
+  _val="$(yaml_plugin_get "copilot" "instructions")"
+  _val="$(printf '%s' "$_val" | tr '[:upper:]' '[:lower:]')"
+  case "$_val" in
+    false|no|0|disabled|off) return 1 ;;
+    *) return 0 ;;
+  esac
+}
+
+copilot_agents_enabled() {
+  copilot_plugin_enabled || return 1
+  _val="$(yaml_plugin_get "copilot" "agents")"
+  _val="$(printf '%s' "$_val" | tr '[:upper:]' '[:lower:]')"
+  case "$_val" in
+    false|no|0|disabled|off) return 1 ;;
+    *) return 0 ;;
+  esac
+}
+
+_yaml_plugin_set_in_file() {
+  _file="$1"; _plugin="$2"; _field="$3"; _value="$4"
+  if [ ! -f "$_file" ]; then
+    mkdir -p "$(dirname "$_file")"
+    printf 'plugins:\n' > "$_file"
+  elif ! grep -q '^plugins:' "$_file" 2>/dev/null; then
+    printf '\nplugins:\n' >> "$_file"
   fi
-  if ! yaml_has_plugin "$_name"; then
+
+  if ! awk -v plugin="$_plugin" '
+    /^plugins:[ ]*$/ || /^plugins:[ ]*#/ { in_p=1; next }
+    in_p && /^[^ #]/ { in_p=0 }
+    in_p && match($0, "^  " plugin ":[ ]*(#.*)?$") { found=1; exit }
+    END { exit !found }
+  ' "$_file" 2>/dev/null; then
+    if grep -qE "^  $_plugin:[ ]*(\{\}|\[\])?$" "$_file" 2>/dev/null; then
+      _tmp="$(mktemp)"
+      awk -v plugin="$_plugin" -v field="$_field" -v value="$_value" '
+        match($0, "^  " plugin ":[ ]*(\\{\\}|\\[\\])?$") {
+          printf "  %s:\n    %s: %s\n", plugin, field, value
+          next
+        }
+        { print }
+      ' "$_file" > "$_tmp" && mv "$_tmp" "$_file"
+      return 0
+    fi
     _tmp="$(mktemp)"
-    awk -v name="$_name" '
-      /^plugins:/ {
+    awk -v plugin="$_plugin" -v field="$_field" -v value="$_value" '
+      /^plugins:[ ]*$/ || /^plugins:[ ]*#/ {
         print
-        printf "  %s: {}\n", name
+        printf "  %s:\n    %s: %s\n", plugin, field, value
         added=1
         next
       }
       { print }
-    ' "$WORKSPACE_YAML" > "$_tmp" && mv "$_tmp" "$WORKSPACE_YAML"
+      END {
+        if (!added) {
+          printf "plugins:\n  %s:\n    %s: %s\n", plugin, field, value
+        }
+      }
+    ' "$_file" > "$_tmp" && mv "$_tmp" "$_file"
+    return 0
+  fi
+
+  _tmp="$(mktemp)"
+  awk -v plugin="$_plugin" -v field="$_field" -v value="$_value" '
+    /^plugins:/ { in_plugins=1; print; next }
+    in_plugins && /^[^ #]/ {
+      if (in_target && !field_set) {
+        printf "    %s: %s\n", field, value
+        field_set=1
+      }
+      in_plugins=0; in_target=0
+    }
+    in_plugins && match($0, "^  " plugin ":[ ]*(#.*)?$") {
+      in_target=1; print; next
+    }
+    in_target && /^  [^ #]/ {
+      if (!field_set) {
+        printf "    %s: %s\n", field, value
+        field_set=1
+      }
+      in_target=0
+    }
+    in_target && match($0, "^    " field ":") {
+      printf "    %s: %s\n", field, value
+      field_set=1
+      next
+    }
+    { print }
+    END {
+      if (in_target && !field_set) {
+        printf "    %s: %s\n", field, value
+      }
+    }
+  ' "$_file" > "$_tmp" && mv "$_tmp" "$_file"
+}
+
+yaml_plugin_set() {
+  _plugin="$1"; _field="$2"; _value="$3"
+  _yaml_plugin_set_in_file "$WORKSPACE_YAML" "$_plugin" "$_field" "$_value"
+}
+
+yaml_plugin_set_local() {
+  _plugin="$1"; _field="$2"; _value="$3"
+  if [ ! -f "$WORKSPACE_LOCAL_YAML" ]; then
+    cat <<'EOF' > "$WORKSPACE_LOCAL_YAML"
+# ==============================================================================
+# .local.rnex.yaml — Repo Nexus Local Configuration (Machine-Specific)
+# ==============================================================================
+# This file is gitignored. Use it to specify local repository paths, overrides,
+# and enable/disable states for this workstation.
+
+plugins:
+EOF
+  fi
+  _yaml_plugin_set_in_file "$WORKSPACE_LOCAL_YAML" "$_plugin" "$_field" "$_value"
+}
+
+yaml_enable_plugin() {
+  _name="$1"
+  _target_file="${2:-$WORKSPACE_YAML}"
+  if [ ! -f "$_target_file" ]; then
+    printf 'plugins:\n' > "$_target_file"
+  elif ! grep -q '^plugins:' "$_target_file" 2>/dev/null; then
+    printf '\nplugins:\n' >> "$_target_file"
+  fi
+  if ! _yaml_list_plugins_from_file "$_target_file" | grep -qx "$_name" 2>/dev/null; then
+    _tmp="$(mktemp)"
+    if [ "$_name" = "copilot" ]; then
+      awk -v name="$_name" '
+        /^plugins:[ ]*$/ || /^plugins:[ ]*#/ {
+          print
+          printf "  %s:\n    prompts: true\n    skills: true\n    instructions: true\n    agents: true\n", name
+          added=1
+          next
+        }
+        { print }
+        END {
+          if (!added) {
+            printf "plugins:\n  %s:\n    prompts: true\n    skills: true\n    instructions: true\n    agents: true\n", name
+          }
+        }
+      ' "$_target_file" > "$_tmp" && mv "$_tmp" "$_target_file"
+    else
+      awk -v name="$_name" '
+        /^plugins:[ ]*$/ || /^plugins:[ ]*#/ {
+          print
+          printf "  %s: {}\n", name
+          added=1
+          next
+        }
+        { print }
+        END {
+          if (!added) {
+            printf "plugins:\n  %s: {}\n", name
+          }
+        }
+      ' "$_target_file" > "$_tmp" && mv "$_tmp" "$_target_file"
+    fi
+  else
+    if [ -f "$WORKSPACE_LOCAL_YAML" ] && [ "$_target_file" = "$WORKSPACE_LOCAL_YAML" ]; then
+      _yaml_plugin_set_in_file "$_target_file" "$_name" "enabled" "true"
+    fi
   fi
 }
 
@@ -734,8 +937,8 @@ EOF
     _dest_pdir="$_r_rnex/plugins/$_pname"
     mkdir -p "$_dest_pdir"
 
-    # Copy rules/workflows/instructions into member plugin dir
-    for _sub in rules workflows instructions; do
+    # Copy rules/workflows/instructions/prompts/skills/agents into member plugin dir
+    for _sub in rules workflows instructions prompts skills agents; do
       if [ -d "$_pdir/$_sub" ]; then
         mkdir -p "$_dest_pdir/$_sub"
         cp -r "$_pdir/$_sub"/* "$_dest_pdir/$_sub"/ 2>/dev/null || true
@@ -846,8 +1049,8 @@ sync_plugins() {
     if [ "$_pdir" != "$_scoped_dest" ]; then
       mkdir -p "$_scoped_dest"
 
-      # Copy rules, workflows, instructions into scoped plugin directory
-      for _sub in rules workflows instructions; do
+      # Copy rules, workflows, instructions, prompts, skills, agents into scoped plugin directory
+      for _sub in rules workflows instructions prompts skills agents; do
         if [ -d "$_pdir/$_sub" ]; then
           mkdir -p "$_scoped_dest/$_sub"
           cp -r "$_pdir/$_sub"/* "$_scoped_dest/$_sub"/ 2>/dev/null || true
@@ -890,14 +1093,11 @@ reconcile_gitignore() {
 repos/*
 !repos/.gitkeep
 
-# Repo Nexus internal state & cache
-.rnex/
-
 # Local machine-specific configuration
 $RNEX_LOCAL_CONFIG_FILE
 .rnex.local.yaml
 GI_EOF
-    log_ok "Created .gitignore (ignoring repos/, .rnex/, and $RNEX_LOCAL_CONFIG_FILE)"
+    log_ok "Created .gitignore (ignoring repos/ and $RNEX_LOCAL_CONFIG_FILE)"
     return 0
   fi
 
@@ -908,18 +1108,19 @@ GI_EOF
     log_ok "Removed legacy lint trigger counter entries from .gitignore"
   fi
 
-  # 2. Ensure repos/* is ignored
+  # 2. Strip legacy .rnex/ entries if present (.rnex/ contains tracked prompts, plugins, and hooks)
+  if grep -qE '^[ ]*#?[ ]*Repo Nexus internal state' "$_gi" 2>/dev/null || grep -qE '^\.rnex/?$' "$_gi" 2>/dev/null; then
+    _tmp="$(mktemp)"
+    grep -vE '(^[ ]*#?[ ]*Repo Nexus internal state|^\.rnex/?$)' "$_gi" > "$_tmp" && mv "$_tmp" "$_gi"
+    log_ok "Removed .rnex/ from .gitignore (.rnex should be tracked in git)"
+  fi
+
+  # 3. Ensure repos/* is ignored
   if ! grep -q "^repos" "$_gi" 2>/dev/null; then
     printf '\n# Member repos (managed by rnex)\nrepos/*\n!repos/.gitkeep\n' >> "$_gi"
     log_dim "Added repos/* to .gitignore"
   fi
 
-  # 3. Ensure .rnex/ is ignored
-  if ! grep -q '^\.rnex/' "$_gi" 2>/dev/null && ! grep -q '^\.rnex$' "$_gi" 2>/dev/null; then
-    printf '\n# Repo Nexus internal state & cache\n.rnex/\n' >> "$_gi"
-    log_dim "Added .rnex/ to .gitignore"
-  fi
-
   # 4. Ensure local config files are ignored
   if ! grep -qF "$RNEX_LOCAL_CONFIG_FILE" "$_gi" 2>/dev/null; then
     printf '\n# Local machine-specific configuration\n%s\n' "$RNEX_LOCAL_CONFIG_FILE" >> "$_gi"
@@ -1132,6 +1333,115 @@ sync_code_workspace() {
   fi
 }
 
+sync_copilot_instructions() {
+  _dst_ci="$NEXUS_DIR/.github/copilot-instructions.md"
+  if ! copilot_instructions_enabled; then
+    if [ -f "$_dst_ci" ]; then
+      if grep -q "$AI_MARKER_START" "$_dst_ci" 2>/dev/null; then
+        _non_rnex="$(awk -v s="$AI_MARKER_START" -v e="$AI_MARKER_END" '
+          $0 ~ s { skip=1; next }
+          $0 ~ e { skip=0; next }
+          !skip { print }
+        ' "$_dst_ci" | tr -d " \t\r\n")"
+        if [ -z "$_non_rnex" ]; then
+          rm -f "$_dst_ci"
+        else
+          _tmp="$(mktemp)"
+          awk -v s="$AI_MARKER_START" -v e="$AI_MARKER_END" '
+            $0 ~ s { skip=1; next }
+            $0 ~ e { skip=0; next }
+            !skip { print }
+          ' "$_dst_ci" > "$_tmp" && mv "$_tmp" "$_dst_ci"
+        fi
+      fi
+    fi
+    return 0
+  fi
+
+  mkdir -p "$NEXUS_DIR/.github"
+  _body_tmp="$(mktemp)"
+
+  {
+    cat <<'EOF'
+# GitHub Copilot Instructions (Repo Nexus Virtual Meta-Repo)
+
+This workspace operates as a **Repo Nexus Virtual Meta-Repo** uniting independent repositories.
+
+## Routing & Operating Protocol
+1. Inspect `.local.rnex.yaml` when present, then `rnex.yaml`.
+2. Master operational prompts are indexed at `.rnex/prompts/index.md` (and mirrored in `.github/prompts/`).
+3. Member repositories reside in `repos/<name>/`. Inspect `repos/<name>/.rnex/` for repository-specific context.
+4. Perform Git commits directly inside member repository roots (`repos/<name>/`).
+EOF
+
+    # Append active plugins instructions & rules
+    _active_p="$(yaml_list_plugins)"
+    if [ -n "$_active_p" ]; then
+      printf '\n## Active Plugins & Guidelines\n'
+      echo "$_active_p" | while read -r _pname; do
+        [ -n "$_pname" ] || continue
+        yaml_plugin_enabled "$_pname" || continue
+        [ "$_pname" != "copilot" ] || continue
+        _pdir="$(find_plugin_dir "$_pname" 2>/dev/null || true)"
+        [ -n "$_pdir" ] || continue
+        _pdesc="$(plugin_get_field "$_pdir" "description")"
+        printf '\n### Plugin: %s\n' "$_pname"
+        [ -n "$_pdesc" ] && printf '%s\n\n' "$_pdesc"
+
+        for _rfile in "$_pdir"/rules/*.md "$NEXUS_DIR/.rnex/plugins/$_pname"/rules/*.md; do
+          if [ -f "$_rfile" ]; then
+            printf '#### Rules (%s)\n' "$(basename "$_rfile")"
+            cat "$_rfile"
+            printf '\n'
+            break
+          fi
+        done
+
+        for _ifile in "$_pdir"/instructions/*.md "$NEXUS_DIR/.rnex/plugins/$_pname"/instructions/*.md; do
+          if [ -f "$_ifile" ]; then
+            printf '#### Instructions (%s)\n' "$(basename "$_ifile")"
+            cat "$_ifile"
+            printf '\n'
+            break
+          fi
+        done
+      done
+    fi
+  } > "$_body_tmp"
+
+  if [ ! -f "$_dst_ci" ]; then
+    {
+      printf '%s\n' "$AI_MARKER_START"
+      cat "$_body_tmp"
+      printf '\n%s\n' "$AI_MARKER_END"
+    } > "$_dst_ci"
+  elif grep -q "$AI_MARKER_START" "$_dst_ci" 2>/dev/null; then
+    _tmp="$(mktemp)"
+    awk -v s="$AI_MARKER_START" -v e="$AI_MARKER_END" -v src="$_body_tmp" '
+      $0 ~ s {
+        print s
+        while ((getline line < src) > 0) print line
+        close(src)
+        print e
+        skip=1
+        next
+      }
+      $0 ~ e { skip=0; next }
+      !skip { print }
+    ' "$_dst_ci" > "$_tmp" && mv "$_tmp" "$_dst_ci"
+  else
+    _tmp="$(mktemp)"
+    cat "$_dst_ci" > "$_tmp"
+    {
+      printf '\n\n%s\n' "$AI_MARKER_START"
+      cat "$_body_tmp"
+      printf '\n%s\n' "$AI_MARKER_END"
+    } >> "$_tmp"
+    mv "$_tmp" "$_dst_ci"
+  fi
+  rm -f "$_body_tmp"
+}
+
 sync_prompts() {
   _src_prompts=""
   if [ -d "$SCRIPT_LOCATION/toolkit/prompts" ]; then
@@ -1152,6 +1462,208 @@ sync_prompts() {
     _b="$(basename "$_pfile")"
     cp -f "$_pfile" "$_dst_prompts/$_b"
   done
+
+  # Copilot prompts sync (.github/prompts/*.prompt.md)
+  if copilot_prompts_enabled; then
+    _copilot_prompts="$NEXUS_DIR/.github/prompts"
+    mkdir -p "$_copilot_prompts"
+
+    # Base toolkit prompts
+    for _pfile in "$_src_prompts"/rnex-*.md; do
+      [ -f "$_pfile" ] || continue
+      _pname="$(basename "$_pfile" .md)"
+      _desc="$(awk '
+        /^#/ { in_title=1; next }
+        in_title && /^[A-Za-z]/ { print; exit }
+      ' "$_pfile" 2>/dev/null)"
+      [ -n "$_desc" ] || _desc="Repo Nexus prompt for $_pname"
+
+      _dst_cp="$_copilot_prompts/$_pname.prompt.md"
+      {
+        printf -- '---\nname: %s\ndescription: %s\n---\n\n' "$_pname" "$_desc"
+        cat "$_pfile"
+      } > "$_dst_cp"
+    done
+
+    # Active plugins prompts & workflows
+    yaml_list_plugins | while read -r _pname; do
+      [ -n "$_pname" ] || continue
+      yaml_plugin_enabled "$_pname" || continue
+      [ "$_pname" != "copilot" ] || continue
+      _pdir="$(find_plugin_dir "$_pname" 2>/dev/null || true)"
+      [ -n "$_pdir" ] || continue
+
+      for _sub in prompts workflows; do
+        for _s_dir in "$_pdir/$_sub" "$NEXUS_DIR/.rnex/plugins/$_pname/$_sub"; do
+          [ -d "$_s_dir" ] || continue
+          for _pfile in "$_s_dir"/*.md; do
+            [ -f "$_pfile" ] || continue
+            _base="$(basename "$_pfile" .md)"
+            case "$_base" in
+              index|README) continue ;;
+            esac
+            _desc="$(awk '
+              /^#/ { in_title=1; next }
+              in_title && /^[A-Za-z]/ { print; exit }
+            ' "$_pfile" 2>/dev/null)"
+            [ -n "$_desc" ] || _desc="Prompt $_base from plugin $_pname"
+
+            _dst_cp="$_copilot_prompts/$_base.prompt.md"
+            {
+              printf -- '---\nname: %s\ndescription: %s\n---\n\n' "$_base" "$_desc"
+              cat "$_pfile"
+            } > "$_dst_cp"
+          done
+        done
+      done
+    done
+  else
+    if [ -d "$NEXUS_DIR/.github/prompts" ]; then
+      rm -f "$NEXUS_DIR/.github/prompts"/*.prompt.md 2>/dev/null || true
+      rmdir "$NEXUS_DIR/.github/prompts" 2>/dev/null || true
+    fi
+  fi
+
+  # Copilot skills sync (.github/skills/<name>/SKILL.md)
+  if copilot_skills_enabled; then
+    _copilot_skills="$NEXUS_DIR/.github/skills"
+    mkdir -p "$_copilot_skills"
+
+    # Base toolkit skills
+    for _pfile in "$_src_prompts"/rnex-*.md; do
+      [ -f "$_pfile" ] || continue
+      _pname="$(basename "$_pfile" .md)"
+      _desc="$(awk '
+        /^#/ { in_title=1; next }
+        in_title && /^[A-Za-z]/ { print; exit }
+      ' "$_pfile" 2>/dev/null)"
+      [ -n "$_desc" ] || _desc="Repo Nexus prompt for $_pname"
+
+      _dst_sk_dir="$_copilot_skills/$_pname"
+      mkdir -p "$_dst_sk_dir"
+      _dst_sk="$_dst_sk_dir/SKILL.md"
+      {
+        printf -- '---\nname: %s\ndescription: %s\n---\n\n' "$_pname" "$_desc"
+        cat "$_pfile"
+      } > "$_dst_sk"
+    done
+
+    # Active plugins skills, prompts, & workflows
+    yaml_list_plugins | while read -r _pname; do
+      [ -n "$_pname" ] || continue
+      yaml_plugin_enabled "$_pname" || continue
+      [ "$_pname" != "copilot" ] || continue
+      _pdir="$(find_plugin_dir "$_pname" 2>/dev/null || true)"
+      [ -n "$_pdir" ] || continue
+
+      # A. Dedicated skills in plugin
+      for _s_dir in "$_pdir/skills" "$NEXUS_DIR/.rnex/plugins/$_pname/skills"; do
+        [ -d "$_s_dir" ] || continue
+        for _s_entry in "$_s_dir"/*; do
+          if [ -d "$_s_entry" ] && [ -f "$_s_entry/SKILL.md" ]; then
+            _sname="$(basename "$_s_entry")"
+            mkdir -p "$_copilot_skills/$_sname"
+            cp -f "$_s_entry/SKILL.md" "$_copilot_skills/$_sname/SKILL.md"
+          elif [ -f "$_s_entry" ]; then
+            _sname="$(basename "$_s_entry" .md)"
+            mkdir -p "$_copilot_skills/$_sname"
+            if grep -q '^---' "$_s_entry" 2>/dev/null; then
+              cp -f "$_s_entry" "$_copilot_skills/$_sname/SKILL.md"
+            else
+              _desc="$(awk '
+                /^#/ { in_title=1; next }
+                in_title && /^[A-Za-z]/ { print; exit }
+              ' "$_s_entry" 2>/dev/null)"
+              [ -n "$_desc" ] || _desc="Skill $_sname from plugin $_pname"
+              {
+                printf -- '---\nname: %s\ndescription: %s\n---\n\n' "$_sname" "$_desc"
+                cat "$_s_entry"
+              } > "$_copilot_skills/$_sname/SKILL.md"
+            fi
+          fi
+        done
+      done
+
+      # B. Plugin prompts & workflows as skills if not already provided
+      for _sub in prompts workflows; do
+        for _s_dir in "$_pdir/$_sub" "$NEXUS_DIR/.rnex/plugins/$_pname/$_sub"; do
+          [ -d "$_s_dir" ] || continue
+          for _pfile in "$_s_dir"/*.md; do
+            [ -f "$_pfile" ] || continue
+            _base="$(basename "$_pfile" .md)"
+            case "$_base" in
+              index|README) continue ;;
+            esac
+            _dst_sk_dir="$_copilot_skills/$_base"
+            if [ ! -f "$_dst_sk_dir/SKILL.md" ]; then
+              mkdir -p "$_dst_sk_dir"
+              _desc="$(awk '
+                /^#/ { in_title=1; next }
+                in_title && /^[A-Za-z]/ { print; exit }
+              ' "$_pfile" 2>/dev/null)"
+              [ -n "$_desc" ] || _desc="Skill $_base from plugin $_pname"
+              {
+                printf -- '---\nname: %s\ndescription: %s\n---\n\n' "$_base" "$_desc"
+                cat "$_pfile"
+              } > "$_dst_sk_dir/SKILL.md"
+            fi
+          done
+        done
+      done
+    done
+  else
+    if [ -d "$NEXUS_DIR/.github/skills" ]; then
+      rm -rf "$NEXUS_DIR/.github/skills" 2>/dev/null || true
+    fi
+  fi
+
+  # Copilot agents sync (.github/agents/*.agent.md)
+  if copilot_agents_enabled; then
+    _copilot_agents="$NEXUS_DIR/.github/agents"
+
+    yaml_list_plugins | while read -r _pname; do
+      [ -n "$_pname" ] || continue
+      yaml_plugin_enabled "$_pname" || continue
+      [ "$_pname" != "copilot" ] || continue
+      _pdir="$(find_plugin_dir "$_pname" 2>/dev/null || true)"
+      [ -n "$_pdir" ] || continue
+
+      for _s_dir in "$_pdir/agents" "$NEXUS_DIR/.rnex/plugins/$_pname/agents"; do
+        [ -d "$_s_dir" ] || continue
+        for _afile in "$_s_dir"/*.md; do
+          [ -f "$_afile" ] || continue
+          _aname="$(basename "$_afile" .agent.md)"
+          _aname="$(basename "$_aname" .md)"
+          mkdir -p "$_copilot_agents"
+          if grep -q '^---' "$_afile" 2>/dev/null; then
+            cp -f "$_afile" "$_copilot_agents/$_aname.agent.md"
+          else
+            _desc="$(awk '
+              /^#/ { in_title=1; next }
+              in_title && /^[A-Za-z]/ { print; exit }
+            ' "$_afile" 2>/dev/null)"
+            [ -n "$_desc" ] || _desc="Agent $_aname from plugin $_pname"
+            {
+              printf -- '---\nname: %s\ndescription: %s\n---\n\n' "$_aname" "$_desc"
+              cat "$_afile"
+            } > "$_copilot_agents/$_aname.agent.md"
+          fi
+          # Also mirror to skills if skills enabled
+          if copilot_skills_enabled; then
+            mkdir -p "$_copilot_skills/$_aname"
+            cp -f "$_copilot_agents/$_aname.agent.md" "$_copilot_skills/$_aname/SKILL.md"
+          fi
+        done
+      done
+    done
+  else
+    if [ -d "$NEXUS_DIR/.github/agents" ]; then
+      rm -rf "$NEXUS_DIR/.github/agents" 2>/dev/null || true
+    fi
+  fi
+
+  # Copilot instructions sync (.github/copilot-instructions.md)
+  sync_copilot_instructions
 }
 
 upgrade_workspace_config() {
@@ -1486,12 +1998,15 @@ cmd_init() {
   _cli_code_workspace=""
   _cli_hooks=""
   _cli_no_hooks=0
+  _cli_copilot=""
 
   while [ $# -gt 0 ]; do
     case "$1" in
       -y|--yes) _non_interactive=1 ;;
       --hooks) _cli_hooks="true" ;;
       --no-hooks) _cli_no_hooks=1; _cli_hooks="false" ;;
+      --copilot) _cli_copilot="true" ;;
+      --no-copilot) _cli_copilot="false" ;;
       --ai|--instructions|--ai-instructions)
         shift
         _cli_ai_instructions="$1"
@@ -1561,11 +2076,15 @@ cmd_init() {
     log_dim "To reconcile repos and plugins, run:"
     log_dim "  rnex fix"
   else
+    _init_plugins=""
+    if [ "$_cli_copilot" = "true" ]; then
+      _init_plugins="  copilot:\n    prompts: true\n    skills: true\n    instructions: true\n    agents: true\n"
+    fi
+
     cat > "$_target_yaml" <<YAML_EOF
-# Repo Nexus workspace configuration (Virtual Meta-Repo)
+# Repo Nexus workspace configuration
 # See docs/rnex.example.yaml for a comprehensive example with all options.
 
-# Workspace configuration version
 version: $RNEX_VERSION
 
 # Directory for member repository clones
@@ -1582,7 +2101,7 @@ git_hooks: $_init_git_hooks
 
 # Workspace plugins
 plugins:
-
+$(printf '%b' "$_init_plugins")
 # Member repositories managed by Repo Nexus
 repos:
 YAML_EOF
@@ -1617,11 +2136,18 @@ YAML_EOF
   mkdir -p "$_target_dir/.rnex/plugins"
   mkdir -p "$_target_dir/.rnex/prompts"
   _orig_nexus="$NEXUS_DIR"
+  _orig_yaml="$WORKSPACE_YAML"
+  _orig_local_yaml="$WORKSPACE_LOCAL_YAML"
   NEXUS_DIR="$_target_dir"
+  WORKSPACE_YAML="$_target_yaml"
+  WORKSPACE_LOCAL_YAML="$_target_dir/$RNEX_LOCAL_CONFIG_FILE"
+  sync_plugins
   sync_prompts
+  WORKSPACE_LOCAL_YAML="$_orig_local_yaml"
+  WORKSPACE_YAML="$_orig_yaml"
   NEXUS_DIR="$_orig_nexus"
 
-  # ---- 5. Ensure repos/, .rnex/, and local configs are gitignored ---------
+  # ---- 5. Ensure repos/ and local configs are gitignored ---------
   reconcile_gitignore "$_target_dir"
 
   # ---- 6. Generate VS Code / Cursor workspace if configured ----------------
@@ -1978,18 +2504,18 @@ cmd_status() {
   fi
 
   _gi="$NEXUS_DIR/.gitignore"
-  _gi_repos=0; _gi_rnex=0; _gi_local=0; _gi_has_counter=0
+  _gi_repos=0; _gi_local=0; _gi_has_counter=0; _gi_has_rnex=0
   if [ -f "$_gi" ]; then
     grep -q '^repos' "$_gi" 2>/dev/null && _gi_repos=1
-    (grep -q '^\.rnex/' "$_gi" 2>/dev/null || grep -q '^\.rnex$' "$_gi" 2>/dev/null) && _gi_rnex=1
     grep -qF "$RNEX_LOCAL_CONFIG_FILE" "$_gi" 2>/dev/null && _gi_local=1
     grep -q "lint_trigger_counter" "$_gi" 2>/dev/null && _gi_has_counter=1
+    (grep -q '^\.rnex/' "$_gi" 2>/dev/null || grep -q '^\.rnex$' "$_gi" 2>/dev/null) && _gi_has_rnex=1
   fi
 
-  if [ "$_gi_repos" -eq 1 ] && [ "$_gi_rnex" -eq 1 ] && [ "$_gi_local" -eq 1 ] && [ "$_gi_has_counter" -eq 0 ]; then
-    printf '  %b✓%b Git Ignore:    repos/, .rnex/, and %s ignored in .gitignore\n' "$_G" "$_NC" "$RNEX_LOCAL_CONFIG_FILE"
+  if [ "$_gi_repos" -eq 1 ] && [ "$_gi_local" -eq 1 ] && [ "$_gi_has_counter" -eq 0 ] && [ "$_gi_has_rnex" -eq 0 ]; then
+    printf '  %b✓%b Git Ignore:    repos/ and %s ignored in .gitignore\n' "$_G" "$_NC" "$RNEX_LOCAL_CONFIG_FILE"
   else
-    printf '  %b!%b Git Ignore:    recommend running "rnex fix" to update .gitignore (repos/, .rnex/, local configs)\n' "$_Y" "$_NC"
+    printf '  %b!%b Git Ignore:    recommend running "rnex fix" to update .gitignore (repos/, local configs)\n' "$_Y" "$_NC"
   fi
 
   _hooks_path="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
@@ -2037,6 +2563,7 @@ cmd_status() {
       fi
       ;;
   esac
+
   printf '\n'
 
   printf '%bWorkspace AI Context (Routing):%b\n' "$_BOLD" "$_NC"
@@ -2069,6 +2596,18 @@ cmd_status() {
   if [ -f "$NEXUS_DIR/.rnex/prompts/index.md" ]; then
     printf '  %b✓%b %s %b(prompts catalog)%b\n' "$_G" "$_NC" ".rnex/prompts/index.md" "$_DIM" "$_NC"
   fi
+  if [ -d "$NEXUS_DIR/.github/prompts" ]; then
+    printf '  %b✓%b %s %b(Copilot prompts)%b\n' "$_G" "$_NC" ".github/prompts/" "$_DIM" "$_NC"
+  fi
+  if [ -d "$NEXUS_DIR/.github/skills" ]; then
+    printf '  %b✓%b %s %b(Copilot skills)%b\n' "$_G" "$_NC" ".github/skills/" "$_DIM" "$_NC"
+  fi
+  if [ -d "$NEXUS_DIR/.github/agents" ]; then
+    printf '  %b✓%b %s %b(Copilot agents)%b\n' "$_G" "$_NC" ".github/agents/" "$_DIM" "$_NC"
+  fi
+  if [ -f "$NEXUS_DIR/.github/copilot-instructions.md" ]; then
+    printf '  %b✓%b %s %b(Copilot instructions)%b\n' "$_G" "$_NC" ".github/copilot-instructions.md" "$_DIM" "$_NC"
+  fi
   printf '\n'
 
   printf '%bActive Plugins:%b\n' "$_BOLD" "$_NC"
@@ -2082,8 +2621,19 @@ cmd_status() {
       if [ -n "$_pdir" ]; then
         _ver="$(plugin_get_field "$_pdir" "version")"
         _desc="$(plugin_get_field "$_pdir" "description")"
-        printf '  %b●%b %-18s %b(v%s)%b %s\n' "$_G" "$_NC" "$_pname" "$_DIM" "${_ver:-0.1.0}" "$_NC" "${_desc:+- $_desc}"
-        printf '    %bScoped directory: .rnex/plugins/%s%b\n' "$_DIM" "$_pname" "$_NC"
+        if ! yaml_plugin_enabled "$_pname"; then
+          printf '  %b○%b %-18s %b[disabled locally]%b\n' "$_DIM" "$_NC" "$_pname" "$_DIM" "$_NC"
+        else
+          printf '  %b●%b %-18s %b(v%s)%b %s\n' "$_G" "$_NC" "$_pname" "$_DIM" "${_ver:-0.1.0}" "$_NC" "${_desc:+- $_desc}"
+          printf '    %bScoped directory: .rnex/plugins/%s%b\n' "$_DIM" "$_pname" "$_NC"
+          if [ "$_pname" = "copilot" ]; then
+            printf '    %b↳ Options: prompts=%s, skills=%s, instructions=%s, agents=%s%b\n' "$_DIM" \
+              "$(copilot_prompts_enabled && echo "true" || echo "false")" \
+              "$(copilot_skills_enabled && echo "true" || echo "false")" \
+              "$(copilot_instructions_enabled && echo "true" || echo "false")" \
+              "$(copilot_agents_enabled && echo "true" || echo "false")" "$_NC"
+          fi
+        fi
       else
         printf '  %b✗%b %-18s %bMISSING%b\n' "$_R" "$_NC" "$_pname" "$_R" "$_NC"
         printf '    %b↳ [!] Issue: plugin declared in config but directory not found on disk%b\n' "$_R" "$_NC"
@@ -2174,6 +2724,7 @@ cmd_fix() {
       _load_ai_instructions_file
       _load_code_workspace
       _load_git_hooks
+      _load_copilot
       [ "$_fix_quiet" -eq 0 ] && log_ok "Upgraded workspace configuration and routing instructions to v$RNEX_VERSION"
     fi
   fi
@@ -2330,8 +2881,10 @@ cmd_plugin_info() {
   _author="$(plugin_get_field "$_pdir" "author")"
   _home="$(plugin_get_field "$_pdir" "homepage")"
 
-  if yaml_has_plugin "$_name"; then
+  if yaml_plugin_enabled "$_name"; then
     _status="${_G}enabled${_NC}"
+  elif yaml_has_plugin "$_name"; then
+    _status="${_DIM}disabled locally (${WORKSPACE_LOCAL_YAML})${_NC}"
   else
     _status="${_DIM}available (not enabled)${_NC}"
   fi
@@ -2344,6 +2897,14 @@ cmd_plugin_info() {
   [ -n "$_home" ] && printf '%bHomepage:%b     %s\n' "$_BOLD" "$_NC" "$_home"
   printf '%bLocation:%b     %s\n' "$_BOLD" "$_NC" "$_pdir"
 
+  if [ "$_name" = "copilot" ]; then
+    printf '\n%bConfigurable Options (in rnex.yaml or .local.rnex.yaml):%b\n' "$_BOLD" "$_NC"
+    printf '  - prompts: true|false  (mirror prompts to .github/prompts/*.prompt.md; current: %s)\n' "$(copilot_prompts_enabled && echo "true" || echo "false")"
+    printf '  - skills: true|false  (mirror skills to .github/skills/<name>/SKILL.md; current: %s)\n' "$(copilot_skills_enabled && echo "true" || echo "false")"
+    printf '  - instructions: true|false  (mirror instructions to .github/copilot-instructions.md; current: %s)\n' "$(copilot_instructions_enabled && echo "true" || echo "false")"
+    printf '  - agents: true|false  (mirror agents to .github/agents/*.agent.md; current: %s)\n' "$(copilot_agents_enabled && echo "true" || echo "false")"
+  fi
+
   printf '\n%bScoped Directory:%b .rnex/plugins/%s\n' "$_BOLD" "$_NC" "$_name"
 
   _tmpl="$(plugin_list_templates "$_pdir")"
@@ -2363,8 +2924,16 @@ cmd_plugin_info() {
 
 cmd_plugin_enable() {
   require_workspace
-  _pname="$1"
-  [ -n "$_pname" ] || die "Usage: rnex plugin enable <name>"
+  _is_local=0
+  _pname=""
+  while [ $# -gt 0 ]; do
+    case "$1" in
+      --local) _is_local=1 ;;
+      *) _pname="$1" ;;
+    esac
+    shift
+  done
+  [ -n "$_pname" ] || die "Usage: rnex plugin enable [--local] <name>"
 
   _pdir="$(find_plugin_dir "$_pname" 2>/dev/null || true)"
   [ -n "$_pdir" ] || die "Plugin '$_pname' not found."
@@ -2372,8 +2941,13 @@ cmd_plugin_enable() {
   _name="$(plugin_get_field "$_pdir" "name")"
   [ -n "$_name" ] || _name="$_pname"
 
-  yaml_enable_plugin "$_name"
-  log_ok "Plugin '$_name' enabled in $(basename "$WORKSPACE_YAML")"
+  if [ "$_is_local" -eq 1 ]; then
+    yaml_enable_plugin "$_name" "$WORKSPACE_LOCAL_YAML"
+    log_ok "Plugin '$_name' enabled locally in $(basename "$WORKSPACE_LOCAL_YAML")"
+  else
+    yaml_enable_plugin "$_name" "$WORKSPACE_YAML"
+    log_ok "Plugin '$_name' enabled in $(basename "$WORKSPACE_YAML")"
+  fi
 
   sync_plugins
   cmd_fix
@@ -2382,8 +2956,16 @@ cmd_plugin_enable() {
 
 cmd_plugin_disable() {
   require_workspace
-  _pname="$1"
-  [ -n "$_pname" ] || die "Usage: rnex plugin disable <name>"
+  _is_local=0
+  _pname=""
+  while [ $# -gt 0 ]; do
+    case "$1" in
+      --local) _is_local=1 ;;
+      *) _pname="$1" ;;
+    esac
+    shift
+  done
+  [ -n "$_pname" ] || die "Usage: rnex plugin disable [--local] <name>"
 
   _pdir="$(find_plugin_dir "$_pname" 2>/dev/null || true)"
   _name="$_pname"
@@ -2392,22 +2974,34 @@ cmd_plugin_disable() {
     [ -n "$_n" ] && _name="$_n"
   fi
 
-  yaml_disable_plugin "$_name"
-
-  # Remove scoped plugin from workspace .rnex/plugins/
-  if [ -d "$NEXUS_DIR/.rnex/plugins/$_name" ]; then
-    rm -rf "$NEXUS_DIR/.rnex/plugins/$_name"
-    log_ok "Removed workspace plugin scope: .rnex/plugins/$_name"
+  if [ "$_is_local" -eq 1 ]; then
+    if _yaml_list_plugins_from_file "$WORKSPACE_YAML" | grep -qx "$_name" 2>/dev/null; then
+      yaml_plugin_set_local "$_name" "enabled" "false"
+      log_ok "Plugin '$_name' disabled locally in $(basename "$WORKSPACE_LOCAL_YAML")"
+    else
+      _yaml_disable_plugin_in_file "$WORKSPACE_LOCAL_YAML" "$_name"
+      log_ok "Plugin '$_name' removed from $(basename "$WORKSPACE_LOCAL_YAML")"
+    fi
+  else
+    yaml_disable_plugin "$_name"
+    log_ok "Plugin '$_name' disabled from workspace"
   fi
 
-  # Remove scoped plugin from member repos .rnex/plugins/
-  yaml_list_repos | while read -r _rname; do
-    _rpath="$(resolve_repo_path "$_rname")"
-    if [ -d "$_rpath/.rnex/plugins/$_name" ]; then
-      rm -rf "$_rpath/.rnex/plugins/$_name"
+  if ! yaml_plugin_enabled "$_name"; then
+    if [ -d "$NEXUS_DIR/.rnex/plugins/$_name" ]; then
+      rm -rf "$NEXUS_DIR/.rnex/plugins/$_name"
+      log_ok "Removed workspace plugin scope: .rnex/plugins/$_name"
     fi
-  done
 
+    yaml_list_repos | while read -r _rname; do
+      _rpath="$(resolve_repo_path "$_rname")"
+      if [ -d "$_rpath/.rnex/plugins/$_name" ]; then
+        rm -rf "$_rpath/.rnex/plugins/$_name"
+      fi
+    done
+  fi
+
+  sync_prompts
   log_ok "Plugin '$_name' disabled from workspace"
 }
 
@@ -2630,7 +3224,7 @@ cmd_help() {
     -v, --version           Show version
 
   WORKSPACE & SYSTEM SETUP
-    init [-y] [--ai <file>] [--code-workspace [file]] [--hooks|--no-hooks] [dir]
+    init [-y] [--ai <file>] [--code-workspace [file]] [--hooks|--no-hooks] [--copilot|--no-copilot] [dir]
                             Initialize a new Repo Nexus workspace (default AI file: AGENTS.md)
     install [dir]           Install rnex & repo-nexus globally into ~/.local/bin (or custom dir)
     fix [-y] [--quiet]      Reconcile workspace, plugins, prompts & member .rnex/ (alias: sync)
@@ -2654,8 +3248,8 @@ cmd_help() {
   PLUGIN MANAGEMENT
     plugin [list]           List available and enabled plugins
     plugin info <name>      Show details of a plugin
-    plugin enable <name>    Enable plugin in workspace (scoped to .rnex/plugins/<name>/)
-    plugin disable <name>   Disable plugin from workspace
+    plugin enable [--local] <name>   Enable plugin in workspace (scoped to .rnex/plugins/<name>/)
+    plugin disable [--local] <name>  Disable plugin from workspace
 
   EXAMPLES
     rnex init                                   # Initialize workspace in current folder

package/toolkit/plugins/copilot/README.md

@@ -0,0 +1,37 @@
+# GitHub Copilot Plugin for Repo Nexus
+
+A built-in Repo Nexus plugin providing bidirectional alignment and operational prompt/skill mirroring for GitHub Copilot.
+
+## Capabilities
+
+1. **Prompts Mirroring**: Standardized Repo Nexus prompts (`rnex-feature`, `rnex-audit`, etc.) and active plugins' prompts/workflows are synchronized into `.github/prompts/*.prompt.md` with YAML frontmatter.
+2. **Agent Skills**: Prompts, active plugin skills, and agent bundles are mirrored into `.github/skills/<name>/SKILL.md` for GitHub Copilot Agent mode.
+3. **Custom Agents**: Active plugins' agents are mirrored into `.github/agents/*.agent.md`.
+4. **Instructions Integration**: Active plugins' rules/instructions and Repo Nexus routing instructions are synthesized into `.github/copilot-instructions.md`.
+
+## Usage
+
+Enable the plugin across the workspace:
+```bash
+rnex plugin enable copilot
+```
+
+Or configure options in `rnex.yaml` or `.local.rnex.yaml`:
+```yaml
+plugins:
+  copilot:
+    prompts: true
+    skills: true
+    instructions: true
+    agents: true
+```
+
+## Options
+
+| Option | Type | Default | Description |
+|--------|------|---------|-------------|
+| `prompts` | boolean | `true` | Mirror prompts to `.github/prompts/*.prompt.md` |
+| `skills` | boolean | `true` | Mirror skills to `.github/skills/<name>/SKILL.md` |
+| `instructions` | boolean | `true` | Mirror guidelines to `.github/copilot-instructions.md` |
+| `agents` | boolean | `true` | Mirror custom agents to `.github/agents/*.agent.md` |
+| `enabled` | boolean | `true` | Set to `false` in `.local.rnex.yaml` to override team config |

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

@@ -0,0 +1,29 @@
+# GitHub Copilot Integration for Repo Nexus
+
+This workspace has the Repo Nexus `copilot` plugin enabled.
+
+## Operating Principles
+- **Prompts (`.github/prompts/*.prompt.md`)**: Operational Repo Nexus prompts and active plugins' prompts/workflows are mirrored here with YAML frontmatter (`name`, `description`) for use in the VS Code Copilot Chat prompt picker and slash commands.
+- **Agent Skills (`.github/skills/<name>/SKILL.md`)**: Standard prompts, active plugin skills, and agent bundles are mirrored as individual skill bundles with frontmatter for GitHub Copilot Agent mode and `gh skill`.
+- **Custom Agents (`.github/agents/*.agent.md`)**: Active plugins' agent definitions (such as `wiki-curator`) are mirrored here for Copilot workspace custom agents.
+- **Copilot Instructions (`.github/copilot-instructions.md`)**: Synthesizes workspace routing and active plugin guidelines between `<!-- REPO-NEXUS:START -->` and `<!-- REPO-NEXUS:END -->`, preserving any manual user instructions outside those markers.
+- **Decoupled Cross-Plugin Discovery**: Plugins remain independent and decoupled; the `copilot` provider discovers and mirrors assets from whatever plugins are currently active.
+
+## Configuration
+Configure plugin options in `rnex.yaml` or override them per developer in `.local.rnex.yaml`:
+
+```yaml
+plugins:
+  copilot:
+    prompts: true        # Mirror prompts to .github/prompts/ (default: true)
+    skills: true         # Mirror skills to .github/skills/ (default: true)
+    instructions: true   # Mirror routing & plugin guidelines to .github/copilot-instructions.md (default: true)
+    agents: true         # Mirror custom agents to .github/agents/ (default: true)
+```
+
+To disable locally without altering team configuration, add to `.local.rnex.yaml`:
+```yaml
+plugins:
+  copilot:
+    enabled: false
+```

package/toolkit/plugins/copilot/plugin.yaml

@@ -0,0 +1,7 @@
+name: copilot
+version: 0.5.1
+description: GitHub Copilot integration (mirrors workspace prompts to .github/prompts and skills to .github/skills)
+author: nu-nenoi
+homepage: https://github.com/nu-nenoi/repo-nexus
+instructions:
+  - instructions/copilot-integration.md: .rnex/plugins/copilot/instructions/copilot-integration.md

package/toolkit/plugins/karpathy-llm/agents/wiki-curator.agent.md

@@ -0,0 +1,8 @@
+---
+name: wiki-curator
+description: Autonomous knowledge librarian for the Karpathy LLM Wiki architecture.
+---
+
+# Wiki Curator Agent
+
+Autonomous knowledge librarian specialized in synthesizing unstructured source documents into the atomic Karpathy LLM Wiki graph.

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

@@ -0,0 +1,10 @@
+# Karpathy LLM Wiki Ingestion Workflow (`wiki-ingest`)
+
+Autonomous workflow for decomposing and ingesting raw source documents from `raw/` into atomic Karpathy LLM Wiki pages.
+
+## Protocol
+1. Scan `raw/` for uningested documents not yet recorded in `wiki/_log.md`.
+2. Read source materials completely; preserve original files in `raw/` unmodified.
+3. Decompose each source document into atomic wiki pages in `wiki/` (5–25 pages per source).
+4. For every page, write required YAML frontmatter with typed relations (`sources`, `related`, `extends`, `contradicts`, `mentioned_in`).
+5. Update `wiki/index.md` and append an entry to `wiki/_log.md`.

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

@@ -0,0 +1,10 @@
+# Karpathy LLM Wiki Lint & Graph Maintenance (`wiki-lint`)
+
+Periodic maintenance workflow to preserve wiki graph integrity, validate typed relations, and recompute bidirectional links.
+
+## Protocol
+1. Verify all frontmatter relation paths (`sources`, `related`, `extends`, `contradicts`) resolve to existing files.
+2. Recompute `mentioned_in` backlinks for every page across the entire wiki graph.
+3. Find orphaned pages not reachable from `wiki/index.md` or any `mentioned_in` link, and index them.
+4. Detect duplicate/overlapping pages and check for factual contradictions.
+5. Identify knowledge gaps and append audit results to `wiki/_log.md`.

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

@@ -0,0 +1,14 @@
+---
+name: wiki-ingest
+description: Autonomous ingestion and atomic decomposition of raw sources into Karpathy LLM Wiki pages.
+---
+
+# Karpathy LLM Wiki Ingestion Skill
+
+Use this skill when decomposing raw documents, research notes, meeting logs, or external articles from `raw/` into atomic wiki pages under `wiki/`.
+
+## Key Rules
+- Source documents stay untouched in `raw/`.
+- Produce 5–25 atomic pages per document (never lump into one large file).
+- Include YAML frontmatter with typed relations (`sources`, `related`, `extends`, `contradicts`, `mentioned_in`).
+- Record completed ingestion in `wiki/_log.md`.

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

@@ -0,0 +1,14 @@
+---
+name: wiki-lint
+description: Autonomous link validation, backlink recalculation, and graph repair for Karpathy LLM Wiki.
+---
+
+# Karpathy LLM Wiki Lint Skill
+
+Use this skill when auditing and maintaining knowledge graph integrity across `/wiki/`.
+
+## Key Steps
+- Validate all relation filepaths exist.
+- Recalculate and update `mentioned_in` backlinks.
+- Check for orphan pages and update `wiki/index.md`.
+- Flag contradictions and record maintenance in `wiki/_log.md`.