repo-nexus 0.7.18 → 0.7.19

package/lib/commands/plugin.sh

@@ -131,8 +131,8 @@ cmd_plugin_info() {
       [ -n "$_item" ] || continue
       _s="${_item%%:*}"
       _d="${_item#*:}"
-      _s="$(printf '%s' "$_s" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')"
-      _d="$(printf '%s' "$_d" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')"
+      _s="$(printf '%s' "$_s" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' -e 's/^["\047]//' -e 's/["\047]$//')"
+      _d="$(printf '%s' "$_d" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' -e 's/^["\047]//' -e 's/["\047]$//')"
       _d="$(plugin_resolve_placeholders "$_name" "$_pdir" "$_d")"
       printf '  - %s → %s\n' "$_s" "$_d"
     done

package/lib/hooks.sh

@@ -115,6 +115,11 @@ run_plugin_git_hooks() {
   RNEX_ARGS="$*"
   RNEX_QUIET="${_sync_quiet:-0}"
 
+  _stdin_data=""
+  if [ ! -t 0 ]; then
+    _stdin_data="$(cat)"
+  fi
+
   _plugins="$(yaml_list_plugins 2>/dev/null || true)"
   for _pname in $_plugins; do
     [ -n "$_pname" ] || continue
@@ -143,7 +148,11 @@ run_plugin_git_hooks() {
       chmod +x "$_h_cand" 2>/dev/null || true
       (
         export RNEX_ROOT RNEX_CONFIG_MERGED RNEX_PLUGIN_DIR RNEX_CMD RNEX_ARGS RNEX_QUIET
-        "$_h_cand" "$@"
+        if [ -n "$_stdin_data" ]; then
+          printf '%s\n' "$_stdin_data" | "$_h_cand" "$@"
+        else
+          "$_h_cand" "$@"
+        fi
       ) || true
     fi
   done
@@ -377,11 +386,27 @@ cmd_hooks() {
           return 0
           ;;
         pre-push)
-          run_plugin_git_hooks "pre-push" "$@"
+          _stdin_data=""
+          if [ ! -t 0 ]; then
+            _stdin_data="$(cat)"
+          fi
+          if [ -n "$_stdin_data" ]; then
+            printf '%s\n' "$_stdin_data" | run_plugin_git_hooks "pre-push" "$@"
+          else
+            run_plugin_git_hooks "pre-push" "$@"
+          fi
           if [ -x "$NEXUS_DIR/scripts/githooks/pre-push" ]; then
-            "$NEXUS_DIR/scripts/githooks/pre-push" "$@" || return $?
+            if [ -n "$_stdin_data" ]; then
+              printf '%s\n' "$_stdin_data" | "$NEXUS_DIR/scripts/githooks/pre-push" "$@" || return $?
+            else
+              "$NEXUS_DIR/scripts/githooks/pre-push" "$@" || return $?
+            fi
           elif [ -x "$NEXUS_DIR/.githooks/pre-push" ]; then
-            "$NEXUS_DIR/.githooks/pre-push" "$@" || return $?
+            if [ -n "$_stdin_data" ]; then
+              printf '%s\n' "$_stdin_data" | "$NEXUS_DIR/.githooks/pre-push" "$@" || return $?
+            else
+              "$NEXUS_DIR/.githooks/pre-push" "$@" || return $?
+            fi
           fi
           return 0
           ;;

package/lib/plugins.sh

@@ -91,7 +91,7 @@ plugin_list_instructions() {
 
 plugin_resolve_placeholders() {
   _p="$1"; _pd="$2"; _str="$3"
-  _res="$_str"
+  _res="$(printf '%s' "$_str" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' -e 's/^["\047]//' -e 's/["\047]$//')"
 
   if [ -f "$_pd/plugin.yaml" ]; then
     _keys="$(awk '
@@ -142,6 +142,8 @@ plugin_resolve_placeholders() {
     -e "s|^wiki/|${_w_val}/|" \
     -e "s|^raw/|${_r_val}/|")"
 
+  _res="$(printf '%s' "$_res" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' -e 's/^["\047]//' -e 's/["\047]$//')"
+
   printf '%s' "$_res"
 }
 
@@ -230,8 +232,8 @@ sync_plugins() {
       [ -n "$_item" ] || continue
       _s="${_item%%:*}"
       _d="${_item#*:}"
-      _s="$(printf '%s' "$_s" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')"
-      _d="$(printf '%s' "$_d" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')"
+      _s="$(printf '%s' "$_s" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' -e 's/^["\047]//' -e 's/["\047]$//')"
+      _d="$(printf '%s' "$_d" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' -e 's/^["\047]//' -e 's/["\047]$//')"
 
       _d="$(plugin_resolve_placeholders "$_pname" "$_pdir" "$_d")"
 

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.7.18",
+  "version": "0.7.19",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",

package/templates/rnex-env.sh

@@ -103,3 +103,137 @@ rnex_unregister_user_skill() {
     fi
   done
 }
+
+# Provider configuration check helper
+if ! command -v provider_option_enabled >/dev/null 2>&1; then
+  provider_option_enabled() {
+    _p="$1"; _opt="$2"
+    _r="${NEXUS_DIR:-${RNEX_ROOT:-.}}"
+    _val=""
+    if [ -f "$_r/.local.rnex.yaml" ]; then
+      _val="$(awk -v p="$_p" -v o="$_opt" '
+        /^plugins:/ { in_p=1; next }
+        in_p && /^[^ #]/ { in_p=0; in_target=0 }
+        in_p && match($0, "^[ ]*" p ":[ ]*(#.*)?$") { in_target=1; next }
+        in_target && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_target=0 }
+        in_target && $0 ~ ("^[ ]*" o ":") {
+          sub("^[ ]*" o ":[ ]*", "")
+          sub(/[ ]*#.*/, "")
+          gsub(/["\047]/, "")
+          print
+          exit
+        }
+      ' "$_r/.local.rnex.yaml")"
+    fi
+    if [ -z "$_val" ] && [ -f "$_r/rnex.yaml" ]; then
+      _val="$(awk -v p="$_p" -v o="$_opt" '
+        /^plugins:/ { in_p=1; next }
+        in_p && /^[^ #]/ { in_p=0; in_target=0 }
+        in_p && match($0, "^[ ]*" p ":[ ]*(#.*)?$") { in_target=1; next }
+        in_target && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_target=0 }
+        in_target && $0 ~ ("^[ ]*" o ":") {
+          sub("^[ ]*" o ":[ ]*", "")
+          sub(/[ ]*#.*/, "")
+          gsub(/["\047]/, "")
+          print
+          exit
+        }
+      ' "$_r/rnex.yaml")"
+    fi
+    _val="$(printf '%s' "$_val" | tr '[:upper:]' '[:lower:]')"
+    case "$_val" in
+      false|no|0|disabled|off) return 1 ;;
+      *) return 0 ;;
+    esac
+  }
+fi
+
+# Instructions routing helpers
+if ! command -v merge_rnex_instructions >/dev/null 2>&1; then
+  merge_rnex_instructions() {
+    _dst="$1"
+    _m_start="<!-- REPO-NEXUS:START -->"
+    _m_end="<!-- REPO-NEXUS:END -->"
+    _instr="CRITICAL: You MUST read and strictly follow all instructions in \`.rnex/ai-instructions.md\` before executing any task or answering any query in this workspace."
+    if [ ! -f "$_dst" ]; then
+      mkdir -p "$(dirname "$_dst")"
+      printf '%s\n%s\n%s\n' "$_m_start" "$_instr" "$_m_end" > "$_dst"
+      return 0
+    fi
+    if grep -qF "$_m_start" "$_dst" 2>/dev/null; then
+      _tmp="$(mktemp)"
+      awk -v s="$_m_start" -v e="$_m_end" -v msg="$_instr" '
+        $0 == s { in_b = 1; print s; print msg; next }
+        $0 == e { in_b = 0; print e; next }
+        !in_b { print }
+      ' "$_dst" > "$_tmp" && mv "$_tmp" "$_dst"
+      return 0
+    fi
+    _tmp="$(mktemp)"
+    cp "$_dst" "$_tmp"
+    if [ -s "$_tmp" ] && [ -n "$(tail -c 1 "$_tmp" 2>/dev/null)" ]; then
+      printf '\n' >> "$_tmp"
+    fi
+    printf '\n%s\n%s\n%s\n' "$_m_start" "$_instr" "$_m_end" >> "$_tmp"
+    mv "$_tmp" "$_dst"
+  }
+fi
+
+if ! command -v clean_rnex_instructions >/dev/null 2>&1; then
+  clean_rnex_instructions() {
+    _dst="$1"
+    [ -f "$_dst" ] || return 0
+    _m_start="<!-- REPO-NEXUS:START -->"
+    _m_end="<!-- REPO-NEXUS:END -->"
+    if grep -qF "$_m_start" "$_dst" 2>/dev/null; then
+      _non_rnex="$(awk -v s="$_m_start" -v e="$_m_end" '
+        $0 == s { skip=1; next }
+        $0 == e { skip=0; next }
+        !skip { print }
+      ' "$_dst" | tr -d " \t\r\n")"
+      if [ -z "$_non_rnex" ]; then
+        rm -f "$_dst"
+      else
+        _tmp="$(mktemp)"
+        awk -v s="$_m_start" -v e="$_m_end" '
+          $0 == s { skip=1; next }
+          $0 == e { skip=0; next }
+          !skip { print }
+        ' "$_dst" > "$_tmp" && mv "$_tmp" "$_dst"
+      fi
+    fi
+  }
+fi
+
+if ! command -v clean_provider_user_skills >/dev/null 2>&1; then
+  clean_provider_user_skills() {
+    _sk_dir="$1"
+    [ -d "$_sk_dir" ] || return 0
+    rm -f "$_sk_dir"/rnex-*.md 2>/dev/null || true
+    for _d in "$_sk_dir"/rnex-*; do
+      [ -d "$_d" ] || continue
+      rm -rf "$_d" 2>/dev/null || true
+    done
+    rmdir "$_sk_dir" 2>/dev/null || true
+  }
+fi
+
+if ! command -v clean_provider_agents >/dev/null 2>&1; then
+  clean_provider_agents() {
+    _ag_dir="$1"
+    _ext="${2:-.md}"
+    _r="${NEXUS_DIR:-${RNEX_ROOT:-.}}"
+    [ -d "$_ag_dir" ] || return 0
+    for _pdir in "$_r/toolkit/plugins"/* "$_r/.rnex/plugins"/*; do
+      [ -d "$_pdir" ] || continue
+      [ -d "$_pdir/agents" ] || continue
+      for _afile in "$_pdir/agents"/*.md; do
+        [ -f "$_afile" ] || continue
+        _aname="$(basename "$_afile" .agent.md)"
+        _aname="$(basename "$_aname" .md)"
+        rm -f "$_ag_dir/${_aname}${_ext}" 2>/dev/null || true
+      done
+    done
+    rmdir "$_ag_dir" 2>/dev/null || true
+  }
+fi

package/toolkit/plugins/copilot/hooks/after_sync.sh

@@ -1,22 +1,162 @@
 #!/bin/sh
 set -e
 _root="${RNEX_ROOT:-${NEXUS_DIR:-$PWD}}"
+NEXUS_DIR="${NEXUS_DIR:-$_root}"
+WORKSPACE_YAML="${WORKSPACE_YAML:-$_root/rnex.yaml}"
+WORKSPACE_LOCAL_YAML="${WORKSPACE_LOCAL_YAML:-$_root/.local.rnex.yaml}"
+export RNEX_ROOT NEXUS_DIR WORKSPACE_YAML WORKSPACE_LOCAL_YAML
 
-if ! command -v merge_rnex_instructions >/dev/null 2>&1; then
+# Explicitly locate and source core helper library if functions not preloaded
+if ! command -v merge_rnex_instructions >/dev/null 2>&1 || ! command -v provider_option_enabled >/dev/null 2>&1; then
+  if [ -z "${RNEX_LIB_DIR:-}" ]; then
+    for _cand in \
+      "$_root/lib" \
+      "$(dirname "$0")/../../../../lib" \
+      "$(dirname "$0")/../../../lib"; do
+      if [ -d "$_cand" ] && [ -f "$_cand/ai.sh" ]; then
+        RNEX_LIB_DIR="$(cd "$_cand" 2>/dev/null && pwd -P)"
+        break
+      fi
+    done
+  fi
+  if [ -n "${RNEX_LIB_DIR:-}" ] && [ -d "$RNEX_LIB_DIR" ]; then
+    [ -f "$RNEX_LIB_DIR/core.sh" ] && . "$RNEX_LIB_DIR/core.sh" 2>/dev/null || true
+    [ -f "$RNEX_LIB_DIR/workspace.sh" ] && . "$RNEX_LIB_DIR/workspace.sh" 2>/dev/null || true
+    [ -f "$RNEX_LIB_DIR/yaml.sh" ] && . "$RNEX_LIB_DIR/yaml.sh" 2>/dev/null || true
+    [ -f "$RNEX_LIB_DIR/ai.sh" ] && . "$RNEX_LIB_DIR/ai.sh" 2>/dev/null || true
+  fi
   if [ -f "$_root/.rnex/bin/rnex-env.sh" ]; then
     . "$_root/.rnex/bin/rnex-env.sh"
   fi
 fi
 
+# Complete guarded fallback contract for standalone or restricted hook runners
+if ! command -v provider_option_enabled >/dev/null 2>&1; then
+  provider_option_enabled() {
+    _p="$1"; _opt="$2"
+    _val=""
+    if [ -f "$_root/.local.rnex.yaml" ]; then
+      _val="$(awk -v p="$_p" -v o="$_opt" '
+        /^plugins:/ { in_p=1; next }
+        in_p && /^[^ #]/ { in_p=0; in_target=0 }
+        in_p && match($0, "^[ ]*" p ":[ ]*(#.*)?$") { in_target=1; next }
+        in_target && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_target=0 }
+        in_target && $0 ~ ("^[ ]*" o ":") {
+          sub("^[ ]*" o ":[ ]*", "")
+          sub(/[ ]*#.*/, "")
+          gsub(/["\047]/, "")
+          print
+          exit
+        }
+      ' "$_root/.local.rnex.yaml")"
+    fi
+    if [ -z "$_val" ] && [ -f "$_root/rnex.yaml" ]; then
+      _val="$(awk -v p="$_p" -v o="$_opt" '
+        /^plugins:/ { in_p=1; next }
+        in_p && /^[^ #]/ { in_p=0; in_target=0 }
+        in_p && match($0, "^[ ]*" p ":[ ]*(#.*)?$") { in_target=1; next }
+        in_target && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_target=0 }
+        in_target && $0 ~ ("^[ ]*" o ":") {
+          sub("^[ ]*" o ":[ ]*", "")
+          sub(/[ ]*#.*/, "")
+          gsub(/["\047]/, "")
+          print
+          exit
+        }
+      ' "$_root/rnex.yaml")"
+    fi
+    _val="$(printf '%s' "$_val" | tr '[:upper:]' '[:lower:]')"
+    case "$_val" in
+      false|no|0|disabled|off) return 1 ;;
+      *) return 0 ;;
+    esac
+  }
+fi
+
+if ! command -v merge_rnex_instructions >/dev/null 2>&1; then
+  merge_rnex_instructions() {
+    _dst="$1"
+    _m_start="<!-- REPO-NEXUS:START -->"
+    _m_end="<!-- REPO-NEXUS:END -->"
+    _instr="CRITICAL: You MUST read and strictly follow all instructions in \`.rnex/ai-instructions.md\` before executing any task or answering any query in this workspace."
+    if [ ! -f "$_dst" ]; then
+      mkdir -p "$(dirname "$_dst")"
+      printf '%s\n%s\n%s\n' "$_m_start" "$_instr" "$_m_end" > "$_dst"
+      return 0
+    fi
+    if grep -qF "$_m_start" "$_dst" 2>/dev/null; then
+      _tmp="$(mktemp)"
+      awk -v s="$_m_start" -v e="$_m_end" -v msg="$_instr" '
+        $0 == s { in_b = 1; print s; print msg; next }
+        $0 == e { in_b = 0; print e; next }
+        !in_b { print }
+      ' "$_dst" > "$_tmp" && mv "$_tmp" "$_dst"
+      return 0
+    fi
+    _tmp="$(mktemp)"
+    cp "$_dst" "$_tmp"
+    if [ -s "$_tmp" ] && [ -n "$(tail -c 1 "$_tmp" 2>/dev/null)" ]; then
+      printf '\n' >> "$_tmp"
+    fi
+    printf '\n%s\n%s\n%s\n' "$_m_start" "$_instr" "$_m_end" >> "$_tmp"
+    mv "$_tmp" "$_dst"
+  }
+fi
+
+if ! command -v clean_rnex_instructions >/dev/null 2>&1; then
+  clean_rnex_instructions() {
+    _dst="$1"
+    [ -f "$_dst" ] || return 0
+    _m_start="<!-- REPO-NEXUS:START -->"
+    _m_end="<!-- REPO-NEXUS:END -->"
+    if grep -qF "$_m_start" "$_dst" 2>/dev/null; then
+      _non_rnex="$(awk -v s="$_m_start" -v e="$_m_end" '
+        $0 == s { skip=1; next }
+        $0 == e { skip=0; next }
+        !skip { print }
+      ' "$_dst" | tr -d " \t\r\n")"
+      if [ -z "$_non_rnex" ]; then
+        rm -f "$_dst"
+      else
+        _tmp="$(mktemp)"
+        awk -v s="$_m_start" -v e="$_m_end" '
+          $0 == s { skip=1; next }
+          $0 == e { skip=0; next }
+          !skip { print }
+        ' "$_dst" > "$_tmp" && mv "$_tmp" "$_dst"
+      fi
+    fi
+  }
+fi
+
+if ! command -v clean_provider_user_skills >/dev/null 2>&1; then
+  clean_provider_user_skills() {
+    _sk_dir="$1"
+    [ -d "$_sk_dir" ] || return 0
+    rm -f "$_sk_dir"/rnex-*.md 2>/dev/null || true
+    for _d in "$_sk_dir"/rnex-*; do
+      [ -d "$_d" ] || continue
+      rm -rf "$_d" 2>/dev/null || true
+    done
+    rmdir "$_sk_dir" 2>/dev/null || true
+  }
+fi
+
 _inst="$(provider_option_enabled "copilot" "instructions" 2>/dev/null && echo "true" || echo "false")"
 if [ "$_inst" = "true" ]; then
   mkdir -p "$_root/.github"
-  merge_rnex_instructions "$_root/.github/copilot-instructions.md"
+  if command -v merge_rnex_instructions >/dev/null 2>&1; then
+    merge_rnex_instructions "$_root/.github/copilot-instructions.md"
+  fi
 else
-  clean_rnex_instructions "$_root/.github/copilot-instructions.md"
+  if command -v clean_rnex_instructions >/dev/null 2>&1; then
+    clean_rnex_instructions "$_root/.github/copilot-instructions.md"
+  fi
 fi
 
 _sk="$(provider_option_enabled "copilot" "skills" 2>/dev/null && echo "true" || echo "false")"
 if [ "$_sk" != "true" ]; then
-  clean_provider_user_skills "$_root/.github/skills"
+  if command -v clean_provider_user_skills >/dev/null 2>&1; then
+    clean_provider_user_skills "$_root/.github/skills"
+  fi
 fi

package/toolkit/plugins/copilot/hooks/before_plugin_disable.sh

@@ -1,15 +1,111 @@
 #!/bin/sh
 set -e
 _root="${RNEX_ROOT:-${NEXUS_DIR:-$PWD}}"
+NEXUS_DIR="${NEXUS_DIR:-$_root}"
+WORKSPACE_YAML="${WORKSPACE_YAML:-$_root/rnex.yaml}"
+WORKSPACE_LOCAL_YAML="${WORKSPACE_LOCAL_YAML:-$_root/.local.rnex.yaml}"
+export RNEX_ROOT NEXUS_DIR WORKSPACE_YAML WORKSPACE_LOCAL_YAML
 
-if ! command -v clean_rnex_instructions >/dev/null 2>&1; then
+# Explicitly locate and source core helper library if functions not preloaded
+if ! command -v clean_rnex_instructions >/dev/null 2>&1 || ! command -v clean_provider_user_skills >/dev/null 2>&1 || ! command -v clean_provider_agents >/dev/null 2>&1; then
+  if [ -z "${RNEX_LIB_DIR:-}" ]; then
+    for _cand in \
+      "$_root/lib" \
+      "$(dirname "$0")/../../../../lib" \
+      "$(dirname "$0")/../../../lib"; do
+      if [ -d "$_cand" ] && [ -f "$_cand/ai.sh" ]; then
+        RNEX_LIB_DIR="$(cd "$_cand" 2>/dev/null && pwd -P)"
+        break
+      fi
+    done
+  fi
+  if [ -n "${RNEX_LIB_DIR:-}" ] && [ -d "$RNEX_LIB_DIR" ]; then
+    [ -f "$RNEX_LIB_DIR/core.sh" ] && . "$RNEX_LIB_DIR/core.sh" 2>/dev/null || true
+    [ -f "$RNEX_LIB_DIR/workspace.sh" ] && . "$RNEX_LIB_DIR/workspace.sh" 2>/dev/null || true
+    [ -f "$RNEX_LIB_DIR/yaml.sh" ] && . "$RNEX_LIB_DIR/yaml.sh" 2>/dev/null || true
+    [ -f "$RNEX_LIB_DIR/ai.sh" ] && . "$RNEX_LIB_DIR/ai.sh" 2>/dev/null || true
+  fi
   if [ -f "$_root/.rnex/bin/rnex-env.sh" ]; then
     . "$_root/.rnex/bin/rnex-env.sh"
   fi
 fi
 
-clean_rnex_instructions "$_root/.github/copilot-instructions.md"
-clean_provider_user_skills "$_root/.github/skills"
-clean_provider_agents "$_root/.github/agents" ".agent.md"
-rm -rf "$_root/.github/prompts" 2>/dev/null || true
+# Complete guarded fallback contract for standalone or restricted hook runners
+if ! command -v clean_rnex_instructions >/dev/null 2>&1; then
+  clean_rnex_instructions() {
+    _dst="$1"
+    [ -f "$_dst" ] || return 0
+    _m_start="<!-- REPO-NEXUS:START -->"
+    _m_end="<!-- REPO-NEXUS:END -->"
+    if grep -qF "$_m_start" "$_dst" 2>/dev/null; then
+      _non_rnex="$(awk -v s="$_m_start" -v e="$_m_end" '
+        $0 == s { skip=1; next }
+        $0 == e { skip=0; next }
+        !skip { print }
+      ' "$_dst" | tr -d " \t\r\n")"
+      if [ -z "$_non_rnex" ]; then
+        rm -f "$_dst"
+      else
+        _tmp="$(mktemp)"
+        awk -v s="$_m_start" -v e="$_m_end" '
+          $0 == s { skip=1; next }
+          $0 == e { skip=0; next }
+          !skip { print }
+        ' "$_dst" > "$_tmp" && mv "$_tmp" "$_dst"
+      fi
+    fi
+  }
+fi
+
+if ! command -v clean_provider_user_skills >/dev/null 2>&1; then
+  clean_provider_user_skills() {
+    _sk_dir="$1"
+    [ -d "$_sk_dir" ] || return 0
+    rm -f "$_sk_dir"/rnex-*.md 2>/dev/null || true
+    for _d in "$_sk_dir"/rnex-*; do
+      [ -d "$_d" ] || continue
+      rm -rf "$_d" 2>/dev/null || true
+    done
+    rmdir "$_sk_dir" 2>/dev/null || true
+  }
+fi
+
+if ! command -v clean_provider_agents >/dev/null 2>&1; then
+  clean_provider_agents() {
+    _ag_dir="$1"
+    _ext="${2:-.md}"
+    [ -d "$_ag_dir" ] || return 0
+    for _pdir in "$_root/toolkit/plugins"/* "$_root/.rnex/plugins"/*; do
+      [ -d "$_pdir" ] || continue
+      [ -d "$_pdir/agents" ] || continue
+      for _afile in "$_pdir/agents"/*.md; do
+        [ -f "$_afile" ] || continue
+        _aname="$(basename "$_afile" .agent.md)"
+        _aname="$(basename "$_aname" .md)"
+        rm -f "$_ag_dir/${_aname}${_ext}" 2>/dev/null || true
+      done
+    done
+    rmdir "$_ag_dir" 2>/dev/null || true
+  }
+fi
+
+if command -v clean_rnex_instructions >/dev/null 2>&1; then
+  clean_rnex_instructions "$_root/.github/copilot-instructions.md"
+fi
+if command -v clean_provider_user_skills >/dev/null 2>&1; then
+  clean_provider_user_skills "$_root/.github/skills"
+fi
+if command -v clean_provider_agents >/dev/null 2>&1; then
+  clean_provider_agents "$_root/.github/agents" ".agent.md"
+fi
+
+# Remove only files owned by this plugin in .github/prompts/ and delete directory only if empty
+if [ -d "$_root/.github/prompts" ]; then
+  rm -f "$_root/.github/prompts"/rnex-*.prompt.md "$_root/.github/prompts"/rnex-*.md 2>/dev/null || true
+  for _p in "$_root/.github/prompts"/rnex-*; do
+    [ -e "$_p" ] || continue
+    rm -rf "$_p" 2>/dev/null || true
+  done
+  rmdir "$_root/.github/prompts" 2>/dev/null || true
+fi
 rmdir "$_root/.github" 2>/dev/null || true

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

@@ -44,12 +44,54 @@ _raw="$(printf '%s' "$_raw" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
 _trigger="$(get_cfg "lint_trigger" "manual")"
 if [ "$_trigger" = "git-pre-push" ] || [ "$_trigger" = "pre-push" ]; then
-  _notify="$(get_cfg "notify_on_changes" "true")"
-  if [ "$_notify" != "false" ]; then
-    _wiki_path="$_root/$_wiki"
-    if [ ! -f "$_wiki_path/index.md" ] || [ ! -f "$_wiki_path/hot.md" ]; then
-      printf '[WIKI] Warning: Required wiki files (index.md or hot.md) missing in %s/.\n' "$_wiki"
+  _has_wiki_changes=0
+  _has_input=0
+  _z40="0000000000000000000000000000000000000000"
+
+  # 1. Inspect pushed revisions if provided on stdin (standard Git pre-push hook contract)
+  if [ ! -t 0 ]; then
+    while read -r _local_ref _local_sha _remote_ref _remote_sha; do
+      [ -z "$_local_sha" ] && continue
+      [ "$_local_sha" = "$_z40" ] && continue
+      _has_input=1
+
+      if [ -z "$_remote_sha" ] || [ "$_remote_sha" = "$_z40" ]; then
+        if git -C "$_root" diff-tree -r --name-only --root "$_local_sha" 2>/dev/null | grep -qE "(^|/)($_raw|$_wiki)/"; then
+          _has_wiki_changes=1
+          break
+        fi
+      else
+        if git -C "$_root" diff-tree -r --name-only "$_remote_sha" "$_local_sha" 2>/dev/null | grep -qE "(^|/)($_raw|$_wiki)/"; then
+          _has_wiki_changes=1
+          break
+        fi
+      fi
+    done
+  fi
+
+  # 2. Fallback when invoked without piped stdin (e.g. CLI direct execution or test runners)
+  if [ "$_has_input" -eq 0 ]; then
+    if [ -n "${1:-}" ] && [ -n "${2:-}" ] && git -C "$_root" cat-file -e "${1:-}" 2>/dev/null && git -C "$_root" cat-file -e "${2:-}" 2>/dev/null; then
+      if git -C "$_root" diff-tree -r --name-only "$1" "$2" 2>/dev/null | grep -qE "(^|/)($_raw|$_wiki)/"; then
+        _has_wiki_changes=1
+      fi
+    elif git -C "$_root" rev-parse --verify HEAD >/dev/null 2>&1; then
+      if git -C "$_root" diff-tree -r --name-only --root HEAD 2>/dev/null | grep -qE "(^|/)($_raw|$_wiki)/"; then
+        _has_wiki_changes=1
+      fi
+    elif git -C "$_root" status --porcelain 2>/dev/null | grep -qE "(^[A-Z? ]+[ ]+|/)($_raw|$_wiki)/"; then
+      _has_wiki_changes=1
+    fi
+  fi
+
+  if [ "$_has_wiki_changes" -eq 1 ]; then
+    _notify="$(get_cfg "notify_on_changes" "true")"
+    if [ "$_notify" != "false" ]; then
+      _wiki_path="$_root/$_wiki"
+      if [ ! -f "$_wiki_path/index.md" ] || [ ! -f "$_wiki_path/hot.md" ]; then
+        printf '[WIKI] Warning: Required wiki files (index.md or hot.md) missing in %s/.\n' "$_wiki"
+      fi
+      printf '[WIKI] Reminder: Wiki files changed. Run the rnex-karpathy-llm-wiki-lint skill to verify.\n'
     fi
-    printf '[WIKI] Reminder: Wiki files changed. Run the rnex-karpathy-llm-wiki-lint skill to verify.\n'
   fi
 fi

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

@@ -34,7 +34,7 @@ Do not create arbitrary or speculative subdirectories during initialization. Sca
 
 ### 2. Index File Format
 
-`/wiki/index.md` uses its own frontmatter schema (it is the wiki navigation file, not an atomic content page):
+`.rnex/wiki/index.md` uses its own frontmatter schema (it is the wiki navigation file, not an atomic content page):
 
 ```yaml
 ---
@@ -58,8 +58,8 @@ Every wiki page is a single atomic markdown file covering one concept, entity, s
 title: ""
 tags: []
 last_updated: YYYY-MM-DD
-# Typed relation fields — paths relative to /wiki/
-sources: []          # /raw/ files this page was derived from
+# Typed relation fields — paths relative to .rnex/wiki/
+sources: []          # ./docs/ files this page was derived from
 related: []          # thematically related wiki pages
 extends: []          # pages this one builds upon or specialises
 contradicts: []      # pages with conflicting information

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

@@ -26,9 +26,9 @@ skills:
 instructions:
   - instructions/rnex-wiki-architecture.md: .rnex/plugins/karpathy-llm/instructions/rnex-wiki-architecture.md
 templates:
-  - templates/index.md: {wiki_dir}/index.md
-  - templates/_log.md: {wiki_dir}/_log.md
-  - templates/hot.md: {wiki_dir}/hot.md
-  - templates/raw.gitkeep: {raw_dir}/.gitkeep
+  - templates/index.md: "{wiki_dir}/index.md"
+  - templates/_log.md: "{wiki_dir}/_log.md"
+  - templates/hot.md: "{wiki_dir}/hot.md"
+  - templates/raw.gitkeep: "{raw_dir}/.gitkeep"
   - templates/rnex-wiki-page.sample.md: .rnex/plugins/karpathy-llm/templates/rnex-wiki-page.template.md
   - templates/rnex-llm-wiki.sample.md: .rnex/plugins/karpathy-llm/templates/rnex-llm-wiki.sample.md