repo-nexus 0.7.19 → 0.7.22

package/lib/commands/completion.sh

@@ -55,8 +55,11 @@ complete -F _rnex_completions repo-nexus
 # Prompt hook for zero-fork auto-synchronization
 _rnex_auto_sync() {
   [ -f rnex.yaml ] || return 0
-  if [ ! -f .rnex/.sync_stamp ] || [ rnex.yaml -nt .rnex/.sync_stamp ] || \
-     { [ -f .local.rnex.yaml ] && [ .local.rnex.yaml -nt .rnex/.sync_stamp ]; }; then
+  _stamp=""
+  [ -f .rnex/sync_stamp ] && _stamp=".rnex/sync_stamp"
+  [ -z "$_stamp" ] && [ -f .rnex/.sync_stamp ] && _stamp=".rnex/.sync_stamp"
+  if [ -z "$_stamp" ] || [ rnex.yaml -nt "$_stamp" ] || \
+     { [ -f .local.rnex.yaml ] && [ .local.rnex.yaml -nt "$_stamp" ]; }; then
     rnex sync -y --quiet
   fi
 }
@@ -143,8 +146,11 @@ _rnex "$@"
 # Prompt hook for zero-fork auto-synchronization
 _rnex_auto_sync() {
   [ -f rnex.yaml ] || return 0
-  if [ ! -f .rnex/.sync_stamp ] || [ rnex.yaml -nt .rnex/.sync_stamp ] || \
-     { [ -f .local.rnex.yaml ] && [ .local.rnex.yaml -nt .rnex/.sync_stamp ]; }; then
+  _stamp=""
+  [ -f .rnex/sync_stamp ] && _stamp=".rnex/sync_stamp"
+  [ -z "$_stamp" ] && [ -f .rnex/.sync_stamp ] && _stamp=".rnex/.sync_stamp"
+  if [ -z "$_stamp" ] || [ rnex.yaml -nt "$_stamp" ] || \
+     { [ -f .local.rnex.yaml ] && [ .local.rnex.yaml -nt "$_stamp" ]; }; then
     rnex sync -y --quiet
   fi
 }
@@ -179,7 +185,13 @@ complete -c rnex -n "__fish_use_subcommand" -a version -d "Show version"
 
 function _rnex_auto_sync --on-event fish_prompt
   test -f rnex.yaml; or return 0
-  if not test -f .rnex/.sync_stamp; or test rnex.yaml -nt .rnex/.sync_stamp; or test -f .local.rnex.yaml -a .local.rnex.yaml -nt .rnex/.sync_stamp
+  set -l _stamp ""
+  if test -f .rnex/sync_stamp
+    set _stamp .rnex/sync_stamp
+  else if test -f .rnex/.sync_stamp
+    set _stamp .rnex/.sync_stamp
+  end
+  if test -z "$_stamp"; or test rnex.yaml -nt "$_stamp"; or test -f .local.rnex.yaml -a .local.rnex.yaml -nt "$_stamp"
     rnex sync -y --quiet
   end
 end

package/lib/commands/plugin.sh

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

package/lib/commands/status.sh

@@ -51,6 +51,7 @@ cmd_status() {
   fi
 
   _stamp_file="$NEXUS_DIR/.rnex/.sync_stamp"
+  [ -f "$_stamp_file" ] || _stamp_file="$NEXUS_DIR/.rnex/sync_stamp"
   _cur_sum="$(get_config_sum "$NEXUS_DIR")"
   if [ ! -f "$_stamp_file" ] || [ "$_cur_sum" != "$(cat "$_stamp_file" 2>/dev/null)" ]; then
     printf '  %b!%b Sync Stamp:    workspace out of sync with configuration (run "rnex sync")\n' "$_Y" "$_NC"

package/lib/commands/sync.sh

@@ -16,6 +16,7 @@ _ws="$(cd "$(dirname "$0")/../.." 2>/dev/null && pwd -P)"
 [ -f "$_ws/rnex.yaml" ] || exit 0
 
 _stamp="$_ws/.rnex/.sync_stamp"
+[ -f "$_stamp" ] || _stamp="$_ws/.rnex/sync_stamp"
 _cur_sum="$(cd "$_ws" 2>/dev/null && cksum rnex.yaml .local.rnex.yaml 2>/dev/null | cksum | awk '{print $1, $2}')"
 _saved_sum=""
 [ -f "$_stamp" ] && _saved_sum="$(cat "$_stamp" 2>/dev/null)"
@@ -70,22 +71,38 @@ cmd_sync() {
     [ "$_sync_quiet" -eq 0 ] && log_ok "Upgraded workspace configuration and routing instructions to v$RNEX_VERSION"
   fi
 
-  # 1. Ensure .gitignore ignores repos/, local configs; ensure .ignore has !repos/*
+  # --------------------------------------------------------------------------
+  # Step 1: Sync hardcoded files & invoke commands that do not depend on config
+  # --------------------------------------------------------------------------
+  # 1.1. Ensure .gitignore ignores repos/, local configs; ensure .ignore has !repos/*
   reconcile_gitignore "$NEXUS_DIR"
 
-  # 2. Reconcile plugins (scopes, deterministic sync, lifecycle hooks copy)
-  sync_plugins
+  # 1.2. Reconcile universal workspace instructions in AGENTS.md
+  merge_rnex_instructions "$NEXUS_DIR/AGENTS.md"
+
+  # 1.3. Generate auto-sync script and AI session-start hooks (hardcoded harness)
+  _write_auto_sync_script "$NEXUS_DIR"
+  _sync_ai_session_start_hooks "$NEXUS_DIR"
+
+  # 1.4. Sync core agentic skills into .rnex/skills/ and write rnex-env.sh
+  sync_skills
 
-  # 3. Compile .rnex/ai-instructions.md
+  # --------------------------------------------------------------------------
+  # Step 2: Generate .rnex/ai-instructions.md and .rnex/sync_stamp
+  # --------------------------------------------------------------------------
+  # 2.1. Compile .rnex/ai-instructions.md
   build_ai_instructions "$NEXUS_DIR"
 
-  # 4. Reconcile universal workspace instructions in AGENTS.md
-  merge_rnex_instructions "$NEXUS_DIR/AGENTS.md"
+  # 2.2. Update sync stamp (.rnex/.sync_stamp and .rnex/sync_stamp)
+  update_sync_stamp "$NEXUS_DIR"
 
-  # 5. Sync core agentic skills and active provider user skills
-  sync_skills
+  # --------------------------------------------------------------------------
+  # Step 3: The rest of synchronization
+  # --------------------------------------------------------------------------
+  # 3.1. Reconcile plugins (scopes, deterministic sync, lifecycle hooks copy, templates, leaked dir cleanup)
+  sync_plugins
 
-  # 6. Reconcile Git hooks according to configuration
+  # 3.2. Reconcile Git hooks according to configuration
   case "$GIT_HOOKS_CONFIG" in
     false|no|0)
       _cur_hp="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
@@ -123,7 +140,7 @@ cmd_sync() {
       ;;
   esac
 
-  # 7. Reconcile member repos (.rnex/ harness sync)
+  # 3.3. Reconcile member repos (.rnex/ harness sync)
   yaml_list_repos | while read -r _name; do
     [ -n "$_name" ] || continue
     if yaml_repo_enabled "$_name"; then
@@ -136,16 +153,9 @@ cmd_sync() {
     fi
   done
 
-  # 8. Reconcile VS Code / Cursor multi-root workspace if configured
+  # 3.4. Reconcile VS Code / Cursor multi-root workspace if configured
   sync_code_workspace
 
-  # 9. Generate auto-sync script and AI session-start hooks
-  _write_auto_sync_script "$NEXUS_DIR"
-  _sync_ai_session_start_hooks "$NEXUS_DIR"
-
-  # 10. Update sync stamp
-  update_sync_stamp "$NEXUS_DIR"
-
   if [ "$_sync_quiet" -eq 0 ]; then
     log_ok "Sync complete — workspace, plugins, skills, and member .rnex directories reconciled"
   fi

package/lib/hooks.sh

@@ -324,7 +324,13 @@ cmd_hooks() {
       case "$_hook_name" in
         post-merge)
           _cfg_changed=0
-          if [ ! -f "$NEXUS_DIR/.rnex/.sync_stamp" ] || [ "$(get_config_sum "$NEXUS_DIR")" != "$(cat "$NEXUS_DIR/.rnex/.sync_stamp" 2>/dev/null)" ]; then
+          _stamp_file=""
+          if [ -f "$NEXUS_DIR/.rnex/sync_stamp" ]; then
+            _stamp_file="$NEXUS_DIR/.rnex/sync_stamp"
+          elif [ -f "$NEXUS_DIR/.rnex/.sync_stamp" ]; then
+            _stamp_file="$NEXUS_DIR/.rnex/.sync_stamp"
+          fi
+          if [ -z "$_stamp_file" ] || [ "$(get_config_sum "$NEXUS_DIR")" != "$(cat "$_stamp_file" 2>/dev/null)" ]; then
             _cfg_changed=1
           elif git -C "$NEXUS_DIR" diff-tree -r --name-only ORIG_HEAD HEAD 2>/dev/null | grep -qE "(^rnex\.yaml$|^\.local\.rnex\.yaml$)"; then
             _cfg_changed=1
@@ -342,7 +348,13 @@ cmd_hooks() {
           ;;
         post-checkout)
           _cfg_changed=0
-          if [ ! -f "$NEXUS_DIR/.rnex/.sync_stamp" ] || [ "$(get_config_sum "$NEXUS_DIR")" != "$(cat "$NEXUS_DIR/.rnex/.sync_stamp" 2>/dev/null)" ]; then
+          _stamp_file=""
+          if [ -f "$NEXUS_DIR/.rnex/sync_stamp" ]; then
+            _stamp_file="$NEXUS_DIR/.rnex/sync_stamp"
+          elif [ -f "$NEXUS_DIR/.rnex/.sync_stamp" ]; then
+            _stamp_file="$NEXUS_DIR/.rnex/.sync_stamp"
+          fi
+          if [ -z "$_stamp_file" ] || [ "$(get_config_sum "$NEXUS_DIR")" != "$(cat "$_stamp_file" 2>/dev/null)" ]; then
             _cfg_changed=1
           elif [ -n "$1" ] && [ -n "$2" ] && git -C "$NEXUS_DIR" diff-tree -r --name-only "$1" "$2" 2>/dev/null | grep -qE "(^rnex\.yaml$|^\.local\.rnex\.yaml$)"; then
             _cfg_changed=1
@@ -369,7 +381,13 @@ cmd_hooks() {
           ;;
         pre-commit)
           _cfg_changed=0
-          if [ ! -f "$NEXUS_DIR/.rnex/.sync_stamp" ] || [ "$(get_config_sum "$NEXUS_DIR")" != "$(cat "$NEXUS_DIR/.rnex/.sync_stamp" 2>/dev/null)" ]; then
+          _stamp_file=""
+          if [ -f "$NEXUS_DIR/.rnex/sync_stamp" ]; then
+            _stamp_file="$NEXUS_DIR/.rnex/sync_stamp"
+          elif [ -f "$NEXUS_DIR/.rnex/.sync_stamp" ]; then
+            _stamp_file="$NEXUS_DIR/.rnex/.sync_stamp"
+          fi
+          if [ -z "$_stamp_file" ] || [ "$(get_config_sum "$NEXUS_DIR")" != "$(cat "$_stamp_file" 2>/dev/null)" ]; then
             _cfg_changed=1
           elif git -C "$NEXUS_DIR" diff --cached --name-only 2>/dev/null | grep -qE "(^rnex\.yaml$|^\.local\.rnex\.yaml$)"; then
             _cfg_changed=1

package/lib/plugins.sh

@@ -8,12 +8,16 @@ find_plugin_dir() {
   _query="$1"
   _sdir="$(dirname "$SCRIPT_LOCATION")"
   for _cand in \
+    "${RNEX_ROOT:-}/toolkit/plugins/$_query" \
+    "${RNEX_TOOLKIT_DIR:-}/plugins/$_query" \
+    "${RNEX_PLUGINS_DIR:-}/$_query" \
     "$NEXUS_DIR/toolkit/plugins/$_query" \
     "$SCRIPT_LOCATION/toolkit/plugins/$_query" \
     "$_sdir/toolkit/plugins/$_query" \
     "$NEXUS_DIR/plugins/$_query" \
     "$NEXUS_DIR/.rnex/plugins/$_query" \
     "$NEXUS_DIR/.nexus/plugins/$_query"; do
+    [ -n "$_cand" ] || continue
     if [ -f "$_cand/plugin.yaml" ]; then
       printf '%s' "$_cand"
       return 0
@@ -26,12 +30,16 @@ list_all_available_plugin_dirs() {
   _sdir="$(dirname "$SCRIPT_LOCATION")"
   _dirs=""
   for _parent in \
+    "${RNEX_ROOT:-}/toolkit/plugins" \
+    "${RNEX_TOOLKIT_DIR:-}/plugins" \
+    "${RNEX_PLUGINS_DIR:-}" \
     "$NEXUS_DIR/toolkit/plugins" \
     "$SCRIPT_LOCATION/toolkit/plugins" \
     "$_sdir/toolkit/plugins" \
     "$NEXUS_DIR/plugins" \
     "$NEXUS_DIR/.rnex/plugins" \
     "$NEXUS_DIR/.nexus/plugins"; do
+    [ -n "$_parent" ] || continue
     if [ -d "$_parent" ]; then
       for _sub in "$_parent"/*; do
         if [ -d "$_sub" ] && [ -f "$_sub/plugin.yaml" ]; then
@@ -70,6 +78,7 @@ plugin_list_templates() {
     t && /^[ ]*-[ ]*/ {
       sub(/^[ ]*-[ ]*/, "");
       sub(/[ ]*#.*/, "");
+      gsub(/["\047]/, "");
       if (length($0) > 0) print $0
     }
   ' "$_pdir/plugin.yaml"
@@ -91,7 +100,7 @@ plugin_list_instructions() {
 
 plugin_resolve_placeholders() {
   _p="$1"; _pd="$2"; _str="$3"
-  _res="$(printf '%s' "$_str" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' -e 's/^["\047]//' -e 's/["\047]$//')"
+  _res="$(printf '%s' "$_str" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"")"
 
   if [ -f "$_pd/plugin.yaml" ]; then
     _keys="$(awk '
@@ -114,7 +123,7 @@ plugin_resolve_placeholders() {
           in_c && $0 ~ ("^[ ]*" k ":") {
             sub("^[ ]*" k ":[ ]*", "")
             sub(/[ ]*#.*/, "")
-            gsub(/^["\047]|["\047]$/, "")
+            gsub(/["\047]/, "")
             print
             exit
           }
@@ -122,27 +131,29 @@ plugin_resolve_placeholders() {
       fi
       case "$_k" in
         *_dir|dir)
-          _v="$(printf '%s' "$_v" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
+          _v="$(printf '%s' "$_v" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
           ;;
       esac
       _res="$(printf '%s' "$_res" | sed -e "s|{$_k}|$_v|g")"
     done
   fi
 
-  # Backward compatibility for legacy template destination paths
+  # Fallback resolution for core wiki/raw placeholders and legacy prefixes
   _w_val="$(yaml_plugin_get "$_p" "wiki_dir" 2>/dev/null || true)"
   [ -z "$_w_val" ] && _w_val=".rnex/wiki"
-  _w_val="$(printf '%s' "$_w_val" | sed -e 's#^/##' -e 's#/$##')"
+  _w_val="$(printf '%s' "$_w_val" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
   _r_val="$(yaml_plugin_get "$_p" "raw_dir" 2>/dev/null || true)"
   [ -z "$_r_val" ] && _r_val="docs"
-  _r_val="$(printf '%s' "$_r_val" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
+  _r_val="$(printf '%s' "$_r_val" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
   _res="$(printf '%s' "$_res" | sed \
-    -e "s|^wiki/|${_w_val}/|" \
-    -e "s|^raw/|${_r_val}/|")"
+    -e "s|{wiki_dir}|${_w_val}|g" \
+    -e "s|{raw_dir}|${_r_val}|g" \
+    -e "s|^\.\{0,1\}\/\{0,1\}wiki/|${_w_val}/|" \
+    -e "s|^\.\{0,1\}\/\{0,1\}raw/|${_r_val}/|")"
 
-  _res="$(printf '%s' "$_res" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' -e 's/^["\047]//' -e 's/["\047]$//')"
+  _res="$(printf '%s' "$_res" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##')"
 
   printf '%s' "$_res"
 }
@@ -152,11 +163,11 @@ plugin_instantiate_template() {
 
   _w_val="$(yaml_plugin_get "$_p" "wiki_dir" 2>/dev/null || true)"
   [ -z "$_w_val" ] && _w_val=".rnex/wiki"
-  _w_val="$(printf '%s' "$_w_val" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' -e 's#^/##' -e 's#/$##')"
+  _w_val="$(printf '%s' "$_w_val" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^/##' -e 's#/$##')"
 
   _r_val="$(yaml_plugin_get "$_p" "raw_dir" 2>/dev/null || true)"
   [ -z "$_r_val" ] && _r_val="docs"
-  _r_val="$(printf '%s' "$_r_val" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
+  _r_val="$(printf '%s' "$_r_val" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
   sed -e "s|{wiki_dir}|$_w_val|g" \
       -e "s|{raw_dir}|$_r_val|g" \
@@ -165,6 +176,79 @@ plugin_instantiate_template() {
 
 # Sync plugins into scoped directories: .rnex/plugins/<plugin-name>/
 sync_plugins() {
+  # Clean up any bogus placeholder directories accidentally created in workspace root
+  for _bogus in \
+    "$NEXUS_DIR/\"{wiki_dir}" \
+    "$NEXUS_DIR/\"{raw_dir}" \
+    "$NEXUS_DIR/{wiki_dir}" \
+    "$NEXUS_DIR/{raw_dir}"; do
+    if [ -d "$_bogus" ]; then
+      rm -rf "$_bogus"
+      log_dim "Cleaned up leaked placeholder directory: $(basename "$_bogus")"
+    fi
+  done
+
+  # Clean up obsolete leaked root ./raw and ./wiki directories if non-default paths are configured
+  _raw_cfg="$(yaml_plugin_get "karpathy-llm" "raw_dir" 2>/dev/null || true)"
+  [ -z "$_raw_cfg" ] && _raw_cfg="docs"
+  _raw_cfg="$(printf '%s' "$_raw_cfg" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
+
+  _wiki_cfg="$(yaml_plugin_get "karpathy-llm" "wiki_dir" 2>/dev/null || true)"
+  [ -z "$_wiki_cfg" ] && _wiki_cfg=".rnex/wiki"
+  _wiki_cfg="$(printf '%s' "$_wiki_cfg" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
+
+  if [ "$_raw_cfg" != "raw" ] && [ -d "$NEXUS_DIR/raw" ]; then
+    if ! rmdir "$NEXUS_DIR/raw" 2>/dev/null; then
+      _can_clean=1
+      for _f in "$NEXUS_DIR/raw"/* "$NEXUS_DIR/raw"/.[!.]* "$NEXUS_DIR/raw"/..?*; do
+        [ -e "$_f" ] || continue
+        _b="$(basename "$_f")"
+        if [ "$_b" = ".gitkeep" ]; then
+          continue
+        fi
+        if [ -f "$NEXUS_DIR/$_raw_cfg/$_b" ] && cmp -s "$_f" "$NEXUS_DIR/$_raw_cfg/$_b"; then
+          continue
+        fi
+        _can_clean=0
+        break
+      done
+      if [ "$_can_clean" -eq 1 ]; then
+        rm -rf "$NEXUS_DIR/raw"
+        log_dim "Cleaned up obsolete root raw/ directory"
+      fi
+    else
+      log_dim "Removed empty obsolete root raw/ directory"
+    fi
+  fi
+
+  if [ "$_wiki_cfg" != "wiki" ] && [ -d "$NEXUS_DIR/wiki" ]; then
+    if ! rmdir "$NEXUS_DIR/wiki" 2>/dev/null; then
+      _can_clean=1
+      for _f in "$NEXUS_DIR/wiki"/* "$NEXUS_DIR/wiki"/.[!.]* "$NEXUS_DIR/wiki"/..?*; do
+        [ -e "$_f" ] || continue
+        _b="$(basename "$_f")"
+        case "$_b" in
+          index.md|_log.md|hot.md|.gitkeep)
+            continue
+            ;;
+          *)
+            if [ -f "$NEXUS_DIR/$_wiki_cfg/$_b" ] && cmp -s "$_f" "$NEXUS_DIR/$_wiki_cfg/$_b"; then
+              continue
+            fi
+            _can_clean=0
+            break
+            ;;
+        esac
+      done
+      if [ "$_can_clean" -eq 1 ]; then
+        rm -rf "$NEXUS_DIR/wiki"
+        log_dim "Cleaned up obsolete root wiki/ directory"
+      fi
+    else
+      log_dim "Removed empty obsolete root wiki/ directory"
+    fi
+  fi
+
   # 1. Prune plugins that are disabled or no longer enabled in config
   if [ -d "$NEXUS_DIR/.rnex/plugins" ]; then
     for _existing in "$NEXUS_DIR/.rnex/plugins"/*; do
@@ -232,11 +316,19 @@ sync_plugins() {
       [ -n "$_item" ] || continue
       _s="${_item%%:*}"
       _d="${_item#*:}"
-      _s="$(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]$//')"
+      _s="$(printf '%s' "$_s" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"")"
+      _d="$(printf '%s' "$_d" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"")"
 
       _d="$(plugin_resolve_placeholders "$_pname" "$_pdir" "$_d")"
 
+      # Defensive guard: never create directories or files if placeholder expansion failed or quotes leaked
+      case "$_d" in
+        *"{"*"}"*|*\"*|*\'*)
+          log_warn "Skipping invalid template destination with unresolved placeholders: $_d"
+          continue
+          ;;
+      esac
+
       _src_path="$_pdir/$_s"
       _dest_path="$NEXUS_DIR/$_d"
 

package/lib/workspace.sh

@@ -42,11 +42,18 @@ update_sync_stamp() {
   _dir="${1:-${NEXUS_DIR:-.}}"
   mkdir -p "$_dir/.rnex"
   if [ ! -f "$_dir/.rnex/.gitignore" ]; then
-    printf ".sync_stamp\n" > "$_dir/.rnex/.gitignore"
-  elif ! grep -q "^\.sync_stamp" "$_dir/.rnex/.gitignore" 2>/dev/null; then
-    printf ".sync_stamp\n" >> "$_dir/.rnex/.gitignore"
+    printf ".sync_stamp\nsync_stamp\n" > "$_dir/.rnex/.gitignore"
+  else
+    if ! grep -q "^\.sync_stamp" "$_dir/.rnex/.gitignore" 2>/dev/null; then
+      printf ".sync_stamp\n" >> "$_dir/.rnex/.gitignore"
+    fi
+    if ! grep -q "^sync_stamp" "$_dir/.rnex/.gitignore" 2>/dev/null; then
+      printf "sync_stamp\n" >> "$_dir/.rnex/.gitignore"
+    fi
   fi
-  get_config_sum "$_dir" > "$_dir/.rnex/.sync_stamp"
+  _csum="$(get_config_sum "$_dir")"
+  printf '%s\n' "$_csum" > "$_dir/.rnex/.sync_stamp"
+  printf '%s\n' "$_csum" > "$_dir/.rnex/sync_stamp"
 }
 
 check_auto_sync() {
@@ -70,6 +77,7 @@ check_auto_sync() {
   fi
   [ -f "$_cfg_file" ] || return 0
   _stamp="$_ws/.rnex/.sync_stamp"
+  [ -f "$_stamp" ] || _stamp="$_ws/.rnex/sync_stamp"
   if [ ! -f "$_stamp" ] || [ "$(get_config_sum "$_ws")" != "$(cat "$_stamp" 2>/dev/null)" ]; then
     cmd_sync -y --quiet
   fi

package/lib/yaml.sh

@@ -8,30 +8,48 @@ _yaml_list_plugins_from_file() {
   _f="$1"
   [ -f "$_f" ] || return 0
   awk '
-    /^plugins:[ ]*$/ || /^plugins:[ ]*#/ { p=1; next }
-    p && /^[^ #]/ { p=0 }
-    p && /^  [a-zA-Z0-9_.-]+:/ {
-      line = $0
-      sub(/^[ ]*/, "", line)
-      sub(/:.*/, "", line)
-      gsub(/[[:space:]]/, "", line)
-      if (length(line) > 0) print line
+    /^[ \t]*plugins:[ \t]*(#.*)?$/ { in_plugins=1; plugin_indent=-1; next }
+    in_plugins && /^[^ \t#]/ { in_plugins=0 }
+    !in_plugins { next }
+    {
+      match($0, /^[ \t]*/)
+      indent = RLENGTH
+      trimmed = substr($0, indent + 1)
     }
-    p && /^  -[ ]+[a-zA-Z0-9_.-]+/ {
-      line = $0
-      sub(/^[ ]*-[ ]*/, "", line)
-      sub(/[ ]*#.*/, "", line)
-      sub(/:.*/, "", line)
-      gsub(/[[:space:]]/, "", line)
-      if (length(line) > 0) print line
+    trimmed ~ /^([#]|$)/ { next }
+
+    in_plugins && (plugin_indent == -1) && (indent > 0) {
+      plugin_indent = indent
+    }
+
+    in_plugins && (indent == plugin_indent) {
+      if (trimmed ~ /^["\047]?[a-zA-Z0-9_.-]+["\047]?:/) {
+        line = trimmed
+        sub(/:.*/, "", line)
+        gsub(/^["\047]|["\047]$/, "", line)
+        gsub(/[[:space:]]/, "", line)
+        if (length(line) > 0) print line
+      } else if (trimmed ~ /^-[ \t]+["\047]?[a-zA-Z0-9_.-]+/) {
+        line = trimmed
+        sub(/^-[ \t]+/, "", line)
+        sub(/[ \t]*#.*/, "", line)
+        sub(/:.*/, "", line)
+        gsub(/^["\047]|["\047]$/, "", line)
+        gsub(/[[:space:]]/, "", line)
+        if (length(line) > 0) print line
+      }
     }
   ' "$_f"
 }
 
 yaml_list_plugins() {
+  _wy="${WORKSPACE_YAML:-}"
+  [ -z "$_wy" ] && _wy="${NEXUS_DIR:-.}/$RNEX_CONFIG_FILE"
+  _wly="${WORKSPACE_LOCAL_YAML:-}"
+  [ -z "$_wly" ] && _wly="${NEXUS_DIR:-.}/$RNEX_LOCAL_CONFIG_FILE"
   {
-    _yaml_list_plugins_from_file "$WORKSPACE_YAML"
-    _yaml_list_plugins_from_file "$WORKSPACE_LOCAL_YAML"
+    _yaml_list_plugins_from_file "$_wy"
+    _yaml_list_plugins_from_file "$_wly"
   } | awk '!seen[$0]++'
 }
 
@@ -39,29 +57,69 @@ _yaml_plugin_get_from_file() {
   _f="$1"; _pname="$2"; _key="$3"
   [ -f "$_f" ] || return 0
   awk -v plugin="$_pname" -v key="$_key" '
-    /^plugins:[ ]*$/ || /^plugins:[ ]*#/ { in_plugins=1; next }
-    in_plugins && /^[^ #]/ { in_plugins=0 }
-    in_plugins && match($0, "^  " plugin ":[ ]*(#.*)?$") { in_target=1; next }
-    in_target && /^  [^ #]/ { in_target=0 }
-    in_target && match($0, "^    " key ":[ ]*") {
-      line = $0
-      sub("^    " key ":[ ]*", "", line)
-      sub(/[ ]*#.*$/, "", line)
-      gsub(/^["\x27]|["\x27]$/, "", line)
-      print line
-      exit
+    /^[ \t]*plugins:[ \t]*(#.*)?$/ { in_plugins=1; in_target=0; plugin_indent=-1; next }
+    in_plugins && /^[^ \t#]/ { in_plugins=0; in_target=0 }
+    !in_plugins { next }
+    {
+      match($0, /^[ \t]*/)
+      indent = RLENGTH
+      trimmed = substr($0, indent + 1)
+    }
+    trimmed ~ /^([#]|$)/ { next }
+
+    in_target && (indent <= plugin_indent) {
+      in_target=0
+    }
+
+    !in_target {
+      k = trimmed
+      sub(/:.*/, "", k)
+      gsub(/^["\047]|["\047]$/, "", k)
+      gsub(/[[:space:]]/, "", k)
+      if (k == plugin && trimmed ~ /:[ \t]*(#.*)?$/) {
+        in_target=1
+        plugin_indent=indent
+        next
+      }
+    }
+
+    in_target && (indent > plugin_indent) {
+      k = trimmed
+      sub(/:.*/, "", k)
+      gsub(/^["\047]|["\047]$/, "", k)
+      gsub(/[[:space:]]/, "", k)
+      if (k == key && trimmed ~ /:[ \t]*/) {
+        val = trimmed
+        sub(/^[^:]*:[ \t]*/, "", val)
+        if (val ~ /^"[^"]*"/) {
+          match(val, /^"[^"]*"/)
+          val = substr(val, 2, RLENGTH - 2)
+        } else if (val ~ /^\047[^\047]*\047/) {
+          match(val, /^\047[^\047]*\047/)
+          val = substr(val, 2, RLENGTH - 2)
+        } else {
+          sub(/[ \t]*#.*$/, "", val)
+          sub(/[ \t]+$/, "", val)
+        }
+        print val
+        exit
+      }
     }
   ' "$_f"
 }
 
 yaml_plugin_get() {
   _pname="$1"; _key="$2"
-  _val="$(_yaml_plugin_get_from_file "$WORKSPACE_LOCAL_YAML" "$_pname" "$_key")"
+  _wy="${WORKSPACE_YAML:-}"
+  [ -z "$_wy" ] && _wy="${NEXUS_DIR:-.}/$RNEX_CONFIG_FILE"
+  _wly="${WORKSPACE_LOCAL_YAML:-}"
+  [ -z "$_wly" ] && _wly="${NEXUS_DIR:-.}/$RNEX_LOCAL_CONFIG_FILE"
+  _val="$(_yaml_plugin_get_from_file "$_wly" "$_pname" "$_key")"
   if [ -n "$_val" ]; then
     printf '%s' "$_val"
     return 0
   fi
-  _yaml_plugin_get_from_file "$WORKSPACE_YAML" "$_pname" "$_key"
+  _yaml_plugin_get_from_file "$_wy" "$_pname" "$_key"
 }
 
 yaml_has_plugin() {
@@ -346,7 +404,7 @@ _yaml_get_from_file() {
       line = $0
       sub("^    " field ":[ ]*", "", line)
       sub(/[ ]*#.*$/, "", line)
-      gsub(/^["\x27]|["\x27]$/, "", line)
+      gsub(/^["\047]|["\047]$/, "", line)
       print line
       exit
     }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.7.19",
+  "version": "0.7.22",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",

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

@@ -12,36 +12,60 @@ _root="$RNEX_ROOT"
 get_cfg() {
   _key="$1"; _def="$2"
   _val=""
-  if [ -f "$_root/.local.rnex.yaml" ]; then
-    _val="$(awk -v k="$_key" '
-      /^plugins:/ { in_p=1; in_k=0; next }
-      in_p && /^[^ #]/ { in_p=0; in_k=0 }
-      in_p && match($0, "^[ ]*karpathy-llm:[ ]*(#.*)?$") { in_k=1; next }
-      in_k && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_k=0 }
-      in_k && $0 ~ ("^[ ]*" k ":") {
-        sub("^[ ]*" k ":[ ]*", "")
-        sub(/[ ]*#.*/, "")
-        gsub(/["\047]/, "")
-        print
-        exit
+  for _cfg in "$_root/.local.rnex.yaml" "$_root/rnex.yaml"; do
+    [ -f "$_cfg" ] || continue
+    _val="$(awk -v plugin="karpathy-llm" -v key="$_key" '
+      /^[ \t]*plugins:[ \t]*(#.*)?$/ { in_plugins=1; in_target=0; plugin_indent=-1; next }
+      in_plugins && /^[^ \t#]/ { in_plugins=0; in_target=0 }
+      !in_plugins { next }
+      {
+        match($0, /^[ \t]*/)
+        indent = RLENGTH
+        trimmed = substr($0, indent + 1)
       }
-    ' "$_root/.local.rnex.yaml")"
-  fi
-  if [ -z "$_val" ] && [ -f "$_root/rnex.yaml" ]; then
-    _val="$(awk -v k="$_key" '
-      /^plugins:/ { in_p=1; in_k=0; next }
-      in_p && /^[^ #]/ { in_p=0; in_k=0 }
-      in_p && match($0, "^[ ]*karpathy-llm:[ ]*(#.*)?$") { in_k=1; next }
-      in_k && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_k=0 }
-      in_k && $0 ~ ("^[ ]*" k ":") {
-        sub("^[ ]*" k ":[ ]*", "")
-        sub(/[ ]*#.*/, "")
-        gsub(/["\047]/, "")
-        print
-        exit
+      trimmed ~ /^([#]|$)/ { next }
+
+      in_target && (indent <= plugin_indent) {
+        in_target=0
       }
-    ' "$_root/rnex.yaml")"
-  fi
+
+      !in_target {
+        k = trimmed
+        sub(/:.*/, "", k)
+        gsub(/^["\047]|["\047]$/, "", k)
+        gsub(/[[:space:]]/, "", k)
+        if (k == plugin && trimmed ~ /:[ \t]*(#.*)?$/) {
+          in_target=1
+          plugin_indent=indent
+          next
+        }
+      }
+
+      in_target && (indent > plugin_indent) {
+        k = trimmed
+        sub(/:.*/, "", k)
+        gsub(/^["\047]|["\047]$/, "", k)
+        gsub(/[[:space:]]/, "", k)
+        if (k == key && trimmed ~ /:[ \t]*/) {
+          val = trimmed
+          sub(/^[^:]*:[ \t]*/, "", val)
+          if (val ~ /^"[^"]*"/) {
+            match(val, /^"[^"]*"/)
+            val = substr(val, 2, RLENGTH - 2)
+          } else if (val ~ /^\047[^\047]*\047/) {
+            match(val, /^\047[^\047]*\047/)
+            val = substr(val, 2, RLENGTH - 2)
+          } else {
+            sub(/[ \t]*#.*$/, "", val)
+            sub(/[ \t]+$/, "", val)
+          }
+          print val
+          exit
+        }
+      }
+    ' "$_cfg")"
+    [ -n "$_val" ] && break
+  done
   [ -n "$_val" ] && printf '%s' "$_val" || printf '%s' "$_def"
 }
 
@@ -59,6 +83,53 @@ _raw_path="$_root/$_raw"
 mkdir -p "$_wiki_path" "$_raw_path"
 [ -f "$_raw_path/.gitkeep" ] || touch "$_raw_path/.gitkeep"
 
+# Clean up obsolete leaked root ./raw and ./wiki directories if non-default paths are configured
+if [ "$_raw" != "raw" ] && [ -d "$_root/raw" ]; then
+  if ! rmdir "$_root/raw" 2>/dev/null; then
+    _clean_raw_leak=1
+    for _rf in "$_root/raw"/* "$_root/raw"/.[!.]* "$_root/raw"/..?*; do
+      [ -e "$_rf" ] || continue
+      _rf_base="$(basename "$_rf")"
+      if [ "$_rf_base" = ".gitkeep" ]; then
+        continue
+      fi
+      if [ -f "$_raw_path/$_rf_base" ] && cmp -s "$_rf" "$_raw_path/$_rf_base"; then
+        continue
+      fi
+      _clean_raw_leak=0
+      break
+    done
+    if [ "$_clean_raw_leak" -eq 1 ]; then
+      rm -rf "$_root/raw" 2>/dev/null || true
+    fi
+  fi
+fi
+
+if [ "$_wiki" != "wiki" ] && [ -d "$_root/wiki" ]; then
+  if ! rmdir "$_root/wiki" 2>/dev/null; then
+    _clean_wiki_leak=1
+    for _wf in "$_root/wiki"/* "$_root/wiki"/.[!.]* "$_root/wiki"/..?*; do
+      [ -e "$_wf" ] || continue
+      _wf_base="$(basename "$_wf")"
+      case "$_wf_base" in
+        index.md|_log.md|hot.md|.gitkeep)
+          continue
+          ;;
+        *)
+          if [ -f "$_wiki_path/$_wf_base" ] && cmp -s "$_wf" "$_wiki_path/$_wf_base"; then
+            continue
+          fi
+          _clean_wiki_leak=0
+          break
+          ;;
+      esac
+    done
+    if [ "$_clean_wiki_leak" -eq 1 ]; then
+      rm -rf "$_root/wiki" 2>/dev/null || true
+    fi
+  fi
+fi
+
 # Clean up legacy staging directory only if empty or positively verified as managed duplicate copies
 if [ -d "$_wiki_path/raw" ]; then
   if ! rmdir "$_wiki_path/raw" 2>/dev/null; then
@@ -369,7 +440,7 @@ if [ "$_skip_all_readmes" -ne 1 ]; then
           line = $0
           sub("^    enabled:[ ]*", "", line)
           sub(/[ ]*#.*$/, "", line)
-          gsub(/^["\x27]|["\x27]$/, "", line)
+          gsub(/^["\047]|["\047]$/, "", line)
           print line
           exit
         }
@@ -390,7 +461,7 @@ if [ "$_skip_all_readmes" -ne 1 ]; then
           line = $0
           sub("^    ingest_member_readmes:[ ]*", "", line)
           sub(/[ ]*#.*$/, "", line)
-          gsub(/^["\x27]|["\x27]$/, "", line)
+          gsub(/^["\047]|["\047]$/, "", line)
           print line
           exit
         }
@@ -412,7 +483,7 @@ if [ "$_skip_all_readmes" -ne 1 ]; then
             line = $0
             sub("^    path:[ ]*", "", line)
             sub(/[ ]*#.*$/, "", line)
-            gsub(/^["\x27]|["\x27]$/, "")
+            gsub(/^["\047]|["\047]$/, "", line)
             print line
             exit
           }

package/toolkit/plugins/karpathy-llm/hooks/git_post-commit.sh

@@ -4,36 +4,60 @@ _root="${RNEX_ROOT:-$PWD}"
 get_cfg() {
   _key="$1"; _def="$2"
   _val=""
-  if [ -f "$_root/.local.rnex.yaml" ]; then
-    _val="$(awk -v k="$_key" '
-      /^plugins:/ { in_p=1; in_k=0; next }
-      in_p && /^[^ #]/ { in_p=0; in_k=0 }
-      in_p && match($0, "^[ ]*karpathy-llm:[ ]*(#.*)?$") { in_k=1; next }
-      in_k && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_k=0 }
-      in_k && $0 ~ ("^[ ]*" k ":") {
-        sub("^[ ]*" k ":[ ]*", "")
-        sub(/[ ]*#.*/, "")
-        gsub(/["\047]/, "")
-        print
-        exit
+  for _cfg in "$_root/.local.rnex.yaml" "$_root/rnex.yaml"; do
+    [ -f "$_cfg" ] || continue
+    _val="$(awk -v plugin="karpathy-llm" -v key="$_key" '
+      /^[ \t]*plugins:[ \t]*(#.*)?$/ { in_plugins=1; in_target=0; plugin_indent=-1; next }
+      in_plugins && /^[^ \t#]/ { in_plugins=0; in_target=0 }
+      !in_plugins { next }
+      {
+        match($0, /^[ \t]*/)
+        indent = RLENGTH
+        trimmed = substr($0, indent + 1)
       }
-    ' "$_root/.local.rnex.yaml")"
-  fi
-  if [ -z "$_val" ] && [ -f "$_root/rnex.yaml" ]; then
-    _val="$(awk -v k="$_key" '
-      /^plugins:/ { in_p=1; in_k=0; next }
-      in_p && /^[^ #]/ { in_p=0; in_k=0 }
-      in_p && match($0, "^[ ]*karpathy-llm:[ ]*(#.*)?$") { in_k=1; next }
-      in_k && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_k=0 }
-      in_k && $0 ~ ("^[ ]*" k ":") {
-        sub("^[ ]*" k ":[ ]*", "")
-        sub(/[ ]*#.*/, "")
-        gsub(/["\047]/, "")
-        print
-        exit
+      trimmed ~ /^([#]|$)/ { next }
+
+      in_target && (indent <= plugin_indent) {
+        in_target=0
       }
-    ' "$_root/rnex.yaml")"
-  fi
+
+      !in_target {
+        k = trimmed
+        sub(/:.*/, "", k)
+        gsub(/^["\047]|["\047]$/, "", k)
+        gsub(/[[:space:]]/, "", k)
+        if (k == plugin && trimmed ~ /:[ \t]*(#.*)?$/) {
+          in_target=1
+          plugin_indent=indent
+          next
+        }
+      }
+
+      in_target && (indent > plugin_indent) {
+        k = trimmed
+        sub(/:.*/, "", k)
+        gsub(/^["\047]|["\047]$/, "", k)
+        gsub(/[[:space:]]/, "", k)
+        if (k == key && trimmed ~ /:[ \t]*/) {
+          val = trimmed
+          sub(/^[^:]*:[ \t]*/, "", val)
+          if (val ~ /^"[^"]*"/) {
+            match(val, /^"[^"]*"/)
+            val = substr(val, 2, RLENGTH - 2)
+          } else if (val ~ /^\047[^\047]*\047/) {
+            match(val, /^\047[^\047]*\047/)
+            val = substr(val, 2, RLENGTH - 2)
+          } else {
+            sub(/[ \t]*#.*$/, "", val)
+            sub(/[ \t]+$/, "", val)
+          }
+          print val
+          exit
+        }
+      }
+    ' "$_cfg")"
+    [ -n "$_val" ] && break
+  done
   [ -n "$_val" ] && printf '%s' "$_val" || printf '%s' "$_def"
 }
 

package/toolkit/plugins/karpathy-llm/hooks/git_post-merge.sh

@@ -4,36 +4,60 @@ _root="${RNEX_ROOT:-$PWD}"
 get_cfg() {
   _key="$1"; _def="$2"
   _val=""
-  if [ -f "$_root/.local.rnex.yaml" ]; then
-    _val="$(awk -v k="$_key" '
-      /^plugins:/ { in_p=1; in_k=0; next }
-      in_p && /^[^ #]/ { in_p=0; in_k=0 }
-      in_p && match($0, "^[ ]*karpathy-llm:[ ]*(#.*)?$") { in_k=1; next }
-      in_k && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_k=0 }
-      in_k && $0 ~ ("^[ ]*" k ":") {
-        sub("^[ ]*" k ":[ ]*", "")
-        sub(/[ ]*#.*/, "")
-        gsub(/["\047]/, "")
-        print
-        exit
+  for _cfg in "$_root/.local.rnex.yaml" "$_root/rnex.yaml"; do
+    [ -f "$_cfg" ] || continue
+    _val="$(awk -v plugin="karpathy-llm" -v key="$_key" '
+      /^[ \t]*plugins:[ \t]*(#.*)?$/ { in_plugins=1; in_target=0; plugin_indent=-1; next }
+      in_plugins && /^[^ \t#]/ { in_plugins=0; in_target=0 }
+      !in_plugins { next }
+      {
+        match($0, /^[ \t]*/)
+        indent = RLENGTH
+        trimmed = substr($0, indent + 1)
       }
-    ' "$_root/.local.rnex.yaml")"
-  fi
-  if [ -z "$_val" ] && [ -f "$_root/rnex.yaml" ]; then
-    _val="$(awk -v k="$_key" '
-      /^plugins:/ { in_p=1; in_k=0; next }
-      in_p && /^[^ #]/ { in_p=0; in_k=0 }
-      in_p && match($0, "^[ ]*karpathy-llm:[ ]*(#.*)?$") { in_k=1; next }
-      in_k && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_k=0 }
-      in_k && $0 ~ ("^[ ]*" k ":") {
-        sub("^[ ]*" k ":[ ]*", "")
-        sub(/[ ]*#.*/, "")
-        gsub(/["\047]/, "")
-        print
-        exit
+      trimmed ~ /^([#]|$)/ { next }
+
+      in_target && (indent <= plugin_indent) {
+        in_target=0
       }
-    ' "$_root/rnex.yaml")"
-  fi
+
+      !in_target {
+        k = trimmed
+        sub(/:.*/, "", k)
+        gsub(/^["\047]|["\047]$/, "", k)
+        gsub(/[[:space:]]/, "", k)
+        if (k == plugin && trimmed ~ /:[ \t]*(#.*)?$/) {
+          in_target=1
+          plugin_indent=indent
+          next
+        }
+      }
+
+      in_target && (indent > plugin_indent) {
+        k = trimmed
+        sub(/:.*/, "", k)
+        gsub(/^["\047]|["\047]$/, "", k)
+        gsub(/[[:space:]]/, "", k)
+        if (k == key && trimmed ~ /:[ \t]*/) {
+          val = trimmed
+          sub(/^[^:]*:[ \t]*/, "", val)
+          if (val ~ /^"[^"]*"/) {
+            match(val, /^"[^"]*"/)
+            val = substr(val, 2, RLENGTH - 2)
+          } else if (val ~ /^\047[^\047]*\047/) {
+            match(val, /^\047[^\047]*\047/)
+            val = substr(val, 2, RLENGTH - 2)
+          } else {
+            sub(/[ \t]*#.*$/, "", val)
+            sub(/[ \t]+$/, "", val)
+          }
+          print val
+          exit
+        }
+      }
+    ' "$_cfg")"
+    [ -n "$_val" ] && break
+  done
   [ -n "$_val" ] && printf '%s' "$_val" || printf '%s' "$_def"
 }
 

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

@@ -4,36 +4,60 @@ _root="${RNEX_ROOT:-$PWD}"
 get_cfg() {
   _key="$1"; _def="$2"
   _val=""
-  if [ -f "$_root/.local.rnex.yaml" ]; then
-    _val="$(awk -v k="$_key" '
-      /^plugins:/ { in_p=1; in_k=0; next }
-      in_p && /^[^ #]/ { in_p=0; in_k=0 }
-      in_p && match($0, "^[ ]*karpathy-llm:[ ]*(#.*)?$") { in_k=1; next }
-      in_k && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_k=0 }
-      in_k && $0 ~ ("^[ ]*" k ":") {
-        sub("^[ ]*" k ":[ ]*", "")
-        sub(/[ ]*#.*/, "")
-        gsub(/["\047]/, "")
-        print
-        exit
+  for _cfg in "$_root/.local.rnex.yaml" "$_root/rnex.yaml"; do
+    [ -f "$_cfg" ] || continue
+    _val="$(awk -v plugin="karpathy-llm" -v key="$_key" '
+      /^[ \t]*plugins:[ \t]*(#.*)?$/ { in_plugins=1; in_target=0; plugin_indent=-1; next }
+      in_plugins && /^[^ \t#]/ { in_plugins=0; in_target=0 }
+      !in_plugins { next }
+      {
+        match($0, /^[ \t]*/)
+        indent = RLENGTH
+        trimmed = substr($0, indent + 1)
       }
-    ' "$_root/.local.rnex.yaml")"
-  fi
-  if [ -z "$_val" ] && [ -f "$_root/rnex.yaml" ]; then
-    _val="$(awk -v k="$_key" '
-      /^plugins:/ { in_p=1; in_k=0; next }
-      in_p && /^[^ #]/ { in_p=0; in_k=0 }
-      in_p && match($0, "^[ ]*karpathy-llm:[ ]*(#.*)?$") { in_k=1; next }
-      in_k && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_k=0 }
-      in_k && $0 ~ ("^[ ]*" k ":") {
-        sub("^[ ]*" k ":[ ]*", "")
-        sub(/[ ]*#.*/, "")
-        gsub(/["\047]/, "")
-        print
-        exit
+      trimmed ~ /^([#]|$)/ { next }
+
+      in_target && (indent <= plugin_indent) {
+        in_target=0
       }
-    ' "$_root/rnex.yaml")"
-  fi
+
+      !in_target {
+        k = trimmed
+        sub(/:.*/, "", k)
+        gsub(/^["\047]|["\047]$/, "", k)
+        gsub(/[[:space:]]/, "", k)
+        if (k == plugin && trimmed ~ /:[ \t]*(#.*)?$/) {
+          in_target=1
+          plugin_indent=indent
+          next
+        }
+      }
+
+      in_target && (indent > plugin_indent) {
+        k = trimmed
+        sub(/:.*/, "", k)
+        gsub(/^["\047]|["\047]$/, "", k)
+        gsub(/[[:space:]]/, "", k)
+        if (k == key && trimmed ~ /:[ \t]*/) {
+          val = trimmed
+          sub(/^[^:]*:[ \t]*/, "", val)
+          if (val ~ /^"[^"]*"/) {
+            match(val, /^"[^"]*"/)
+            val = substr(val, 2, RLENGTH - 2)
+          } else if (val ~ /^\047[^\047]*\047/) {
+            match(val, /^\047[^\047]*\047/)
+            val = substr(val, 2, RLENGTH - 2)
+          } else {
+            sub(/[ \t]*#.*$/, "", val)
+            sub(/[ \t]+$/, "", val)
+          }
+          print val
+          exit
+        }
+      }
+    ' "$_cfg")"
+    [ -n "$_val" ] && break
+  done
   [ -n "$_val" ] && printf '%s' "$_val" || printf '%s' "$_def"
 }
 

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

@@ -4,36 +4,60 @@ _root="${RNEX_ROOT:-$PWD}"
 get_cfg() {
   _key="$1"; _def="$2"
   _val=""
-  if [ -f "$_root/.local.rnex.yaml" ]; then
-    _val="$(awk -v k="$_key" '
-      /^plugins:/ { in_p=1; in_k=0; next }
-      in_p && /^[^ #]/ { in_p=0; in_k=0 }
-      in_p && match($0, "^[ ]*karpathy-llm:[ ]*(#.*)?$") { in_k=1; next }
-      in_k && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_k=0 }
-      in_k && $0 ~ ("^[ ]*" k ":") {
-        sub("^[ ]*" k ":[ ]*", "")
-        sub(/[ ]*#.*/, "")
-        gsub(/["\047]/, "")
-        print
-        exit
+  for _cfg in "$_root/.local.rnex.yaml" "$_root/rnex.yaml"; do
+    [ -f "$_cfg" ] || continue
+    _val="$(awk -v plugin="karpathy-llm" -v key="$_key" '
+      /^[ \t]*plugins:[ \t]*(#.*)?$/ { in_plugins=1; in_target=0; plugin_indent=-1; next }
+      in_plugins && /^[^ \t#]/ { in_plugins=0; in_target=0 }
+      !in_plugins { next }
+      {
+        match($0, /^[ \t]*/)
+        indent = RLENGTH
+        trimmed = substr($0, indent + 1)
       }
-    ' "$_root/.local.rnex.yaml")"
-  fi
-  if [ -z "$_val" ] && [ -f "$_root/rnex.yaml" ]; then
-    _val="$(awk -v k="$_key" '
-      /^plugins:/ { in_p=1; in_k=0; next }
-      in_p && /^[^ #]/ { in_p=0; in_k=0 }
-      in_p && match($0, "^[ ]*karpathy-llm:[ ]*(#.*)?$") { in_k=1; next }
-      in_k && (/^[ ]{1,2}[^ #]/ || /^[^ #]/) { in_k=0 }
-      in_k && $0 ~ ("^[ ]*" k ":") {
-        sub("^[ ]*" k ":[ ]*", "")
-        sub(/[ ]*#.*/, "")
-        gsub(/["\047]/, "")
-        print
-        exit
+      trimmed ~ /^([#]|$)/ { next }
+
+      in_target && (indent <= plugin_indent) {
+        in_target=0
       }
-    ' "$_root/rnex.yaml")"
-  fi
+
+      !in_target {
+        k = trimmed
+        sub(/:.*/, "", k)
+        gsub(/^["\047]|["\047]$/, "", k)
+        gsub(/[[:space:]]/, "", k)
+        if (k == plugin && trimmed ~ /:[ \t]*(#.*)?$/) {
+          in_target=1
+          plugin_indent=indent
+          next
+        }
+      }
+
+      in_target && (indent > plugin_indent) {
+        k = trimmed
+        sub(/:.*/, "", k)
+        gsub(/^["\047]|["\047]$/, "", k)
+        gsub(/[[:space:]]/, "", k)
+        if (k == key && trimmed ~ /:[ \t]*/) {
+          val = trimmed
+          sub(/^[^:]*:[ \t]*/, "", val)
+          if (val ~ /^"[^"]*"/) {
+            match(val, /^"[^"]*"/)
+            val = substr(val, 2, RLENGTH - 2)
+          } else if (val ~ /^\047[^\047]*\047/) {
+            match(val, /^\047[^\047]*\047/)
+            val = substr(val, 2, RLENGTH - 2)
+          } else {
+            sub(/[ \t]*#.*$/, "", val)
+            sub(/[ \t]+$/, "", val)
+          }
+          print val
+          exit
+        }
+      }
+    ' "$_cfg")"
+    [ -n "$_val" ] && break
+  done
   [ -n "$_val" ] && printf '%s' "$_val" || printf '%s' "$_def"
 }