repo-nexus 0.7.28 → 0.7.30

package/docs/plugins/karpathy-llm.md

@@ -105,9 +105,6 @@ plugins:
     # Notify developer when changes are committed to intake sources or .rnex/wiki/
     notify_on_changes: true
 
-    # Ingest member repository READMEs into atomic wiki pages
-    ingest_member_readmes: true
-
     # Enable or disable
     enabled: true
 ```
@@ -116,10 +113,8 @@ plugins:
 |:---|:---|:---|:---|
 | `wiki_dir` | string | `.rnex/wiki` | Directory containing curated atomic markdown pages. |
 | `sources` | list | `[docs, "repos/**/README.md"]` | Intake directories and/or glob patterns relative to workspace root. Overridable in `.local.rnex.yaml`. |
-| `raw_dir` | string | *(deprecated)* | Deprecated legacy intake directory. Transparently treated as a single `sources` entry with a migration warning. |
 | `lint_trigger` | string | `manual` | Git hook event that triggers wiki change detection (`git-post-merge`, `git-post-commit`, `git-pre-commit`, `git-pre-push`, `manual`). |
 | `notify_on_changes` | boolean | `true` | Show notification banner when changes are committed to intake sources or `.rnex/wiki/`. |
-| `ingest_member_readmes` | boolean | `true` | Automatically ingest member repository READMEs into atomic wiki pages. |
 | `enabled` | boolean | `true` | Enable or disable the plugin. Overridable in `.local.rnex.yaml`. |
 
 ---
@@ -133,7 +128,7 @@ The `sources` setting defines where the Karpathy LLM Wiki discovers raw intake d
 - **Single-Level Globs (e.g. `repos/*/README.md` or `docs/*.md`)**: Matches files at a fixed directory level.
 - **Active Repository Filtering**: Any resolved path located within `repos/<name>/` is checked against member repository status. If a repository is disabled (`enabled: false`) in `rnex.yaml` or `.local.rnex.yaml`, its files are automatically excluded.
 - **Two-Level Configuration Precedence**: If `sources` is declared in `.local.rnex.yaml`, it completely overrides the `sources` list defined in `rnex.yaml`.
-- **Legacy Fallback & Migration**: Existing configurations with `raw_dir: ./path` continue to work without disruption. Repo Nexus reads `raw_dir` as a single-element sources list and emits a non-fatal deprecation notice advising you to migrate to `sources`.
+- **Legacy Migration**: Existing configurations with `raw_dir: <dir>` are automatically rewritten to a `sources` list during `rnex sync`.
 - **Directory Provisioning**: When running `rnex sync`, explicit directory entries (such as `docs`) are created automatically if missing. Glob patterns (containing `*`, `?`, or `[`) and file targets are never converted into directories.
 
 ---

package/docs/rnex.example.yaml

@@ -105,11 +105,9 @@ plugins:
   #     - docs                    #   directory: all files (hidden dirs and node_modules pruned)
   #     - "repos/**/README.md"    #   recursive glob (quote it); disabled repos are excluded
   #                               # A sources list in .local.rnex.yaml replaces this list entirely.
-  #                               # Legacy 'raw_dir' is still read as a single source (deprecated).
   #   wiki_dir: ".rnex/wiki"      # Directory for curated atomic markdown pages (default: .rnex/wiki)
   #   lint_trigger: "manual"      # Runs manually via 'rnex sync' or validation checklists (git-post-merge, git-post-commit, git-pre-commit, git-pre-push, manual)
   #   notify_on_changes: true     # Show notification when changes are committed to ./docs or .rnex/wiki
-  #   ingest_member_readmes: true # Automatically ingest member repository READMEs into atomic wiki pages (default: true)
 
 
 # ------------------------------------------------------------------------------

package/lib/commands/status.sh

@@ -228,7 +228,7 @@ cmd_status() {
               printf '    %b↳ Options: %s%b\n' "$_DIM" "$_opts" "$_NC"
             fi
             if [ "$_pname" = "karpathy-llm" ] && [ -n "$(plugin_legacy_raw_dir "$_pname" 2>/dev/null)" ]; then
-              printf '    %b↳ [!] Deprecated: raw_dir — replace it with a sources list and run rnex sync%b\n' "$_Y" "$_NC"
+              printf '    %b↳ [!] Deprecated: raw_dir — run "rnex sync" to rewrite to sources%b\n' "$_Y" "$_NC"
             fi
           fi
         fi

package/lib/commands/sync.sh

@@ -71,6 +71,10 @@ cmd_sync() {
     [ "$_sync_quiet" -eq 0 ] && log_ok "Upgraded workspace configuration and routing instructions to v$RNEX_VERSION"
   fi
 
+  # Reconcile legacy plugin settings (e.g. karpathy-llm raw_dir -> sources, strip ingest_member_readmes)
+  migrate_karpathy_llm_config "$WORKSPACE_YAML"
+  [ -f "$WORKSPACE_LOCAL_YAML" ] && migrate_karpathy_llm_config "$WORKSPACE_LOCAL_YAML"
+
   # --------------------------------------------------------------------------
   # Step 1: Sync hardcoded files & invoke commands that do not depend on config
   # --------------------------------------------------------------------------

package/lib/core.sh

@@ -52,6 +52,29 @@ resolve_path() {
   esac
 }
 
+# Return 0 unless value is explicitly falsy (false, no, 0, disabled, off, none)
+is_enabled_val() {
+  _iev="$(printf '%s' "$1" | tr '[:upper:]' '[:lower:]')"
+  case "$_iev" in
+    false|no|0|disabled|off|none) return 1 ;;
+    *) return 0 ;;
+  esac
+}
+
+# Return 0 if value is explicitly truthy (true, yes, 1, on, enabled)
+is_truthy() {
+  _it="$(printf '%s' "$1" | tr '[:upper:]' '[:lower:]')"
+  case "$_it" in
+    true|yes|1|on|enabled) return 0 ;;
+    *) return 1 ;;
+  esac
+}
+
+# Strip surrounding whitespace, quotes, leading ./ or /, and trailing /
+normalize_rel_path() {
+  printf '%s' "$1" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##'
+}
+
 
 # ---- Version Resolution (package.json is single source of truth) ----------
 

package/lib/plugins.sh

@@ -180,11 +180,6 @@ plugin_instantiate_template() {
 
 # Sync plugins into scoped directories: .rnex/plugins/<plugin-name>/
 sync_plugins() {
-  # Emit the legacy raw_dir deprecation notice once per sync (stdout discarded)
-  if yaml_plugin_enabled "karpathy-llm" 2>/dev/null; then
-    get_plugin_config_list "karpathy-llm" "sources" >/dev/null
-  fi
-
   # Clean up any bogus placeholder directories accidentally created in workspace root
   for _bogus in \
     "$NEXUS_DIR/\"{wiki_dir}" \

package/lib/workspace.sh

@@ -144,26 +144,11 @@ _init_local_yaml() {
 }
 
 _load_workspace_version() {
-  _wv=""
-  if [ -f "$WORKSPACE_LOCAL_YAML" ]; then
-    _wv="$(awk '/^version:/ { sub(/^version:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$WORKSPACE_LOCAL_YAML")"
-  fi
-  if [ -z "$_wv" ] && [ -f "$WORKSPACE_YAML" ]; then
-    _wv="$(awk '/^version:/ { sub(/^version:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$WORKSPACE_YAML")"
-  fi
-  _wv="$(echo "$_wv" | tr -d " \t\r\n'\"")"
-  WORKSPACE_CONFIG_VERSION="$_wv"
+  WORKSPACE_CONFIG_VERSION="$(yaml_get_top_level "version")"
 }
 
 _load_repos_dir() {
-  _rd=""
-  if [ -f "$WORKSPACE_LOCAL_YAML" ]; then
-    _rd="$(awk '/^repos_dir:/ { sub(/^repos_dir:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$WORKSPACE_LOCAL_YAML")"
-  fi
-  if [ -z "$_rd" ] && [ -f "$WORKSPACE_YAML" ]; then
-    _rd="$(awk '/^repos_dir:/ { sub(/^repos_dir:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$WORKSPACE_YAML")"
-  fi
-  _rd="${_rd:-./repos}"
+  _rd="$(yaml_get_top_level "repos_dir" "./repos")"
   case "$_rd" in
     /*) REPOS_DIR="$_rd" ;;
     *)  REPOS_DIR="$NEXUS_DIR/$_rd" ;;
@@ -171,14 +156,7 @@ _load_repos_dir() {
 }
 
 _load_code_workspace() {
-  _cw=""
-  if [ -f "$WORKSPACE_LOCAL_YAML" ]; then
-    _cw="$(awk '/^(code_workspace|vscode_workspace):/ { sub(/^[a-zA-Z0-9_]+:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$WORKSPACE_LOCAL_YAML")"
-  fi
-  if [ -z "$_cw" ] && [ -f "$WORKSPACE_YAML" ]; then
-    _cw="$(awk '/^(code_workspace|vscode_workspace):/ { sub(/^[a-zA-Z0-9_]+:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$WORKSPACE_YAML")"
-  fi
-  _cw="$(echo "$_cw" | tr -d " \t\r\n'\"")"
+  _cw="$(yaml_get_top_level "code_workspace|vscode_workspace")"
   case "$_cw" in
     true|yes|1)
       _ws_basename="$(basename "$NEXUS_DIR")"
@@ -197,15 +175,98 @@ _load_code_workspace() {
 }
 
 _load_git_hooks() {
-  _gh=""
-  if [ -f "$WORKSPACE_LOCAL_YAML" ]; then
-    _gh="$(awk '/^(git_hooks|hooks):/ { sub(/^[a-zA-Z0-9_]+:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$WORKSPACE_LOCAL_YAML")"
+  GIT_HOOKS_CONFIG="$(yaml_get_top_level "git_hooks|hooks")"
+}
+
+migrate_karpathy_llm_config() {
+  _mkc_f="$1"
+  [ -f "$_mkc_f" ] || return 0
+
+  _mkc_has_sources=0
+  if command -v _yaml_plugin_list_from_file >/dev/null 2>&1; then
+    [ -n "$(_yaml_plugin_list_from_file "$_mkc_f" "karpathy-llm" "sources")" ] && _mkc_has_sources=1
+  elif grep -q '^[ \t]*sources:[ \t]*' "$_mkc_f" 2>/dev/null; then
+    _mkc_has_sources=1
   fi
-  if [ -z "$_gh" ] && [ -f "$WORKSPACE_YAML" ]; then
-    _gh="$(awk '/^(git_hooks|hooks):/ { sub(/^[a-zA-Z0-9_]+:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$WORKSPACE_YAML")"
+
+  _mkc_tmp="$(mktemp)"
+  awk -v has_sources="$_mkc_has_sources" '
+    /^[ \t]*plugins:[ \t]*(#.*)?$/ { in_plugins=1; in_target=0; plugin_indent=-1; print; next }
+    in_plugins && /^[^ \t#]/ { in_plugins=0; in_target=0 }
+    {
+      match($0, /^[ \t]*/)
+      indent = RLENGTH
+      trimmed = substr($0, indent + 1)
+    }
+    trimmed ~ /^ingest_member_readmes:[ \t]*/ {
+      next
+    }
+    !in_plugins || trimmed ~ /^([#]|$)/ {
+      print
+      next
+    }
+
+    in_target && (indent <= plugin_indent) {
+      in_target=0
+    }
+
+    !in_target {
+      k = trimmed
+      sub(/:.*/, "", k)
+      gsub(/^["\047]|["\047]$/, "", k)
+      gsub(/[[:space:]]/, "", k)
+      if (k == "karpathy-llm" && trimmed ~ /:[ \t]*(#.*)?$/) {
+        in_target=1
+        plugin_indent=indent
+      }
+      print
+      next
+    }
+
+    in_target && (indent > plugin_indent) {
+      k = trimmed
+      sub(/:.*/, "", k)
+      gsub(/^["\047]|["\047]$/, "", k)
+      gsub(/[[:space:]]/, "", k)
+      if (k == "raw_dir" && trimmed ~ /:[ \t]*/) {
+        if (has_sources == 1) {
+          next
+        }
+        val = trimmed
+        sub(/^[^:]*:[ \t]*/, "", val)
+        if (val ~ /^"[^"]*"/) {
+          match(val, /^"[^"]*"/)
+          val = substr(val, 2, RLENGTH - 2)
+        } else if (val ~ /^\047[^\047]*\047/) {
+          match(val, /^\047[^\047]*\047/)
+          val = substr(val, 2, RLENGTH - 2)
+        } else {
+          sub(/[ \t]*#.*$/, "", val)
+          sub(/[ \t]+$/, "", val)
+        }
+        while (sub(/^\.\//, "", val)) {}
+        if (val != "." && val != "/") {
+          sub(/\/+$/, "", val)
+        }
+        if (length(val) == 0) val = "docs"
+        ind = substr($0, 1, indent)
+        if (val ~ /[*?\[]|[ \t]/) {
+          printf "%ssources:\n%s  - \"%s\"\n", ind, ind, val
+        } else {
+          printf "%ssources:\n%s  - %s\n", ind, ind, val
+        }
+        has_sources=1
+        next
+      }
+    }
+    { print }
+  ' "$_mkc_f" > "$_mkc_tmp"
+
+  if ! cmp -s "$_mkc_f" "$_mkc_tmp"; then
+    mv "$_mkc_tmp" "$_mkc_f"
+  else
+    rm -f "$_mkc_tmp"
   fi
-  _gh="$(echo "$_gh" | tr -d " \t\r\n'\"")"
-  GIT_HOOKS_CONFIG="$_gh"
 }
 
 upgrade_workspace_config() {
@@ -303,5 +364,8 @@ upgrade_workspace_config() {
     ' "$_f" > "$_tmp" && mv "$_tmp" "$_f"
   fi
 
+  # 5. Migrate legacy karpathy-llm raw_dir to sources and strip obsolete ingest_member_readmes
+  migrate_karpathy_llm_config "$_f"
+
   rm -f "$_tmp"
 }

package/lib/yaml.sh

@@ -4,13 +4,68 @@
 # lib/yaml.sh — YAML Parser / Manipulator (for rnex.yaml & .local.rnex.yaml)
 # ============================================================================
 
-_yaml_list_plugins_from_file() {
-  _f="$1"
-  [ -f "$_f" ] || return 0
-  awk '
-    /^[ \t]*plugins:[ \t]*(#.*)?$/ { in_plugins=1; plugin_indent=-1; next }
-    in_plugins && /^[^ \t#]/ { in_plugins=0 }
-    !in_plugins { next }
+# ---- Config Path & File Initialization Helpers -----------------------------
+
+_yaml_resolve_files() {
+  _wy="${WORKSPACE_YAML:-}"
+  [ -n "$_wy" ] || _wy="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_CONFIG_FILE:-rnex.yaml}"
+  _wly="${WORKSPACE_LOCAL_YAML:-}"
+  [ -n "$_wly" ] || _wly="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}"
+}
+
+_ensure_local_yaml_file() {
+  _ely_sec="${1:-}"
+  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.
+${_ely_sec:+
+${_ely_sec}:}
+EOF
+  fi
+}
+
+# ---- Generic Top-Level & Section YAML Primitives ---------------------------
+
+_yaml_top_level_from_file() {
+  _ytf_f="$1"; _ytf_pat="$2"
+  [ -f "$_ytf_f" ] || return 0
+  awk -v pat="^(${_ytf_pat})[ \t]*:" '
+    $0 ~ pat {
+      line = $0
+      sub(/^[a-zA-Z0-9_.-]+[ \t]*:[ \t]*/, "", line)
+      sub(/[ \t]*#.*/, "", line)
+      sub(/^[ \t]+/, "", line)
+      sub(/[ \t\r]+$/, "", line)
+      gsub(/^["\047]|["\047]$/, "", line)
+      val = line
+    }
+    END { if (length(val) > 0) print val }
+  ' "$_ytf_f"
+}
+
+yaml_get_top_level() {
+  _ygt_pat="$1"; _ygt_def="${2:-}"
+  _yaml_resolve_files
+  _ygt_val="$(_yaml_top_level_from_file "$_wly" "$_ygt_pat")"
+  [ -n "$_ygt_val" ] || _ygt_val="$(_yaml_top_level_from_file "$_wy" "$_ygt_pat")"
+  if [ -n "$_ygt_val" ]; then
+    printf '%s' "$_ygt_val"
+  elif [ -n "$_ygt_def" ]; then
+    printf '%s' "$_ygt_def"
+  fi
+}
+
+_yaml_section_keys() {
+  _ysk_f="$1"; _ysk_sec="$2"
+  [ -f "$_ysk_f" ] || return 0
+  awk -v sec="$_ysk_sec" '
+    $0 ~ ("^[ \t]*" sec ":[ \t]*(#.*)?$") { in_sec=1; sec_indent=-1; next }
+    in_sec && /^[^ \t#]/ { in_sec=0 }
+    !in_sec { next }
     {
       match($0, /^[ \t]*/)
       indent = RLENGTH
@@ -18,18 +73,18 @@ _yaml_list_plugins_from_file() {
     }
     trimmed ~ /^([#]|$)/ { next }
 
-    in_plugins && (plugin_indent == -1) && (indent > 0) {
-      plugin_indent = indent
+    in_sec && (sec_indent == -1) && (indent > 0) {
+      sec_indent = indent
     }
 
-    in_plugins && (indent == plugin_indent) {
+    in_sec && (indent == sec_indent) {
       if (trimmed ~ /^["\047]?[a-zA-Z0-9_.-]+["\047]?:/) {
         line = trimmed
         sub(/:.*/, "", line)
         gsub(/^["\047]|["\047]$/, "", line)
         gsub(/[[:space:]]/, "", line)
         if (length(line) > 0) print line
-      } else if (trimmed ~ /^-[ \t]+["\047]?[a-zA-Z0-9_.-]+/) {
+      } else if (sec == "plugins" && trimmed ~ /^-[ \t]+["\047]?[a-zA-Z0-9_.-]+/) {
         line = trimmed
         sub(/^-[ \t]+/, "", line)
         sub(/[ \t]*#.*/, "", line)
@@ -39,27 +94,16 @@ _yaml_list_plugins_from_file() {
         if (length(line) > 0) print line
       }
     }
-  ' "$_f"
-}
-
-yaml_list_plugins() {
-  _wy="${WORKSPACE_YAML:-}"
-  [ -z "$_wy" ] && _wy="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_CONFIG_FILE:-rnex.yaml}"
-  _wly="${WORKSPACE_LOCAL_YAML:-}"
-  [ -z "$_wly" ] && _wly="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}"
-  {
-    _yaml_list_plugins_from_file "$_wy"
-    _yaml_list_plugins_from_file "$_wly"
-  } | awk '!seen[$0]++'
+  ' "$_ysk_f"
 }
 
-_yaml_plugin_get_from_file() {
-  _f="$1"; _pname="$2"; _key="$3"
-  [ -f "$_f" ] || return 0
-  awk -v plugin="$_pname" -v key="$_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 }
+_yaml_section_get() {
+  _ysg_f="$1"; _ysg_sec="$2"; _ysg_item="$3"; _ysg_key="$4"
+  [ -f "$_ysg_f" ] || return 0
+  awk -v sec="$_ysg_sec" -v item="$_ysg_item" -v key="$_ysg_key" '
+    $0 ~ ("^[ \t]*" sec ":[ \t]*(#.*)?$") { in_sec=1; in_target=0; item_indent=-1; next }
+    in_sec && /^[^ \t#]/ { in_sec=0; in_target=0 }
+    !in_sec { next }
     {
       match($0, /^[ \t]*/)
       indent = RLENGTH
@@ -67,7 +111,7 @@ _yaml_plugin_get_from_file() {
     }
     trimmed ~ /^([#]|$)/ { next }
 
-    in_target && (indent <= plugin_indent) {
+    in_target && (indent <= item_indent) {
       in_target=0
     }
 
@@ -76,14 +120,14 @@ _yaml_plugin_get_from_file() {
       sub(/:.*/, "", k)
       gsub(/^["\047]|["\047]$/, "", k)
       gsub(/[[:space:]]/, "", k)
-      if (k == plugin && trimmed ~ /:[ \t]*(#.*)?$/) {
+      if (k == item && trimmed ~ /:[ \t]*(\{\})?[ \t]*(#.*)?$/) {
         in_target=1
-        plugin_indent=indent
+        item_indent=indent
         next
       }
     }
 
-    in_target && (indent > plugin_indent) {
+    in_target && (indent > item_indent) {
       k = trimmed
       sub(/:.*/, "", k)
       gsub(/^["\047]|["\047]$/, "", k)
@@ -105,15 +149,122 @@ _yaml_plugin_get_from_file() {
         exit
       }
     }
-  ' "$_f"
+  ' "$_ysg_f"
+}
+
+_yaml_section_set() {
+  _yss_file="$1"; _yss_sec="$2"; _yss_item="$3"; _yss_field="$4"; _yss_value="$5"
+  if [ ! -f "$_yss_file" ]; then
+    mkdir -p "$(dirname "$_yss_file")"
+    printf '%s:\n' "$_yss_sec" > "$_yss_file"
+  elif ! grep -q "^${_yss_sec}:" "$_yss_file" 2>/dev/null; then
+    printf '\n%s:\n' "$_yss_sec" >> "$_yss_file"
+  fi
+
+  if ! awk -v sec="$_yss_sec" -v item="$_yss_item" '
+    $0 ~ ("^" sec ":[ ]*$") || $0 ~ ("^" sec ":[ ]*#") { in_s=1; next }
+    in_s && /^[^ #]/ { in_s=0 }
+    in_s && match($0, "^  " item ":[ ]*(#.*)?$") { found=1; exit }
+    END { exit !found }
+  ' "$_yss_file" 2>/dev/null; then
+    if grep -qE "^  $_yss_item:[ ]*(\{\}|\[\])?$" "$_yss_file" 2>/dev/null; then
+      _tmp="$(mktemp)"
+      awk -v item="$_yss_item" -v field="$_yss_field" -v value="$_yss_value" '
+        match($0, "^  " item ":[ ]*(\\{\\}|\\[\\])?$") {
+          printf "  %s:\n    %s: %s\n", item, field, value
+          next
+        }
+        { print }
+      ' "$_yss_file" > "$_tmp" && mv "$_tmp" "$_yss_file"
+      return 0
+    fi
+    _tmp="$(mktemp)"
+    awk -v sec="$_yss_sec" -v item="$_yss_item" -v field="$_yss_field" -v value="$_yss_value" '
+      $0 ~ ("^" sec ":[ ]*$") || $0 ~ ("^" sec ":[ ]*#") {
+        print
+        printf "  %s:\n    %s: %s\n", item, field, value
+        added=1
+        next
+      }
+      { print }
+      END {
+        if (!added) {
+          printf "%s:\n  %s:\n    %s: %s\n", sec, item, field, value
+        }
+      }
+    ' "$_yss_file" > "$_tmp" && mv "$_tmp" "$_yss_file"
+    return 0
+  fi
+
+  _tmp="$(mktemp)"
+  awk -v sec="$_yss_sec" -v item="$_yss_item" -v field="$_yss_field" -v value="$_yss_value" '
+    $0 ~ ("^" sec ":") { in_sec=1; print; next }
+    in_sec && /^[^ #]/ {
+      if (in_target && !field_set) {
+        printf "    %s: %s\n", field, value
+        field_set=1
+      }
+      in_sec=0; in_target=0
+    }
+    in_sec && match($0, "^  " item ":[ ]*(#.*)?$") {
+      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($0, "^    " field ":") {
+      printf "    %s: %s\n", field, value
+      field_set=1
+      next
+    }
+    { print }
+    END {
+      if (in_target && !field_set) {
+        printf "    %s: %s\n", field, value
+      }
+    }
+  ' "$_yss_file" > "$_tmp" && mv "$_tmp" "$_yss_file"
+}
+
+_yaml_section_remove() {
+  _ysr_file="$1"; _ysr_sec="$2"; _ysr_name="$3"
+  [ -f "$_ysr_file" ] || return 0
+  _tmp="$(mktemp)"
+  awk -v sec="$_ysr_sec" -v name="$_ysr_name" '
+    $0 ~ ("^" sec ":") { in_sec=1; print; next }
+    in_sec && /^[^ #]/ { in_sec=0; skip=0 }
+    in_sec && match($0, "^  " name ":[ ]*(\\{\\})?[ ]*(#.*)?$") { skip=1; next }
+    in_sec && skip && /^  [^ #]/ { skip=0 }
+    skip && /^    / { next }
+    { print }
+  ' "$_ysr_file" > "$_tmp" && mv "$_tmp" "$_ysr_file"
+}
+
+# ---- Plugin Configuration Operations ---------------------------------------
+
+_yaml_list_plugins_from_file() {
+  _yaml_section_keys "$1" "plugins"
+}
+
+yaml_list_plugins() {
+  _yaml_resolve_files
+  {
+    _yaml_list_plugins_from_file "$_wy"
+    _yaml_list_plugins_from_file "$_wly"
+  } | awk '!seen[$0]++'
+}
+
+_yaml_plugin_get_from_file() {
+  _yaml_section_get "$1" "plugins" "$2" "$3"
 }
 
 yaml_plugin_get() {
   _pname="$1"; _key="$2"
-  _wy="${WORKSPACE_YAML:-}"
-  [ -z "$_wy" ] && _wy="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_CONFIG_FILE:-rnex.yaml}"
-  _wly="${WORKSPACE_LOCAL_YAML:-}"
-  [ -z "$_wly" ] && _wly="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}"
+  _yaml_resolve_files
   _val="$(_yaml_plugin_get_from_file "$_wly" "$_pname" "$_key")"
   if [ -n "$_val" ]; then
     printf '%s' "$_val"
@@ -217,13 +368,10 @@ _yaml_plugin_list_from_file() {
 # deprecation warning on stderr), then to the defaults "docs" and "repos/**/README.md".
 get_plugin_config_list() {
   _gpl_plugin="$1"; _gpl_key="$2"
-  _gpl_wy="${WORKSPACE_YAML:-}"
-  [ -z "$_gpl_wy" ] && _gpl_wy="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_CONFIG_FILE:-rnex.yaml}"
-  _gpl_wly="${WORKSPACE_LOCAL_YAML:-}"
-  [ -z "$_gpl_wly" ] && _gpl_wly="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}"
+  _yaml_resolve_files
 
-  _gpl_items="$(_yaml_plugin_list_from_file "$_gpl_wly" "$_gpl_plugin" "$_gpl_key")"
-  [ -z "$_gpl_items" ] && _gpl_items="$(_yaml_plugin_list_from_file "$_gpl_wy" "$_gpl_plugin" "$_gpl_key")"
+  _gpl_items="$(_yaml_plugin_list_from_file "$_wly" "$_gpl_plugin" "$_gpl_key")"
+  [ -n "$_gpl_items" ] || _gpl_items="$(_yaml_plugin_list_from_file "$_wy" "$_gpl_plugin" "$_gpl_key")"
   if [ -n "$_gpl_items" ]; then
     printf '%s\n' "$_gpl_items"
     return 0
@@ -233,7 +381,7 @@ get_plugin_config_list() {
     karpathy-llm:sources)
       _gpl_raw="$(plugin_legacy_raw_dir "$_gpl_plugin")"
       if [ -n "$_gpl_raw" ]; then
-        log_warn "plugins.$_gpl_plugin.raw_dir is deprecated; replace it with a 'sources' list in ${RNEX_CONFIG_FILE:-rnex.yaml} (or ${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}) and run 'rnex sync'." >&2
+        log_warn "plugins.$_gpl_plugin.raw_dir is deprecated; run 'rnex sync' to rewrite it to 'sources' in ${RNEX_CONFIG_FILE:-rnex.yaml}." >&2
         printf '%s\n' "$_gpl_raw"
       else
         printf '%s\n' "docs" "repos/**/README.md"
@@ -246,12 +394,9 @@ get_plugin_config_list() {
 # 'sources' list is configured in either config file. Prints nothing otherwise.
 plugin_legacy_raw_dir() {
   _plr_plugin="$1"
-  _plr_wy="${WORKSPACE_YAML:-}"
-  [ -z "$_plr_wy" ] && _plr_wy="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_CONFIG_FILE:-rnex.yaml}"
-  _plr_wly="${WORKSPACE_LOCAL_YAML:-}"
-  [ -z "$_plr_wly" ] && _plr_wly="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}"
-  [ -n "$(_yaml_plugin_list_from_file "$_plr_wly" "$_plr_plugin" "sources")" ] && return 0
-  [ -n "$(_yaml_plugin_list_from_file "$_plr_wy" "$_plr_plugin" "sources")" ] && return 0
+  _yaml_resolve_files
+  [ -n "$(_yaml_plugin_list_from_file "$_wly" "$_plr_plugin" "sources")" ] && return 0
+  [ -n "$(_yaml_plugin_list_from_file "$_wy" "$_plr_plugin" "sources")" ] && return 0
   yaml_plugin_get "$_plr_plugin" "raw_dir" 2>/dev/null || true
 }
 
@@ -284,45 +429,26 @@ yaml_has_plugin() {
 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 "$_val" in
-    false|no|0|disabled|off) return 1 ;;
-    *) return 0 ;;
-  esac
+  is_enabled_val "$(yaml_plugin_get "$_plugin" "enabled")"
 }
 
 provider_plugin_enabled() {
-  _p="$1"
-  if yaml_plugin_enabled "$_p"; then
-    return 0
-  fi
-  return 1
+  yaml_plugin_enabled "$1"
 }
 
 provider_option_enabled() {
-  _p="$1"
-  _opt="$2"
+  _p="$1"; _opt="$2"
   provider_plugin_enabled "$_p" || return 1
-  _val="$(yaml_plugin_get "$_p" "$_opt")"
-  _val="$(printf '%s' "$_val" | tr '[:upper:]' '[:lower:]')"
-  case "$_val" in
-    false|no|0|disabled|off) return 1 ;;
-    *) return 0 ;;
-  esac
+  is_enabled_val "$(yaml_plugin_get "$_p" "$_opt")"
 }
 
 provider_auto_sync_enabled() {
   _p="$1"
   provider_plugin_enabled "$_p" || return 1
   _val="$(yaml_plugin_get "$_p" "auto_sync_on")"
-  [ -z "$_val" ] && _val="$(yaml_plugin_get "$_p" "autoSyncOn")"
-  [ -z "$_val" ] && _val="SessionStart"
-  _val="$(printf '%s' "$_val" | tr '[:upper:]' '[:lower:]')"
-  case "$_val" in
-    false|no|0|disabled|off|none) return 1 ;;
-    *) return 0 ;;
-  esac
+  [ -n "$_val" ] || _val="$(yaml_plugin_get "$_p" "autoSyncOn")"
+  [ -n "$_val" ] || _val="SessionStart"
+  is_enabled_val "$_val"
 }
 
 copilot_plugin_enabled() { provider_plugin_enabled "copilot"; }
@@ -348,7 +474,6 @@ windsurf_instructions_enabled() { provider_plugin_enabled "windsurf"; }
 windsurf_skills_enabled() { provider_option_enabled "windsurf" "skills"; }
 
 has_active_provider_instructions() {
-  _dir="${1:-${NEXUS_DIR:-$PWD}}"
   _saved_ws_yaml="${WORKSPACE_YAML:-}"
   _saved_local_yaml="${WORKSPACE_LOCAL_YAML:-}"
   if [ -n "$1" ] && [ -d "$1" ]; then
@@ -371,102 +496,16 @@ has_active_provider_instructions() {
 }
 
 _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' >> "$_file"
-  fi
-
-  if ! awk -v plugin="$_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="$(mktemp)"
-    awk -v plugin="$_plugin" -v field="$_field" -v value="$_value" '
-      /^plugins:[ ]*$/ || /^plugins:[ ]*#/ {
-        print
-        printf "  %s:\n    %s: %s\n", plugin, field, value
-        added=1
-        next
-      }
-      { print }
-      END {
-        if (!added) {
-          printf "plugins:\n  %s:\n    %s: %s\n", plugin, field, value
-        }
-      }
-    ' "$_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_section_set "$1" "plugins" "$2" "$3" "$4"
 }
 
 yaml_plugin_set() {
-  _plugin="$1"; _field="$2"; _value="$3"
-  _yaml_plugin_set_in_file "$WORKSPACE_YAML" "$_plugin" "$_field" "$_value"
+  _yaml_plugin_set_in_file "$WORKSPACE_YAML" "$1" "$2" "$3"
 }
 
 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" "$_value"
+  _ensure_local_yaml_file "plugins"
+  _yaml_plugin_set_in_file "$WORKSPACE_LOCAL_YAML" "$1" "$2" "$3"
 }
 
 yaml_enable_plugin() {
@@ -532,17 +571,7 @@ yaml_enable_plugin() {
 }
 
 _yaml_disable_plugin_in_file() {
-  _file="$1"; _name="$2"
-  [ -f "$_file" ] || return 0
-  _tmp="$(mktemp)"
-  awk -v name="$_name" '
-    /^plugins:/ { in_plugins=1; print; next }
-    in_plugins && /^[^ #]/ { in_plugins=0 }
-    in_plugins && match($0, "^  " name ":") { skip=1; next }
-    in_plugins && skip && /^  [^ #]/ { skip=0 }
-    skip && /^    / { next }
-    { print }
-  ' "$_file" > "$_tmp" && mv "$_tmp" "$_file"
+  _yaml_section_remove "$1" "plugins" "$2"
 }
 
 yaml_disable_plugin() {
@@ -551,68 +580,37 @@ yaml_disable_plugin() {
   _yaml_disable_plugin_in_file "$WORKSPACE_LOCAL_YAML" "$_name"
 }
 
+# ---- Repository Configuration Operations -----------------------------------
+
 # Parse list of repos from a single config file
 _yaml_list_repos_from_file() {
-  _f="$1"
-  [ -f "$_f" ] || return 0
-  awk '
-    /^repos:[ ]*$/ || /^repos:[ ]*#/ { r=1; next }
-    r && /^[^ #]/ { r=0 }
-    r && /^  [a-zA-Z0-9_.-]+:[ ]*(\{\})?[ ]*(#.*)?$/ {
-      line = $0
-      sub(/^[ ]*/, "", line)
-      sub(/:.*/, "", line)
-      gsub(/[[:space:]]/, "", line)
-      if (length(line) > 0) print line
-    }
-  ' "$_f"
+  _yaml_section_keys "$1" "repos"
 }
 
 # Parse list of repos merged from repo and local configs (order preserved, deduplicated)
 yaml_list_repos() {
-  _w_y="${WORKSPACE_YAML:-}"
-  [ -z "$_w_y" ] && _w_y="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_CONFIG_FILE:-rnex.yaml}"
-  _w_ly="${WORKSPACE_LOCAL_YAML:-}"
-  [ -z "$_w_ly" ] && _w_ly="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}"
+  _yaml_resolve_files
   {
-    _yaml_list_repos_from_file "$_w_y"
-    _yaml_list_repos_from_file "$_w_ly"
+    _yaml_list_repos_from_file "$_wy"
+    _yaml_list_repos_from_file "$_wly"
   } | awk '!seen[$0]++'
 }
 
 # Get a field value for a repo from a specific config file
 _yaml_get_from_file() {
-  _f="$1"; _repo="$2"; _field="$3"
-  [ -f "$_f" ] || return 0
-  awk -v repo="$_repo" -v field="$_field" '
-    /^repos:[ ]*$/ || /^repos:[ ]*#/ { r=1; next }
-    r && /^[^ #]/ { r=0 }
-    r && match($0, "^  " repo ":[ ]*(\\{\\})?[ ]*(#.*)?$") { in_target=1; next }
-    in_target && /^  [^ #]/ { in_target=0 }
-    in_target && match($0, "^    " field ":[ ]*") {
-      line = $0
-      sub("^    " field ":[ ]*", "", line)
-      sub(/[ ]*#.*$/, "", line)
-      gsub(/^["\047]|["\047]$/, "", line)
-      print line
-      exit
-    }
-  ' "$_f"
+  _yaml_section_get "$1" "repos" "$2" "$3"
 }
 
 # Get field value (local config overrides repo config)
 yaml_get() {
   _repo="$1"; _field="$2"
-  _w_y="${WORKSPACE_YAML:-}"
-  [ -z "$_w_y" ] && _w_y="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_CONFIG_FILE:-rnex.yaml}"
-  _w_ly="${WORKSPACE_LOCAL_YAML:-}"
-  [ -z "$_w_ly" ] && _w_ly="${NEXUS_DIR:-${RNEX_ROOT:-.}}/${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}"
-  _val="$(_yaml_get_from_file "$_w_ly" "$_repo" "$_field")"
+  _yaml_resolve_files
+  _val="$(_yaml_get_from_file "$_wly" "$_repo" "$_field")"
   if [ -n "$_val" ]; then
     printf '%s' "$_val"
     return 0
   fi
-  _yaml_get_from_file "$_w_y" "$_repo" "$_field"
+  _yaml_get_from_file "$_wy" "$_repo" "$_field"
 }
 
 yaml_has_repo() {
@@ -621,13 +619,7 @@ yaml_has_repo() {
 
 # Check if a repo is enabled: default is true unless explicitly set to false/no/0/disabled
 yaml_repo_enabled() {
-  _repo="$1"
-  _val="$(yaml_get "$_repo" "enabled")"
-  _val="$(printf '%s' "$_val" | tr '[:upper:]' '[:lower:]')"
-  case "$_val" in
-    false|no|0|disabled|off) return 1 ;;
-    *) return 0 ;;
-  esac
+  is_enabled_val "$(yaml_get "$1" "enabled")"
 }
 
 yaml_add_repo() {
@@ -650,17 +642,7 @@ yaml_add_repo() {
 }
 
 _yaml_remove_repo_from_file() {
-  _file="$1"; _name="$2"
-  [ -f "$_file" ] || return 0
-  _tmp="$(mktemp)"
-  awk -v name="$_name" '
-    /^repos:/ { r=1; print; next }
-    r && /^[^ #]/ { r=0 }
-    r && match($0, "^  " name ":[ ]*(#.*)?$") { skip=1; next }
-    r && skip && /^  [^ #]/ { skip=0 }
-    skip && /^    / { next }
-    { print }
-  ' "$_file" > "$_tmp" && mv "$_tmp" "$_file"
+  _yaml_section_remove "$1" "repos" "$2"
 }
 
 yaml_remove_repo() {
@@ -670,97 +652,22 @@ yaml_remove_repo() {
 }
 
 _yaml_set_in_file() {
-  _file="$1"; _repo="$2"; _field="$3"; _value="$4"
-  if [ ! -f "$_file" ]; then
-    mkdir -p "$(dirname "$_file")"
-    printf 'repos:\n' > "$_file"
-  elif ! grep -q '^repos:' "$_file" 2>/dev/null; then
-    printf '\nrepos:\n' >> "$_file"
-  fi
-
-  if ! awk -v repo="$_repo" '
-    /^repos:[ ]*$/ || /^repos:[ ]*#/ { in_r=1; next }
-    in_r && /^[^ #]/ { in_r=0 }
-    in_r && match($0, "^  " repo ":[ ]*(#.*)?$") { found=1; exit }
-    END { exit !found }
-  ' "$_file" 2>/dev/null; then
-    _tmp="$(mktemp)"
-    awk -v repo="$_repo" -v field="$_field" -v value="$_value" '
-      /^repos:[ ]*$/ || /^repos:[ ]*#/ {
-        print
-        printf "  %s:\n    %s: %s\n", repo, field, value
-        added=1
-        next
-      }
-      { print }
-      END {
-        if (!added) {
-          printf "repos:\n  %s:\n    %s: %s\n", repo, field, value
-        }
-      }
-    ' "$_file" > "$_tmp" && mv "$_tmp" "$_file"
-    return 0
-  fi
-
-  _tmp="$(mktemp)"
-  awk -v repo="$_repo" -v field="$_field" -v value="$_value" '
-    /^repos:/ { in_repos=1; print; next }
-    in_repos && /^[^ #]/ {
-      if (in_target && !field_set) {
-        printf "    %s: %s\n", field, value
-        field_set=1
-      }
-      in_repos=0; in_target=0
-    }
-    in_repos && match($0, "^  " repo ":[ ]*(#.*)?$") {
-      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_section_set "$1" "repos" "$2" "$3" "$4"
 }
 
 yaml_set() {
-  _repo="$1"; _field="$2"; _value="$3"
-  _yaml_set_in_file "$WORKSPACE_YAML" "$_repo" "$_field" "$_value"
+  _yaml_set_in_file "$WORKSPACE_YAML" "$1" "$2" "$3"
 }
 
 yaml_set_local() {
-  _repo="$1"; _field="$2"; _value="$3"
-  if [ ! -f "$WORKSPACE_LOCAL_YAML" ]; then
-    cat <<'EOF' > "$WORKSPACE_LOCAL_YAML"
-# ==============================================================================
-# .local.rnex.yaml — Repo Nexus Local Configuration (Machine-Specific)
-# ==============================================================================
-# This file is gitignored. Use it to specify local repository paths, overrides,
-# and enable/disable states for this workstation.
-
-repos:
-EOF
-  fi
-  _yaml_set_in_file "$WORKSPACE_LOCAL_YAML" "$_repo" "$_field" "$_value"
+  _ensure_local_yaml_file "repos"
+  _yaml_set_in_file "$WORKSPACE_LOCAL_YAML" "$1" "$2" "$3"
 }
 
+# ---- Top-Level Key Setters -------------------------------------------------
+
 _yaml_set_top_level_in_file() {
-  _file="$1"
-  _key="$2"
-  _val="$3"
+  _file="$1"; _key="$2"; _val="$3"
   [ -f "$_file" ] || return 0
   _tmp="$(mktemp)"
   if grep -q "^[ ]*${_key}:" "$_file" 2>/dev/null; then
@@ -792,21 +699,10 @@ _yaml_set_top_level_in_file() {
 }
 
 yaml_set_top_level() {
-  _key="$1"; _val="$2"
-  _yaml_set_top_level_in_file "$WORKSPACE_YAML" "$_key" "$_val"
+  _yaml_set_top_level_in_file "$WORKSPACE_YAML" "$1" "$2"
 }
 
 yaml_set_top_level_local() {
-  _key="$1"; _val="$2"
-  if [ ! -f "$WORKSPACE_LOCAL_YAML" ]; then
-    cat <<'EOF' > "$WORKSPACE_LOCAL_YAML"
-# ==============================================================================
-# .local.rnex.yaml — Repo Nexus Local Configuration (Machine-Specific)
-# ==============================================================================
-# This file is gitignored. Use it to specify local repository paths, overrides,
-# and enable/disable states for this workstation.
-
-EOF
-  fi
-  _yaml_set_top_level_in_file "$WORKSPACE_LOCAL_YAML" "$_key" "$_val"
+  _ensure_local_yaml_file ""
+  _yaml_set_top_level_in_file "$WORKSPACE_LOCAL_YAML" "$1" "$2"
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.7.28",
+  "version": "0.7.30",
   "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.example.yaml

@@ -105,11 +105,9 @@ plugins:
   #     - docs                    #   directory: all files (hidden dirs and node_modules pruned)
   #     - "repos/**/README.md"    #   recursive glob (quote it); disabled repos are excluded
   #                               # A sources list in .local.rnex.yaml replaces this list entirely.
-  #                               # Legacy 'raw_dir' is still read as a single source (deprecated).
   #   wiki_dir: ".rnex/wiki"      # Directory for curated atomic markdown pages (default: .rnex/wiki)
   #   lint_trigger: "manual"      # Runs manually via 'rnex sync' or validation checklists (git-post-merge, git-post-commit, git-pre-commit, git-pre-push, manual)
   #   notify_on_changes: true     # Show notification when changes are committed to ./docs or .rnex/wiki
-  #   ingest_member_readmes: true # Automatically ingest member repository READMEs into atomic wiki pages (default: true)
 
 
 # ------------------------------------------------------------------------------

package/toolkit/plugins/karpathy-llm/README.md

@@ -131,10 +131,6 @@ plugins:
 
     # Directory paths relative to workspace root (defaults shown)
     wiki_dir: .rnex/wiki        # Directory for curated atomic markdown pages
-
-    # Member repository README auto-ingestion (default: true)
-    # Automatically registers member repos into wiki pages and hot.md during rnex sync
-    ingest_member_readmes: true
 ```
 
 ### 2. Local Machine Configuration (`.local.rnex.yaml`)
@@ -158,11 +154,6 @@ plugins:
 
 ### Detailed Option Descriptions
 
-#### `ingest_member_readmes` (Repo Config)
-* **What it does:** Automatically ingests member repository READMEs into atomic wiki pages (`repo-<name>.md`) and registers them in `hot.md`.
-* **How it works:** During `rnex sync`, the plugin discovers configured repositories in `rnex.yaml`, extracts top-level README summaries, creates initial `repo-<name>.md` pages non-destructively, logs ingestion in `_log.md`, and updates the catalog in `hot.md`.
-* **Why you need it:** Provides newly onboarded AI assistants immediate context and navigation for all member repositories in the multi-repo workspace. If set to `false`, member repositories are not automatically scanned or ingested during sync.
-
 #### `lint_trigger` (Local Config)
 * **What it does:** Optional git hook trigger to automate wiki graph audits and maintenance workflows (`wiki-lint` and `wiki-ingest`).
 * **Default:** Unset / omitted. Automated triggers are **disabled by default**; wiki maintenance is purely manual unless you explicitly opt into a Git hook here.
@@ -183,10 +174,8 @@ plugins:
 
 | Field | Scope / File | Type | Default | Values / Behavior |
 |:---|:---|:---|:---|:---|
-| `ingest_member_readmes` | Repo (`rnex.yaml`) | `boolean` | `true` | Automatically ingests member repo READMEs into `repo-<name>.md` and `hot.md` during `rnex sync`. |
 | `sources` | Repo (`rnex.yaml`) | `list` | `[docs, "repos/**/README.md"]` | Directory paths and/or glob patterns for intake documents. |
 | `wiki_dir` | Repo (`rnex.yaml`) | `string` | `.rnex/wiki` | Directory containing atomic domain pages. |
-| `raw_dir` | Repo (`rnex.yaml`) | `string` | `./docs` | *(Deprecated)* Append-only directory for unmodified source materials. Use `sources` instead. |
 | `lint_trigger` | Local (`.local.rnex.yaml`) | `string` | *(unset)* | Optional opt-in Git hook: `git-post-commit`, `git-pre-push`, `git-post-merge`. Unset = purely manual. |
 | `notify_on_changes` | Local (`.local.rnex.yaml`) | `boolean` | `true` | Terminal alerts printed right after git commit/push when `./docs/` or `.rnex/wiki/` needs attention. |
 

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

@@ -72,7 +72,6 @@ get_cfg() {
 _wiki="$(get_cfg "wiki_dir" ".rnex/wiki")"
 _wiki="$(printf '%s' "$_wiki" | sed -e 's#^/##' -e 's#/$##')"
 _wiki_path="$_root/$_wiki"
-_ingest_readmes="$(get_cfg "ingest_member_readmes" "true")"
 
 mkdir -p "$_wiki_path"
 
@@ -420,12 +419,7 @@ LOG_EOF
   fi
 }
 
-# 2. Automatically ingest README.md from all registered/enabled member repositories
-case "$(printf '%s' "$_ingest_readmes" | tr '[:upper:]' '[:lower:]')" in
-  false|no|0|disabled|off) _skip_all_readmes=1 ;;
-  *) _skip_all_readmes=0 ;;
-esac
-
+# 2. Automatically ingest README.md from registered/enabled member repositories when included in sources
 _rd=""
 for _cfg in "$_root/.local.rnex.yaml" "$_root/rnex.yaml"; do
   [ -f "$_cfg" ] || continue
@@ -448,6 +442,24 @@ done
 REPOS_DIR="${_rd:-./repos}"
 _clean_repos="$(printf '%s' "$REPOS_DIR" | sed -e 's#^[[:space:]]*##' -e 's#[[:space:]]*$##' -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
+_skip_all_readmes=0
+if command -v get_plugin_config_list >/dev/null 2>&1; then
+  _src_list="$(NEXUS_DIR="$_root" WORKSPACE_YAML="$_root/rnex.yaml" WORKSPACE_LOCAL_YAML="$_root/.local.rnex.yaml" get_plugin_config_list "karpathy-llm" "sources" 2>/dev/null || true)"
+  if [ -n "$_src_list" ]; then
+    _skip_all_readmes=1
+    while IFS= read -r _s_item || [ -n "$_s_item" ]; do
+      case "$_s_item" in
+        *README*|*readme*|repos/*|"./repos/"*|"$_clean_repos"/*|*"**"*)
+          _skip_all_readmes=0
+          break
+          ;;
+      esac
+    done <<EOF_SRC
+$_src_list
+EOF_SRC
+  fi
+fi
+
 list_configured_repos() {
   for _cfg_file in "$_root/.local.rnex.yaml" "$_root/rnex.yaml"; do
     [ -f "$_cfg_file" ] || continue
@@ -475,7 +487,6 @@ if [ "$_skip_all_readmes" -ne 1 ]; then
     
     # Check if this repository is explicitly disabled in .local.rnex.yaml or rnex.yaml (block-scoped)
     _is_disabled=""
-    _repo_ingest=""
     for _cfg_file in "$RNEX_ROOT/.local.rnex.yaml" "$RNEX_ROOT/rnex.yaml"; do
       [ -f "$_cfg_file" ] || continue
       _en="$(awk -v repo="$repo_name" '
@@ -499,27 +510,6 @@ if [ "$_skip_all_readmes" -ne 1 ]; then
         esac
       fi
 
-      _ingest_val="$(awk -v repo="$repo_name" '
-        /^repos:[ ]*$/ || /^repos:[ ]*#/ { r=1; next }
-        r && /^[^ #]/ { r=0 }
-        r && match($0, "^  " repo ":[ ]*(\\{\\})?[ ]*(#.*)?$") { in_target=1; next }
-        in_target && /^  [^ #]/ { in_target=0 }
-        in_target && match($0, "^    ingest_member_readmes:[ ]*") {
-          line = $0
-          sub("^    ingest_member_readmes:[ ]*", "", line)
-          sub(/[ ]*#.*$/, "", line)
-          gsub(/^["\047]|["\047]$/, "", line)
-          print line
-          exit
-        }
-      ' "$_cfg_file")"
-      if [ -n "$_ingest_val" ] && [ -z "$_repo_ingest" ]; then
-        case "$(printf '%s' "$_ingest_val" | tr '[:upper:]' '[:lower:]')" in
-          false|no|0|disabled|off) _repo_ingest=0 ;;
-          *) _repo_ingest=1 ;;
-        esac
-      fi
-
       if [ -z "$_custom_path" ]; then
         _cp="$(awk -v repo="$repo_name" '
           /^repos:[ ]*$/ || /^repos:[ ]*#/ { r=1; next }
@@ -539,7 +529,6 @@ if [ "$_skip_all_readmes" -ne 1 ]; then
       fi
     done
     [ "$_is_disabled" = "1" ] && continue
-    [ "$_repo_ingest" = "0" ] && continue
 
     # Resolve physical repository path and relative location
     _repo_rel=""

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

@@ -11,15 +11,12 @@ config_defaults:
   wiki_dir: ".rnex/wiki"
   lint_trigger: "manual" # Default changed to manual to avoid unsolicited background trigger tasks
   notify_on_changes: true
-  ingest_member_readmes: true
 
 config_descriptions:
   sources: "<list>  (intake directories and/or glob patterns; .local.rnex.yaml list replaces rnex.yaml list)"
   wiki_dir: "<dir>  (directory for curated markdown pages)"
-  raw_dir: "<dir>   (deprecated: single intake directory, used only when sources is unset)"
   lint_trigger: "git-post-merge|git-post-commit|git-pre-commit|git-pre-push|manual"
   notify_on_changes: "true|false  (show notification when raw/wiki changes are committed)"
-  ingest_member_readmes: "true|false  (automatically track member repository READMEs in wiki)"
 
 rules:
   - rules/behavioral.md: .rnex/plugins/karpathy-llm/rules/behavioral.md