repo-nexus 0.7.28 → 0.7.29

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/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

@@ -208,6 +208,97 @@ _load_git_hooks() {
   GIT_HOOKS_CONFIG="$_gh"
 }
 
+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]*' "$_mkc_f" 2>/dev/null; then
+    _mkc_has_sources=1
+  fi
+
+  _mkc_tmp="$(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
+}
+
 upgrade_workspace_config() {
   _f="$1"
   _ver="$2"
@@ -303,5 +394,8 @@ upgrade_workspace_config() {
     ' "$_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

@@ -233,7 +233,7 @@ 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"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.7.28",
+  "version": "0.7.29",
   "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