repo-nexus 0.7.26 → 0.7.28

package/CHANGELOG.md

@@ -5,6 +5,27 @@ All notable changes to Repo Nexus (`rnex`) will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.7.26] - 2026-10-21
+
+### Added
+- **Multi-Source Intake Configuration for Karpathy LLM Wiki (`sources`)**:
+  - Replaced single `raw_dir` scalar configuration with multi-value `sources` list under `plugins.karpathy-llm.sources`.
+  - Added pure POSIX `/bin/sh` glob and directory resolver (`resolve_plugin_sources`) supporting both explicit directory paths (e.g. `docs`) and recursive/single-level glob patterns (e.g. `"repos/**/README.md"`, `repos/*/README.md`).
+  - Implemented automatic exclusion of member repositories disabled locally or globally (`enabled: false`) from resolved intake paths.
+  - Enforced two-level configuration precedence: `.local.rnex.yaml` takes full precedence over `rnex.yaml` when defining `sources`.
+  - Added automatic directory pruning for `.git`, `.rnex`, and `node_modules` during recursive file traversal.
+  - Added safe directory provisioning in `rnex sync` that creates explicit directory sources (such as `docs`) while skipping wildcard patterns and file targets.
+
+### Changed
+- **Default Intake Sources**:
+  - Default sources for `karpathy-llm` plugin are now `docs` and `"repos/**/README.md"`.
+  - Updated `rnex init` templates, `rnex status`, and plugin scaffolding to render and configure multi-line `sources`.
+  - Updated plugin lifecycle hooks (`after_sync.sh`, `git_*.sh`) and agentic skills (`wiki-ingest.md`, `wiki-lint.md`) to resolve documentation from `sources`.
+
+### Deprecated
+- **Legacy `raw_dir` Configuration**:
+  - `plugins.karpathy-llm.raw_dir` is deprecated in favor of `sources`. Workspaces configuring `raw_dir` are automatically read via transparent fallback with a non-fatal deprecation notice advising migration to `sources`.
+
 ## [0.7.7] - 2026-10-15
 
 ### Added

package/docs/CLI.md

@@ -93,7 +93,7 @@ Hooks have access to POSIX helper functions for managing User Skill pointers:
 ### Karpathy LLM Wiki Plugin
 The `karpathy-llm` plugin uses lifecycle hooks to manage its domain directories:
 - **Default curated knowledge base (`wiki_dir`)**: `.rnex/wiki`
-- **Default append-only raw intake (`raw_dir`)**: `./docs`
+- **Default intake sources (`sources`)**: `docs` directory and `"repos/**/README.md"` glob pattern (legacy scalar `raw_dir` supported with deprecation notice)
 - **Master navigation index**: `.rnex/wiki/index.md`
 - **Rolling orientation cache**: `.rnex/wiki/hot.md`
 - **Operation log**: `.rnex/wiki/_log.md`

package/docs/plugins/karpathy-llm.md

@@ -93,15 +93,21 @@ plugins:
   karpathy-llm:
     # Directory paths relative to workspace root (defaults shown)
     wiki_dir: .rnex/wiki        # Directory for curated atomic markdown pages
-    raw_dir: ./docs             # Append-only directory for unmodified intake documents
+    sources:                    # Intake documents: directories and/or glob patterns
+      - 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.
 
     # Automated Git hook trigger for wiki verification
     # Options: git-post-merge, git-post-commit, git-pre-commit, git-pre-push, manual
     lint_trigger: manual
 
-    # Notify developer when changes are committed to ./docs/ or .rnex/wiki/
+    # 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
 ```
@@ -109,17 +115,33 @@ plugins:
 | Option | Type | Default | Description |
 |:---|:---|:---|:---|
 | `wiki_dir` | string | `.rnex/wiki` | Directory containing curated atomic markdown pages. |
-| `raw_dir` | string | `./docs` | Append-only directory for unmodified source intake documents. |
+| `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 `./docs/` or `.rnex/wiki/`. |
+| `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`. |
 
 ---
 
+### Intake Sources (`sources`)
+
+The `sources` setting defines where the Karpathy LLM Wiki discovers raw intake documents for `wiki-ingest` and change verification:
+
+- **Directory Paths (e.g. `docs`, `notes`)**: Repo Nexus recursively scans the directory for all files. Hidden directories (starting with `.`) and `node_modules` are automatically pruned.
+- **Recursive Globs (e.g. `"repos/**/README.md"`)**: Pure POSIX `/bin/sh` pattern resolution matches files at arbitrary directory depths. Always quote globs containing `*` in YAML. Directories named `.git`, `.rnex`, and `node_modules` are pruned during traversal.
+- **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`.
+- **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.
+
+---
+
 ## Automated Git Hooks Integration
 
 When workspace Git hooks are installed (`rnex hooks install`), the `karpathy-llm` plugin links directly into Git events:
-- **`post-merge`**: Detects if incoming commits touched `./docs/` or `.rnex/wiki/`, warning the developer to review or re-lint.
+- **`post-merge`**: Detects if incoming commits touched intake sources or `.rnex/wiki/`, warning the developer to review or re-lint.
 - **`post-commit`**: Reminds the developer to run `wiki-lint` or `wiki-ingest` if wiki files were committed.
 - **`pre-commit` & `pre-push`**: Emits trigger notices if unvalidated wiki files are staged or about to be pushed.
 

package/docs/rnex.example.yaml

@@ -101,7 +101,11 @@ plugins:
   # windsurf:
   #   skills: true              # generate user skills in .windsurf/rules/ (default: true)
   # karpathy-llm:
-  #   raw_dir: "./docs"           # Append-only directory for unmodified intake documents (default: ./docs)
+  #   sources:                    # Intake documents: directories and/or glob patterns (default below)
+  #     - 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

package/lib/commands/init.sh

@@ -107,15 +107,7 @@ cmd_init() {
       _pdir="$(find_plugin_dir "$_p" 2>/dev/null || true)"
       _cfg_lines=""
       if [ -n "$_pdir" ] && [ -f "$_pdir/plugin.yaml" ]; then
-        _cfg_lines="$(awk '
-          /^config_defaults:[ ]*$/ || /^config_defaults:[ ]*#/ { in_c=1; next }
-          in_c && /^[^ #]/ { exit }
-          in_c && /^[ ]*[a-zA-Z0-9_.-]+:[ ]*/ {
-            line = $0
-            sub(/^[ ]*/, "    ", line)
-            print line
-          }
-        ' "$_pdir/plugin.yaml")"
+        _cfg_lines="$(plugin_config_default_lines "$_pdir/plugin.yaml")"
       fi
       if [ -n "$_cfg_lines" ]; then
         _init_plugins="${_init_plugins}  ${_p}:\n${_cfg_lines}\n"

package/lib/commands/plugin.sh

@@ -99,6 +99,10 @@ cmd_plugin_info() {
         [ -n "$_skill_target" ] && _desc="$(printf '%s' "$_desc" | sed -e "s|{skill_dir}|$_skill_target|g")"
 
         _cur="$(yaml_plugin_get "$_name" "$_opt" 2>/dev/null || true)"
+        if [ -z "$_cur" ]; then
+          # List-valued options (e.g. sources): show the effective list, comma-separated
+          _cur="$(get_plugin_config_list "$_name" "$_opt" 2>/dev/null | awk '{ out = (NR == 1) ? $0 : out ", " $0 } END { if (NR) print out }')"
+        fi
         if [ -z "$_cur" ]; then
           _cur="$(awk -v k="$_opt" '
             /^config_defaults:[ ]*$/ || /^config_defaults:[ ]*#/ { in_c=1; next }

package/lib/commands/status.sh

@@ -227,6 +227,9 @@ cmd_status() {
             if [ -n "$_opts" ]; then
               printf '    %b↳ Options: %s%b\n' "$_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"
+            fi
           fi
         fi
       else

package/lib/hooks.sh

@@ -146,14 +146,35 @@ run_plugin_git_hooks() {
 
     if [ -n "$_h_cand" ] && [ -f "$_h_cand" ]; then
       chmod +x "$_h_cand" 2>/dev/null || true
-      (
-        export RNEX_ROOT RNEX_CONFIG_MERGED RNEX_PLUGIN_DIR RNEX_CMD RNEX_ARGS RNEX_QUIET
-        if [ -n "$_stdin_data" ]; then
-          printf '%s\n' "$_stdin_data" | "$_h_cand" "$@"
-        else
-          "$_h_cand" "$@"
-        fi
-      ) || true
+      if [ -n "$_stdin_data" ]; then
+        printf '%s\n' "$_stdin_data" | env \
+          NEXUS_DIR="$RNEX_ROOT" \
+          WORKSPACE_YAML="$RNEX_ROOT/${RNEX_CONFIG_FILE:-rnex.yaml}" \
+          WORKSPACE_LOCAL_YAML="$RNEX_ROOT/${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}" \
+          RNEX_ROOT="$RNEX_ROOT" \
+          RNEX_CONFIG_MERGED="$RNEX_CONFIG_MERGED" \
+          RNEX_PLUGIN_DIR="$RNEX_PLUGIN_DIR" \
+          RNEX_CMD="$RNEX_CMD" \
+          RNEX_ARGS="$RNEX_ARGS" \
+          RNEX_QUIET="$RNEX_QUIET" \
+          RNEX_CONFIG_FILE="${RNEX_CONFIG_FILE:-rnex.yaml}" \
+          RNEX_LOCAL_CONFIG_FILE="${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}" \
+          "$_h_cand" "$@" || true
+      else
+        env \
+          NEXUS_DIR="$RNEX_ROOT" \
+          WORKSPACE_YAML="$RNEX_ROOT/${RNEX_CONFIG_FILE:-rnex.yaml}" \
+          WORKSPACE_LOCAL_YAML="$RNEX_ROOT/${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}" \
+          RNEX_ROOT="$RNEX_ROOT" \
+          RNEX_CONFIG_MERGED="$RNEX_CONFIG_MERGED" \
+          RNEX_PLUGIN_DIR="$RNEX_PLUGIN_DIR" \
+          RNEX_CMD="$RNEX_CMD" \
+          RNEX_ARGS="$RNEX_ARGS" \
+          RNEX_QUIET="$RNEX_QUIET" \
+          RNEX_CONFIG_FILE="${RNEX_CONFIG_FILE:-rnex.yaml}" \
+          RNEX_LOCAL_CONFIG_FILE="${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}" \
+          "$_h_cand" "$@" || true
+      fi
     fi
   done
 }

package/lib/plugins.sh

@@ -143,15 +143,14 @@ plugin_resolve_placeholders() {
   [ -z "$_w_val" ] && _w_val=".rnex/wiki"
   _w_val="$(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' "$_r_val" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
+  # {raw_dir} (legacy alias) resolves to the first explicit directory source; when no
+  # directory source exists it stays unresolved so callers can skip the destination.
+  _r_val="$(plugin_primary_source_dir "$_p" 2>/dev/null || true)"
 
-  _res="$(printf '%s' "$_res" | sed \
-    -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|{wiki_dir}|${_w_val}|g" -e "s|^\.\{0,1\}\/\{0,1\}wiki/|${_w_val}/|")"
+  if [ -n "$_r_val" ]; then
+    _res="$(printf '%s' "$_res" | sed -e "s|{raw_dir}|${_r_val}|g" -e "s|^\.\{0,1\}\/\{0,1\}raw/|${_r_val}/|")"
+  fi
 
   _res="$(printf '%s' "$_res" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##')"
 
@@ -165,17 +164,27 @@ plugin_instantiate_template() {
   [ -z "$_w_val" ] && _w_val=".rnex/wiki"
   _w_val="$(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)"
+  _r_val="$(plugin_primary_source_dir "$_p" 2>/dev/null || true)"
   [ -z "$_r_val" ] && _r_val="docs"
-  _r_val="$(printf '%s' "$_r_val" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
+
+  # {sources}: human-readable list of configured intake sources (sed-escaped)
+  _s_val="$(plugin_sources_display "$_p" 2>/dev/null || true)"
+  [ -z "$_s_val" ] && _s_val="$(printf '\140%s/\140' "$_r_val")"
+  _s_val="$(printf '%s' "$_s_val" | sed -e 's/[\\&|]/\\&/g')"
 
   sed -e "s|{wiki_dir}|$_w_val|g" \
       -e "s|{raw_dir}|$_r_val|g" \
+      -e "s|{sources}|$_s_val|g" \
       "$_src" > "$_dest"
 }
 
 # 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}" \
@@ -189,15 +198,15 @@ sync_plugins() {
   done
 
   # Clean up obsolete leaked root ./raw and ./wiki directories if non-default paths are configured
-  _raw_cfg="$(yaml_plugin_get "karpathy-llm" "raw_dir" 2>/dev/null || true)"
+  _raw_cfg="$(plugin_primary_source_dir "karpathy-llm" 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 [ "$_raw_cfg" != "raw" ] && [ -d "$NEXUS_DIR/raw" ] && \
+     ! plugin_source_dirs "karpathy-llm" 2>/dev/null | grep -qx '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
@@ -293,7 +302,9 @@ sync_plugins() {
           rm -rf "${_scoped_dest:?}/$_sub"
           mkdir -p "$_scoped_dest/$_sub"
           cp -R "$_pdir/$_sub"/. "$_scoped_dest/$_sub"/ 2>/dev/null || true
-          [ "$_sub" = "hooks" ] && chmod +x "$_scoped_dest/hooks"/* 2>/dev/null || true
+          if [ "$_sub" = "hooks" ]; then
+            chmod +x "$_scoped_dest/hooks"/* 2>/dev/null || true
+          fi
         else
           rm -rf "${_scoped_dest:?}/$_sub"
         fi
@@ -311,6 +322,17 @@ sync_plugins() {
       fi
     fi
 
+    # Provision explicit directory sources declared under plugins.<name>.sources (e.g. ./docs)
+    for _sdir in $(plugin_source_dirs "$_pname" 2>/dev/null); do
+      [ -n "$_sdir" ] || continue
+      _full_sdir="$NEXUS_DIR/$_sdir"
+      if [ ! -d "$_full_sdir" ]; then
+        mkdir -p "$_full_sdir"
+        [ -f "$_full_sdir/.gitkeep" ] || touch "$_full_sdir/.gitkeep"
+        log_ok "Created intake source directory: $_sdir"
+      fi
+    done
+
     # Initialize templates declared in plugin (functional external dirs like raw/, wiki/)
     plugin_list_templates "$_pdir" | while read -r _item; do
       [ -n "$_item" ] || continue
@@ -321,6 +343,11 @@ sync_plugins() {
 
       _d="$(plugin_resolve_placeholders "$_pname" "$_pdir" "$_d")"
 
+      # No explicit directory source configured (e.g. glob-only sources): nothing to provision
+      case "$_d" in
+        *"{raw_dir}"*) continue ;;
+      esac
+
       # Defensive guard: never create directories or files if placeholder expansion failed or quotes leaked
       case "$_d" in
         *"{"*"}"*|*\"*|*\'*)
@@ -335,9 +362,235 @@ sync_plugins() {
       if [ -f "$_src_path" ] && [ ! -f "$_dest_path" ]; then
         mkdir -p "$(dirname "$_dest_path")"
         plugin_instantiate_template "$_pname" "$_pdir" "$_src_path" "$_dest_path"
-        [ -x "$_src_path" ] && chmod +x "$_dest_path" 2>/dev/null || true
+        if [ -x "$_src_path" ]; then
+          chmod +x "$_dest_path" 2>/dev/null || true
+        fi
         log_ok "Initialized template: $_d"
       fi
     done
   done
 }
+
+# ----------------------------------------------------------------------------
+# Plugin source resolution (directories + POSIX glob patterns)
+# ----------------------------------------------------------------------------
+
+# True if the argument contains a glob metacharacter (*, ?, [)
+_src_has_glob() {
+  case "$1" in
+    *'*'*|*'?'*|*'['*) return 0 ;;
+  esac
+  return 1
+}
+
+# Workspace-relative member repositories directory (default: repos)
+_plugin_repos_rel_dir() {
+  _prd="${REPOS_DIR:-}"
+  if [ -n "$_prd" ]; then
+    _prd="${_prd#"${NEXUS_DIR:-.}"/}"
+  else
+    _prd="repos"
+  fi
+  while [ "${_prd#./}" != "$_prd" ]; do _prd="${_prd#./}"; done
+  printf '%s' "${_prd%/}"
+}
+
+# Normalize a source entry: trim whitespace/CR, strip leading ./ and trailing /
+_src_normalize_entry() {
+  _sne="$(printf '%s' "$1" | tr -d '\r' | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')"
+  while [ "${_sne#./}" != "$_sne" ]; do _sne="${_sne#./}"; done
+  [ "$_sne" = "." ] || _sne="${_sne%/}"
+  printf '%s' "$_sne"
+}
+
+# True if a normalized entry names a file rather than a directory
+# (glob pattern, .md/.txt suffix, or an existing regular file)
+_src_is_file_like() {
+  _src_has_glob "$1" && return 0
+  case "$1" in
+    *.md|*.txt) return 0 ;;
+  esac
+  [ -f "${NEXUS_DIR:-.}/$1" ] && return 0
+  return 1
+}
+
+# List explicit directory sources of a plugin that rnex may provision (mkdir).
+# Skips glob patterns, file entries, absolute paths, '..' traversal, the workspace
+# root, and paths inside the member repositories directory.
+plugin_source_dirs() {
+  _psd_rdir="$(_plugin_repos_rel_dir)"
+  get_plugin_config_list "$1" "sources" 2>/dev/null | while IFS= read -r _psd_e || [ -n "$_psd_e" ]; do
+    _psd_e="$(_src_normalize_entry "$_psd_e")"
+    case "$_psd_e" in
+      ''|.|/*|..|../*|*/..|*/../*) continue ;;
+    esac
+    _src_is_file_like "$_psd_e" && continue
+    case "$_psd_e" in
+      "$_psd_rdir"|"$_psd_rdir"/*) continue ;;
+    esac
+    printf '%s\n' "$_psd_e"
+  done
+}
+
+# First provisionable directory source (legacy {raw_dir} placeholder); may be empty
+plugin_primary_source_dir() {
+  plugin_source_dirs "$1" | sed -n '1p'
+}
+
+# Human-readable source list for templates, e.g.: `docs/`, `repos/**/README.md`
+plugin_sources_display() {
+  get_plugin_config_list "$1" "sources" 2>/dev/null | while IFS= read -r _psy_e || [ -n "$_psy_e" ]; do
+    _psy_e="$(_src_normalize_entry "$_psy_e")"
+    [ -n "$_psy_e" ] || continue
+    if _src_is_file_like "$_psy_e"; then
+      printf '\140%s\140\n' "$_psy_e"
+    else
+      printf '\140%s/\140\n' "$_psy_e"
+    fi
+  done | awk '{ out = (NR == 1) ? $0 : out ", " $0 } END { if (NR) print out }'
+}
+
+# Split a pattern into its leading wildcard-free directory prefix and the rest.
+# The last component always stays in the rest. Sets _sp_base (default ".") and _sp_rest.
+_src_static_prefix() {
+  _sp_base=""
+  _sp_rest="$1"
+  while :; do
+    _sp_comp="${_sp_rest%%/*}"
+    [ "$_sp_comp" = "$_sp_rest" ] && break
+    _src_has_glob "$_sp_comp" && break
+    _sp_base="${_sp_base:+$_sp_base/}$_sp_comp"
+    _sp_rest="${_sp_rest#*/}"
+  done
+  [ -z "$_sp_base" ] && _sp_base="."
+  return 0
+}
+
+# List all files under a directory, pruning hidden directories/files and node_modules
+_src_find_dir() {
+  find "$1" ! -path "$1" -type d \( -name '.*' -o -name node_modules \) -prune -o -type f ! -name '.*' -print 2>/dev/null
+}
+
+# Resolve a recursive glob: <base>/**/<rest>  (base "." for a leading **/)
+_src_find_recursive() {
+  _fr_base="$1"; _fr_rest="$2"
+  if [ "${_fr_rest#*/}" = "$_fr_rest" ] && ! _src_has_glob "$_fr_base"; then
+    # Single trailing component: exact semantics via -name at any depth
+    [ -d "$_fr_base" ] || return 0
+    find "$_fr_base" ! -path "$_fr_base" -type d \( -name .git -o -name .rnex -o -name node_modules \) -prune \
+      -o -type f -name "$_fr_rest" -print 2>/dev/null
+    return 0
+  fi
+  _fr_start="$_fr_base"
+  if _src_has_glob "$_fr_base"; then
+    _src_static_prefix "$_fr_base/x"
+    _fr_start="$_sp_base"
+  fi
+  [ -d "$_fr_start" ] || return 0
+  find "$_fr_start" ! -path "$_fr_start" -type d \( -name .git -o -name .rnex -o -name node_modules \) -prune \
+    -o -type f \( -path "$_fr_base/$_fr_rest" -o -path "$_fr_base/*/$_fr_rest" \) -print 2>/dev/null
+}
+
+# Resolve a single-level glob (e.g. repos/*/README.md, docs/*.md) with bounded depth
+_src_find_glob() {
+  _src_static_prefix "$1"
+  [ -d "$_sp_base" ] || return 0
+  # Prune directories at (or below) the pattern depth so find never descends further
+  _fg_depth="$_sp_base"
+  _fg_r="$_sp_rest"
+  while :; do
+    _fg_depth="$_fg_depth/*"
+    case "$_fg_r" in
+      */*) _fg_r="${_fg_r#*/}" ;;
+      *) break ;;
+    esac
+  done
+  find "$_sp_base" ! -path "$_sp_base" -type d \( -name .git -o -name .rnex -o -name node_modules -o -path "$_fg_depth" \) -prune \
+    -o -type f -path "$_sp_base/$_sp_rest" -print 2>/dev/null
+}
+
+# Resolve one normalized source entry (run from the workspace root)
+_src_resolve_entry() {
+  _re="$1"
+  case "$_re" in
+    '**')
+      _src_find_dir "."
+      ;;
+    */'**')
+      _re="${_re%/\*\*}"
+      [ -d "$_re" ] && _src_find_dir "$_re"
+      ;;
+    '**/'*)
+      _src_find_recursive "." "${_re#\*\*/}"
+      ;;
+    *'/**/'*)
+      _src_find_recursive "${_re%%/\*\*/*}" "${_re#*/\*\*/}"
+      ;;
+    *)
+      if [ -d "$_re" ]; then
+        _src_find_dir "$_re"
+      elif [ -f "$_re" ]; then
+        printf '%s\n' "$_re"
+      elif _src_has_glob "$_re"; then
+        _src_find_glob "$_re"
+      fi
+      ;;
+  esac
+  return 0
+}
+
+# Resolve plugin source entries (directories, files, glob patterns) into a
+# deduplicated, sorted list of workspace-relative file paths.
+# Input: newline-separated entries as $1 (or stdin), e.g. from get_plugin_config_list.
+# Files inside member repositories disabled via `enabled: false` are excluded.
+resolve_plugin_sources() {
+  _rs_root="${NEXUS_DIR:-${RNEX_ROOT:-.}}"
+
+  _saved_wy="${WORKSPACE_YAML:-}"
+  _saved_wly="${WORKSPACE_LOCAL_YAML:-}"
+  [ -z "$WORKSPACE_YAML" ] && WORKSPACE_YAML="$_rs_root/${RNEX_CONFIG_FILE:-rnex.yaml}"
+  [ -z "$WORKSPACE_LOCAL_YAML" ] && WORKSPACE_LOCAL_YAML="$_rs_root/${RNEX_LOCAL_CONFIG_FILE:-.local.rnex.yaml}"
+
+  # Workspace-relative member repositories directory (default: repos)
+  _rs_rdir="$(_plugin_repos_rel_dir)"
+
+  # Space-separated list of disabled repositories (local config overrides repo config)
+  _rs_disabled="$(yaml_list_repos 2>/dev/null | while IFS= read -r _rs_r; do
+    [ -n "$_rs_r" ] || continue
+    yaml_repo_enabled "$_rs_r" || printf '%s ' "$_rs_r"
+  done)"
+
+  _rs_out="$(
+    if [ "$#" -gt 0 ]; then
+      printf '%s\n' "$1"
+    else
+      cat
+    fi | (
+      cd "$_rs_root" || exit 0
+      while IFS= read -r _rs_e || [ -n "$_rs_e" ]; do
+        _rs_e="$(printf '%s' "$_rs_e" | tr -d '\r' | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//')"
+        while [ "${_rs_e#./}" != "$_rs_e" ]; do _rs_e="${_rs_e#./}"; done
+        [ "$_rs_e" = "." ] || _rs_e="${_rs_e%/}"
+        [ -n "$_rs_e" ] || continue
+        _src_resolve_entry "$_rs_e"
+      done
+    ) | sed -e 's#^\(\./\)*##' | awk -v prefix="$_rs_rdir/" -v disabled="$_rs_disabled" '
+      BEGIN {
+        n = split(disabled, d, " ")
+        for (i = 1; i <= n; i++) off[d[i]] = 1
+      }
+      length($0) == 0 { next }
+      index($0, prefix) == 1 {
+        name = substr($0, length(prefix) + 1)
+        sub(/\/.*/, "", name)
+        if (name in off) next
+      }
+      { print }
+    ' | sort -u
+  )"
+
+  WORKSPACE_YAML="$_saved_wy"
+  WORKSPACE_LOCAL_YAML="$_saved_wly"
+
+  printf '%s\n' "$_rs_out" | awk 'NF'
+}

package/lib/repos.sh

@@ -115,7 +115,9 @@ EOF
         rm -rf "${_dest_pdir:?}/$_sub"
         mkdir -p "$_dest_pdir/$_sub"
         cp -R "$_pdir/$_sub"/. "$_dest_pdir/$_sub"/ 2>/dev/null || true
-        [ "$_sub" = "hooks" ] && chmod +x "$_dest_pdir/hooks"/* 2>/dev/null || true
+        if [ "$_sub" = "hooks" ]; then
+          chmod +x "$_dest_pdir/hooks"/* 2>/dev/null || true
+        fi
       else
         rm -rf "${_dest_pdir:?}/$_sub"
       fi