repo-nexus 0.7.24 → 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/examples/monorepo-coexistence.md

@@ -52,7 +52,6 @@ repos:
 
 plugins:
   claude:
-    instructions: true
     skills: true
 ```
 

package/docs/examples/multi-repo-workspace.md

@@ -50,10 +50,8 @@ repos:
 
 plugins:
   claude:
-    instructions: true
     skills: true
   cursor:
-    instructions: true
     skills: true
 ```
 

package/docs/guide/configuration.md

@@ -64,11 +64,10 @@ repos:
 plugins:
   # AI Provider Plugins
   claude:
-    instructions: true
     skills: true
+    auto_sync_on: SessionStart
 
   cursor:
-    instructions: true
     skills: true
 
   # Knowledge & Agent Protocol Plugins
@@ -116,7 +115,7 @@ repos:
 
 plugins:
   gemini:
-    instructions: true
+    skills: true
 ```
 
 After modifying configuration files directly, reconcile the workspace state:

package/docs/plugins/claude.md

@@ -21,8 +21,8 @@ Operational skills, rules, and subagents remain cleanly encapsulated within `.rn
 
 2. **Native Instruction Support via `CLAUDE.md` & `AGENTS.md`**:
    - Claude Code natively reads `CLAUDE.md` as its primary instructions file; it only falls back to `AGENTS.md` when no `CLAUDE.md` exists in the project.
-   - When enabled (`instructions: true`), the Claude plugin synchronizes Repo Nexus routing instructions to `CLAUDE.md` (or merges them cleanly if you already have custom instructions).
-   - If `CLAUDE.md` is absent and `instructions: false`, Claude Code falls back to reading `AGENTS.md` directly.
+   - When enabled, the Claude plugin automatically synchronizes Repo Nexus routing instructions to `CLAUDE.md` (or merges them cleanly if you already have custom instructions).
+   - If the plugin is disabled, the routing block is removed, allowing Claude Code to read `AGENTS.md` directly.
 
 3. **Subagent & Skill Execution**:
    - Core skills reside under `.rnex/skills/`.
@@ -58,15 +58,15 @@ Configure options under `plugins.claude` in `rnex.yaml` or `.local.rnex.yaml`:
 ```yaml
 plugins:
   claude:
-    instructions: true   # Sync routing instructions to CLAUDE.md (default: true)
     skills: true         # Generate user skills in .claude/skills/ (default: true)
+    auto_sync_on: SessionStart # Trigger auto-sync on lifecycle event (default: SessionStart, or false)
     enabled: true        # Set to false to disable
 ```
 
 | Option | Type | Default | Description |
 |:---|:---|:---|:---|
-| `instructions` | boolean | `true` | Merge routing instructions into `CLAUDE.md`. |
 | `skills` | boolean | `true` | Generate user skill pointers in `.claude/skills/rnex-*.md`. |
+| `auto_sync_on` | string/boolean | `SessionStart` | Lifecycle event triggering auto-sync in `.claude/settings.json` (or `false` to disable). |
 | `enabled` | boolean | `true` | Enable or disable the plugin. Overridable in `.local.rnex.yaml`. |
 
 ---
@@ -78,7 +78,7 @@ When `claude` is enabled with functional plugins like `karpathy-llm`, it generat
 ```text
 my-workspace/
 ├── AGENTS.md                          # Universal workspace instructions & routing
-├── CLAUDE.md                          # Claude-specific instructions (if instructions: true)
+├── CLAUDE.md                          # Claude-specific instructions
 ├── .claude/
 │   └── skills/                        # Zero-logic User Skill pointers
 │       ├── rnex-clone-sync.md

package/docs/plugins/copilot.md

@@ -11,7 +11,7 @@ The `copilot` plugin integrates GitHub Copilot with Repo Nexus by projecting wor
 
 GitHub Copilot operates natively within VS Code, Visual Studio, JetBrains, and GitHub.com:
 - **Universal Routing (`AGENTS.md`)**: GitHub Copilot natively reads `AGENTS.md` at the workspace root.
-- **Custom Instructions (`.github/copilot-instructions.md`)**: When `instructions: true`, Repo Nexus injects its non-destructive routing block inside `<!-- REPO-NEXUS:START -->` and `<!-- REPO-NEXUS:END -->`. Custom developer rules outside these markers are strictly preserved.
+- **Custom Instructions (`.github/copilot-instructions.md`)**: When enabled, Repo Nexus injects its non-destructive routing block inside `<!-- REPO-NEXUS:START -->` and `<!-- REPO-NEXUS:END -->`. Custom developer rules outside these markers are strictly preserved.
 - **User Skills (`.github/skills/`)**: When `skills: true`, Repo Nexus generates native `SKILL.md` directory bundles (`.github/skills/rnex-<name>/SKILL.md`) with YAML frontmatter, making them automatically discoverable in VS Code and Copilot Chat skill-pickers while redirecting to the underlying agentic skills under `.rnex/skills/` and active plugins.
 
 ## Configuration
@@ -21,7 +21,6 @@ Enable in `rnex.yaml`:
 ```yaml
 plugins:
   copilot:
-    instructions: true   # Maintain routing in .github/copilot-instructions.md
     skills: true         # Generate user skills in .github/skills/
 ```
 

package/docs/plugins/cursor.md

@@ -20,7 +20,7 @@ Operational skills, rules, and subagents remain cleanly encapsulated within `.rn
    - Contains zero inline heuristics—redirects Cursor directly to the underlying agentic skill protocols inside `.rnex/`.
 
 2. **Native Instructions & Rules Support**:
-   - Synchronizes Repo Nexus routing instructions to `.cursorrules` when `instructions: true` (default).
+   - Automatically synchronizes Repo Nexus routing instructions to `.cursorrules` and `.cursor/rules/rnex-context.mdc`.
    - Preserves user custom rules and custom sections in `.cursorrules`.
 
 3. **Subagent & Skill Execution**:
@@ -57,14 +57,12 @@ Configure options under `plugins.cursor` in `rnex.yaml` or `.local.rnex.yaml`:
 ```yaml
 plugins:
   cursor:
-    instructions: true   # Sync routing instructions to .cursorrules (default: true)
     skills: true         # Generate user skills in .cursor/rules/ (default: true)
     enabled: true        # Set to false to disable
 ```
 
 | Option | Type | Default | Description |
 |:---|:---|:---|:---|
-| `instructions` | boolean | `true` | Merge routing instructions into `.cursorrules`. |
 | `skills` | boolean | `true` | Generate user skill pointers in `.cursor/rules/rnex-*.md`. |
 | `enabled` | boolean | `true` | Enable or disable the plugin. Overridable in `.local.rnex.yaml`. |
 
@@ -77,7 +75,7 @@ When `cursor` is enabled with functional plugins like `karpathy-llm`, it generat
 ```text
 my-workspace/
 ├── AGENTS.md                          # Universal workspace instructions & routing
-├── .cursorrules                       # Cursor root instructions (if instructions: true)
+├── .cursorrules                       # Cursor root instructions
 ├── .cursor/
 │   └── rules/                         # Zero-logic User Skill pointers
 │       ├── rnex-clone-sync.md

package/docs/plugins/gemini.md

@@ -20,7 +20,7 @@ Operational skills, rules, and subagents remain cleanly encapsulated within `.rn
    - Contains zero inline heuristics—redirects Gemini/Antigravity directly to the underlying agentic skill protocols inside `.rnex/`.
 
 2. **Native Instructions Support via `GEMINI.md`**:
-   - Synchronizes Repo Nexus routing instructions to `GEMINI.md` (when `instructions: true`, default) for native support by the Google Gemini CLI.
+   - Automatically synchronizes Repo Nexus routing instructions to `GEMINI.md` for native support by the Google Gemini CLI and Antigravity.
    - Preserves user-defined custom sections in `GEMINI.md` across updates.
 
 3. **Subagent & Skill Execution**:
@@ -57,15 +57,15 @@ Configure options under `plugins.gemini` in `rnex.yaml` or `.local.rnex.yaml`:
 ```yaml
 plugins:
   gemini:
-    instructions: true   # Sync routing instructions to GEMINI.md (default: true)
     skills: true         # Generate user skills in .agents/skills/ (default: true)
+    auto_sync_on: SessionStart # Trigger auto-sync on lifecycle event (default: SessionStart, or false)
     enabled: true        # Set to false to disable
 ```
 
 | Option | Type | Default | Description |
 |:---|:---|:---|:---|
-| `instructions` | boolean | `true` | Merge routing instructions into `GEMINI.md`. |
 | `skills` | boolean | `true` | Generate user skill pointers in `.agents/skills/rnex-*/SKILL.md`. |
+| `auto_sync_on` | string/boolean | `SessionStart` | Lifecycle event triggering auto-sync in `.agents/hooks.json` (or `false` to disable). |
 | `enabled` | boolean | `true` | Enable or disable the plugin. Overridable in `.local.rnex.yaml`. |
 
 ---
@@ -76,7 +76,7 @@ When `gemini` is enabled with functional plugins like `karpathy-llm`, it generat
 
 ```text
 my-workspace/
-├── GEMINI.md                          # Gemini-specific instructions (if instructions: true)
+├── GEMINI.md                          # Gemini-specific instructions
 ├── .agents/
 │   └── skills/                        # Zero-logic User Skill pointers
 │       ├── rnex-clone-sync/

package/docs/plugins/index.md

@@ -97,12 +97,12 @@ repos_dir: ./repos
 plugins:
   # AI Provider Plugins
   claude:
-    instructions: true
     skills: true
+    auto_sync_on: SessionStart
 
   gemini:
-    instructions: true
     skills: true
+    auto_sync_on: SessionStart
 
   # Functional / Knowledge Plugins
   karpathy-llm:

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/plugins/windsurf.md

@@ -20,7 +20,7 @@ Operational skills, rules, and subagents remain cleanly encapsulated within `.rn
    - Contains zero inline heuristics—redirects Cascade directly to the underlying agentic skill protocols inside `.rnex/`.
 
 2. **Native Instructions Support via `.windsurfrules`**:
-   - Synchronizes Repo Nexus routing instructions to `.windsurfrules` when `instructions: true` (default).
+   - Automatically synchronizes Repo Nexus routing instructions to `.windsurfrules`.
    - Preserves user custom rules and custom sections in `.windsurfrules`.
 
 3. **Subagent & Skill Execution**:
@@ -57,14 +57,12 @@ Configure options under `plugins.windsurf` in `rnex.yaml` or `.local.rnex.yaml`:
 ```yaml
 plugins:
   windsurf:
-    instructions: true   # Sync routing instructions to .windsurfrules (default: true)
     skills: true         # Generate user skills in .windsurf/rules/ (default: true)
     enabled: true        # Set to false to disable
 ```
 
 | Option | Type | Default | Description |
 |:---|:---|:---|:---|
-| `instructions` | boolean | `true` | Merge routing instructions into `.windsurfrules`. |
 | `skills` | boolean | `true` | Generate user skill pointers in `.windsurf/rules/rnex-*.md`. |
 | `enabled` | boolean | `true` | Enable or disable the plugin. Overridable in `.local.rnex.yaml`. |
 
@@ -77,7 +75,7 @@ When `windsurf` is enabled with functional plugins like `karpathy-llm`, it gener
 ```text
 my-workspace/
 ├── AGENTS.md                          # Universal workspace instructions & routing
-├── .windsurfrules                     # Windsurf instructions (if instructions: true)
+├── .windsurfrules                     # Windsurf instructions
 ├── .windsurf/
 │   └── rules/                         # Zero-logic User Skill pointers
 │       ├── rnex-clone-sync.md

package/docs/rnex.example.yaml

@@ -84,26 +84,28 @@ git_hooks: true
 #   AGENTS.md at workspace root is the universal cross-tool standard. Assistants that read AGENTS.md
 #   all the time need no separate top-level instructions file. Assistants with native
 #   formats (Claude with CLAUDE.md, Gemini with GEMINI.md, Cursor with .cursorrules, Windsurf with .windsurfrules)
-#   have their instruction files maintained when their plugin is enabled (instructions: true).
+#   have their instruction files maintained automatically when their plugin is enabled.
 #   Agentic skills live self-contained inside .rnex/skills/ (core) and .rnex/plugins/<plugin>/skills/ (plugins).
 #   Provider plugins generate zero-logic User Skills (prefixed with rnex-) into IDE-specific skill directories
 #   linking directly to the agentic skill protocols inside .rnex/.
 
 plugins:
   # claude:
-  #   instructions: true   # sync routing instructions to CLAUDE.md (default: true)
-  #   skills: true         # generate user skills in .claude/skills/ (default: true)
+  #   skills: true              # generate user skills in .claude/skills/ (default: true)
+  #   auto_sync_on: SessionStart # trigger auto-sync on lifecycle event (default: SessionStart, or false)
   # gemini:
-  #   instructions: true   # sync routing instructions to GEMINI.md (default: true)
-  #   skills: true         # generate user skills in .agents/skills/ (default: true)
+  #   skills: true              # generate user skills in .agents/skills/ (default: true)
+  #   auto_sync_on: SessionStart # trigger auto-sync on lifecycle event (default: SessionStart, or false)
   # cursor:
-  #   instructions: true   # sync routing instructions to .cursorrules (default: true)
-  #   skills: true         # generate user skills in .cursor/rules/ (default: true)
+  #   skills: true              # generate user skills in .cursor/rules/ (default: true)
   # windsurf:
-  #   instructions: true   # sync routing instructions to .windsurfrules (default: true)
-  #   skills: true         # generate user skills in .windsurf/rules/ (default: true)
+  #   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/ai.sh

@@ -495,6 +495,96 @@ clean_provider_agents() {
   rmdir "$_ag_dir" 2>/dev/null || true
 }
 
+clean_claude_auto_sync_hook() {
+  _settings="$1"
+  [ -f "$_settings" ] || return 0
+  if grep -q "auto-sync.sh" "$_settings" 2>/dev/null; then
+    _tmp="$(mktemp)"
+    awk '
+      /\{[ \t]*"command"[ \t]*:[ \t]*"\.rnex\/bin\/auto-sync\.sh"[ \t]*\}/ { next }
+      /"command"[ \t]*:[ \t]*"\.rnex\/bin\/auto-sync\.sh"/ { next }
+      { print }
+    ' "$_settings" > "$_tmp"
+    _clean="$(sed -e 's/"hooks"//g' -e 's/"SessionStart"//g' < "$_tmp" | tr -d ' \t\r\n[]{}:,"')"
+    if [ -z "$_clean" ]; then
+      rm -f "$_tmp" "$_settings"
+    else
+      awk '
+        { lines[NR] = $0 }
+        END {
+          for (i = 1; i <= NR; i++) {
+            if (i < NR && lines[i] ~ /,[ \t]*$/) {
+              next_is_bracket = 0
+              for (j = i + 1; j <= NR; j++) {
+                if (lines[j] ~ /^[ \t]*$/) continue
+                if (lines[j] ~ /^[ \t]*[\]\}]/) next_is_bracket = 1
+                break
+              }
+              if (next_is_bracket) {
+                sub(/,[ \t]*$/, "", lines[i])
+              }
+            }
+            print lines[i]
+          }
+        }
+      ' "$_tmp" > "$_settings"
+      rm -f "$_tmp"
+    fi
+  fi
+}
+
+clean_agents_auto_sync_hook() {
+  _hooks="$1"
+  [ -f "$_hooks" ] || return 0
+  if grep -q '"rnex-auto-sync"' "$_hooks" 2>/dev/null; then
+    _tmp="$(mktemp)"
+    awk '
+      BEGIN { skip=0; depth=0 }
+      /"rnex-auto-sync"[ \t]*:[ \t]*\{/ { skip=1; depth=1; next }
+      skip {
+        for (i=1; i<=length($0); i++) {
+          c = substr($0, i, 1)
+          if (c == "{") depth++
+          if (c == "}") {
+            depth--
+            if (depth == 0) {
+              skip = 0
+              next
+            }
+          }
+        }
+        next
+      }
+      { print }
+    ' "$_hooks" > "$_tmp"
+    _clean="$(tr -d " \t\r\n{}" < "$_tmp")"
+    if [ -z "$_clean" ]; then
+      rm -f "$_tmp" "$_hooks"
+    else
+      awk '
+        { lines[NR] = $0 }
+        END {
+          for (i = 1; i <= NR; i++) {
+            if (i < NR && lines[i] ~ /,[ \t]*$/) {
+              next_is_brace = 0
+              for (j = i + 1; j <= NR; j++) {
+                if (lines[j] ~ /^[ \t]*$/) continue
+                if (lines[j] ~ /^[ \t]*\}/) next_is_brace = 1
+                break
+              }
+              if (next_is_brace) {
+                sub(/,[ \t]*$/, "", lines[i])
+              }
+            }
+            print lines[i]
+          }
+        }
+      ' "$_tmp" > "$_hooks"
+      rm -f "$_tmp"
+    fi
+  fi
+}
+
 sync_rnex_base_assets() {
   _src_toolkit=""
   if [ -d "$SCRIPT_LOCATION/toolkit" ]; then

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

@@ -213,10 +213,23 @@ cmd_status() {
         else
           printf '  %b●%b %-18s %b(v%s)%b %s\n' "$_G" "$_NC" "$_pname" "$_DIM" "${_ver:-0.1.0}" "$_NC" "${_desc:+- $_desc}"
           printf '    %bScoped directory: .rnex/plugins/%s%b\n' "$_DIM" "$_pname" "$_NC"
-          if [ -n "$_pdir" ] && { grep -q "instructions:" "$_pdir/plugin.yaml" 2>/dev/null || [ -n "$(yaml_plugin_get "$_pname" "instructions" 2>/dev/null)" ]; }; then
-            printf '    %b↳ Options: instructions=%s, skills=%s%b\n' "$_DIM" \
-              "$(provider_option_enabled "$_pname" "instructions" && echo "true" || echo "false")" \
-              "$(provider_option_enabled "$_pname" "skills" && echo "true" || echo "false")" "$_NC"
+          if [ -n "$_pdir" ] && [ -f "$_pdir/plugin.yaml" ]; then
+            _opts=""
+            if grep -q "skills:" "$_pdir/plugin.yaml" 2>/dev/null || [ -n "$(yaml_plugin_get "$_pname" "skills" 2>/dev/null)" ]; then
+              _opts="${_opts:+$_opts, }skills=$(provider_option_enabled "$_pname" "skills" && echo "true" || echo "false")"
+            fi
+            if grep -q "auto_sync_on:" "$_pdir/plugin.yaml" 2>/dev/null || grep -q "autoSyncOn:" "$_pdir/plugin.yaml" 2>/dev/null || [ -n "$(yaml_plugin_get "$_pname" "auto_sync_on" 2>/dev/null)" ] || [ -n "$(yaml_plugin_get "$_pname" "autoSyncOn" 2>/dev/null)" ]; then
+              _aso="$(yaml_plugin_get "$_pname" "auto_sync_on" 2>/dev/null || true)"
+              [ -z "$_aso" ] && _aso="$(yaml_plugin_get "$_pname" "autoSyncOn" 2>/dev/null || true)"
+              [ -z "$_aso" ] && _aso="SessionStart"
+              _opts="${_opts:+$_opts, }auto_sync_on=$_aso"
+            fi
+            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
 }