repo-nexus 0.2.9 → 0.2.11

package/README.md

@@ -202,7 +202,7 @@ rnex plugin disable karpathy-llm
 ### Built-in Plugin: `karpathy-llm`
 The `karpathy-llm` plugin packages Andrej Karpathy's verified LLM agent design patterns, context engineering principles, and the autonomous **Karpathy LLM Wiki** architecture (based on [`setup-karpathy-wiki.md`](https://github.com/nu-nenoi/ai-toolkit/blob/main/prompts/setup-karpathy-wiki.md), available locally in `toolkit/prompts/setup-karpathy-wiki.md`):
 * **Step 0 — Configuration Interview:** Guides setup decisions including target agent instruction file (`AGENTS.md`, `CLAUDE.md`, `.cursor/rules/wiki.mdc`, etc.), wiki purpose (codebase, second brain, research, content archive), organization layout (flat vs structured), and automation enablement.
-* **The 4 Cardinal Agent Rules** (`.agents/rules/KARPATHY_RULES.md`):
+* **The 4 Cardinal Agent Rules** (`.rnex/rules/KARPATHY_RULES.md`):
   1. *Think Before Coding:* Formulate explicit assumptions, boundary checks, and trade-offs before writing code.
   2. *Simplicity First:* Minimal abstractions, readable implementations, zero speculative boilerplate.
   3. *Surgical Changes:* Minimal blast radius, preserved comments/docstrings, and tight diffs.
@@ -213,9 +213,9 @@ The `karpathy-llm` plugin packages Andrej Karpathy's verified LLM agent design p
   * **Control Index (`/wiki/index.md`):** Master navigation index with `lint_trigger: enabled|disabled` toggle.
   * **Rolling Context (`/wiki/hot.md`):** ~500-word quick-orient context cache for AI agents.
   * **Operation Log (`/wiki/_log.md`):** Append-only audit trail of ingest and lint operations.
-  * **Session Counter (`/wiki/.lint_trigger_counter`):** Machine-local state tracking session activity (gitignored).
-* **Autonomous Lint Trigger (`scripts/wiki-lint-trigger.sh`):** Session counter and maintenance alerts on session 1 and every 15 sessions.
-* **Standardized Workflows (`.agent/workflows/`):**
+  * **Session Counter (`.rnex/.lint_trigger_counter`):** Machine-local state tracking session activity (gitignored).
+* **Autonomous Lint Trigger (`.rnex/scripts/wiki-lint-trigger.sh`):** Session counter and maintenance alerts on session 1 and every 15 sessions.
+* **Standardized Workflows (`.rnex/workflows/`):**
   * `wiki-ingest.md`: 8-step protocol decomposing raw source documents into 5–25 atomic wiki pages.
   * `wiki-lint.md`: 10-step protocol validating paths, recomputing `mentioned_in`, removing orphans, resolving contradictions, identifying gaps, suggesting source candidates, and rebuilding indexes.
 
@@ -238,7 +238,8 @@ ai_files:
 
 # Workspace plugins
 plugins:
-  - karpathy-llm
+  karpathy-llm:
+    lint_trigger_enabled: true
 
 # Member repositories
 repos:

package/docs/rnex.example.yaml

@@ -71,10 +71,11 @@ ai_files:
 #   karpathy-llm   — Andrej Karpathy's agent behavioral principles,
 #                    multi-repo context engineering, and LLM Wiki pattern
 #
-# Local / custom plugins can also be placed in .nexus/plugins/<name>/
+# Local / custom plugins can also be placed in .rnex/plugins/<name>/
 
 plugins:
-  # - karpathy-llm
+  # karpathy-llm:
+  #   lint_trigger_enabled: true
 
 # ------------------------------------------------------------------------------
 # repos — Member repositories managed by Repo Nexus

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.2.9",
+  "version": "0.2.11",
   "description": "Lightweight, zero-dependency companion tool for multi-repo workspaces and shared AI context via symlinks (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",

package/rnex

@@ -171,17 +171,60 @@ yaml_list_ai_files() {
   '
 }
 
-# Parse list of plugins from rnex.yaml
+# Parse list of plugins from rnex.yaml (supports both mapping and list formats)
 yaml_list_plugins() {
   [ -f "$WORKSPACE_YAML" ] || return 0
   awk '
-    /^plugins:/ { p=1; next }
+    /^plugins:[ ]*$/ || /^plugins:[ ]*#/ { p=1; next }
     p && /^[^ #]/ { exit }
     p && /^[ ]*-[ ]*/ {
-      sub(/^[ ]*-[ ]*/, "");
-      sub(/[ ]*#.*/, "");
-      if (length($0) > 0) print $0
+      line = $0
+      sub(/^[ ]*-[ ]*/, "", line)
+      sub(/[ ]*#.*/, "", line)
+      sub(/[ ]*:.*$/, "", line)
+      gsub(/[[:space:]]/, "", line)
+      if (length(line) > 0) print line
+      next
+    }
+    p && /^  [a-zA-Z0-9_.-]+:[ ]*(#.*)?$/ {
+      line = $0
+      sub(/^[ ]*/, "", line)
+      sub(/:.*/, "", line)
+      gsub(/[[:space:]]/, "", line)
+      if (length(line) > 0) print line
+      next
+    }
+    p && /^  [a-zA-Z0-9_.-]+:[ ]+[^#[:space:]]/ {
+      line = $0
+      sub(/^[ ]*/, "", line)
+      sub(/:.*/, "", line)
+      gsub(/[[:space:]]/, "", line)
+      if (length(line) > 0) print line
+      next
+    }
+  ' "$WORKSPACE_YAML"
+}
+
+# Get a configuration field value for a plugin under plugins.<plugin>.<field>
+yaml_plugin_get() {
+  _plugin="$1"; _field="$2"
+  [ -f "$WORKSPACE_YAML" ] || return 0
+  awk -v plugin="$_plugin" -v field="$_field" '
+    /^plugins:[ ]*$/ || /^plugins:[ ]*#/ { in_plugins=1; next }
+    in_plugins && /^[^ #]/ { in_plugins=0 }
+    in_plugins && match($0, "^  " plugin ":[ ]*") { in_target=1; next }
+    in_target && /^    / {
+      line = $0
+      sub(/^[ ]*/, "", line)
+      if (match(line, "^" field ":[ ]*")) {
+        sub("^" field ":[ ]*", "", line)
+        sub(/[ ]*#.*$/, "", line)
+        gsub(/^["\x27]|["\x27]$/, "", line)
+        print line
+        exit
+      }
     }
+    in_target && !/^    / && !/^[ ]*#/ { in_target=0 }
   ' "$WORKSPACE_YAML"
 }
 
@@ -196,28 +239,44 @@ yaml_enable_plugin() {
     printf '\nplugins:\n' >> "$WORKSPACE_YAML"
   fi
   _tmp="$(mktemp)"
-  awk -v name="$_name" '
-    /^plugins:/ {
-      print
-      printf "  - %s\n", name
-      added=1
-      next
-    }
-    { print }
-  ' "$WORKSPACE_YAML" > "$_tmp" && mv "$_tmp" "$WORKSPACE_YAML"
+  if [ "$_name" = "karpathy-llm" ]; then
+    awk -v name="$_name" '
+      /^plugins:[ ]*$/ || /^plugins:[ ]*#/ {
+        print
+        printf "  %s:\n    lint_trigger_enabled: true\n", name
+        added=1
+        next
+      }
+      { print }
+    ' "$WORKSPACE_YAML" > "$_tmp" && mv "$_tmp" "$WORKSPACE_YAML"
+  else
+    awk -v name="$_name" '
+      /^plugins:[ ]*$/ || /^plugins:[ ]*#/ {
+        print
+        printf "  %s: {}\n", name
+        added=1
+        next
+      }
+      { print }
+    ' "$WORKSPACE_YAML" > "$_tmp" && mv "$_tmp" "$WORKSPACE_YAML"
+  fi
 }
 
 yaml_disable_plugin() {
   _name="$1"
   _tmp="$(mktemp)"
   awk -v name="$_name" '
-    /^plugins:/ { in_plugins=1; print; next }
+    /^plugins:[ ]*$/ || /^plugins:[ ]*#/ { in_plugins=1; print; next }
     in_plugins && /^[^ #]/ { in_plugins=0 }
+    in_plugins && match($0, "^  " name ":[ ]*") { in_target=1; next }
+    in_target && (/^    / || /^[ ]*$/) { next }
+    in_target && !/^    / { in_target=0 }
     in_plugins && $0 ~ ("^[ ]*-[ ]*" name "[ ]*($|#)") { next }
     { print }
   ' "$WORKSPACE_YAML" > "$_tmp" && mv "$_tmp" "$WORKSPACE_YAML"
 }
 
+
 # Parse list of repos from rnex.yaml
 yaml_list_repos() {
   [ -f "$WORKSPACE_YAML" ] || return 0
@@ -461,6 +520,7 @@ find_plugin_dir() {
   _query="$1"
   _sdir="$(dirname "$SCRIPT_LOCATION")"
   for _cand in \
+    "$NEXUS_DIR/.rnex/plugins/$_query" \
     "$NEXUS_DIR/.nexus/plugins/$_query" \
     "$NEXUS_DIR/plugins/$_query" \
     "$NEXUS_DIR/toolkit/plugins/$_query" \
@@ -479,6 +539,7 @@ list_all_available_plugin_dirs() {
   for _parent in \
     "$_sdir/toolkit/plugins" \
     "$NEXUS_DIR/toolkit/plugins" \
+    "$NEXUS_DIR/.rnex/plugins" \
     "$NEXUS_DIR/.nexus/plugins" \
     "$NEXUS_DIR/plugins"; do
     if [ -d "$_parent" ]; then
@@ -599,6 +660,16 @@ sync_plugins() {
         log_ok "Initialized template: $_d"
       fi
     done
+
+    # Reconcile plugin configuration (e.g., lint_trigger_enabled for karpathy-llm)
+    if [ "$_pname" = "karpathy-llm" ] && [ -f "$NEXUS_DIR/wiki/index.md" ]; then
+      _lte="$(yaml_plugin_get "karpathy-llm" "lint_trigger_enabled")"
+      if [ "$_lte" = "false" ]; then
+        sed -i.bak 's/lint_trigger:[ ]*enabled/lint_trigger: disabled/' "$NEXUS_DIR/wiki/index.md" 2>/dev/null && rm -f "$NEXUS_DIR/wiki/index.md.bak"
+      elif [ "$_lte" = "true" ]; then
+        sed -i.bak 's/lint_trigger:[ ]*disabled/lint_trigger: enabled/' "$NEXUS_DIR/wiki/index.md" 2>/dev/null && rm -f "$NEXUS_DIR/wiki/index.md.bak"
+      fi
+    fi
   done
 }
 
@@ -1018,6 +1089,12 @@ cmd_plugin_info() {
   [ -n "$_author" ] && printf '%bAuthor:%b       %s\n' "$_BOLD" "$_NC" "$_author"
   [ -n "$_home" ] && printf '%bHomepage:%b     %s\n' "$_BOLD" "$_NC" "$_home"
   printf '%bLocation:%b     %s\n' "$_BOLD" "$_NC" "$_pdir"
+  if yaml_has_plugin "$_name"; then
+    _lte="$(yaml_plugin_get "$_name" "lint_trigger_enabled")"
+    if [ -n "$_lte" ]; then
+      printf '%bConfiguration:%b  lint_trigger_enabled: %s\n' "$_BOLD" "$_NC" "$_lte"
+    fi
+  fi
 
   printf '\n%bProvided AI Context Files:%b\n' "$_BOLD" "$_NC"
   plugin_list_ai_files "$_pdir" | while read -r _item; do
@@ -1102,12 +1179,12 @@ cmd_plugin_enable() {
     fi
   done
 
-  # Ensure machine-local state files (like wiki/.lint_trigger_counter) are gitignored
+  # Ensure machine-local state files (like .rnex/.lint_trigger_counter) are gitignored
   _gi="$NEXUS_DIR/.gitignore"
-  if [ -f "$NEXUS_DIR/scripts/wiki-lint-trigger.sh" ]; then
-    if [ ! -f "$_gi" ] || ! grep -qF "wiki/.lint_trigger_counter" "$_gi" 2>/dev/null; then
-      printf '\n# Karpathy LLM Wiki session counter\nwiki/.lint_trigger_counter\n.lint_trigger_counter\n' >> "$_gi"
-      log_dim "Added 'wiki/.lint_trigger_counter' to .gitignore"
+  if [ -f "$NEXUS_DIR/.rnex/scripts/wiki-lint-trigger.sh" ] || [ -f "$NEXUS_DIR/scripts/wiki-lint-trigger.sh" ]; then
+    if [ ! -f "$_gi" ] || ! grep -qF ".rnex/.lint_trigger_counter" "$_gi" 2>/dev/null; then
+      printf '\n# Repo Nexus internal state\n.rnex/.lint_trigger_counter\nwiki/.lint_trigger_counter\n.lint_trigger_counter\n' >> "$_gi"
+      log_dim "Added '.rnex/.lint_trigger_counter' to .gitignore"
     fi
   fi
 

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

@@ -85,18 +85,20 @@ my-workspace/
 ├── wiki/
 │   ├── index.md                     # Master catalog + lint_trigger toggle
 │   ├── hot.md                       # Rolling ~500-word quick-orient context
-│   ├── _log.md                      # Ingestion & lint audit history
+│   └── _log.md                      # Ingestion & lint audit history
+├── .rnex/
+│   ├── rules/
+│   │   └── KARPATHY_RULES.md        # Cardinal principles & wiki rules (auto-symlinked)
+│   ├── workflows/
+│   │   ├── wiki-ingest.md           # 8-step decomposition & ingestion workflow
+│   │   └── wiki-lint.md             # 10-step graph validation & maintenance workflow
+│   ├── scripts/
+│   │   └── wiki-lint-trigger.sh     # Executable session counter & lint alert
+│   ├── templates/
+│   │   ├── wiki-page.template.md    # Atomic page template with typed relations
+│   │   └── LLM_WIKI.sample.md       # Sample wiki walkthrough
 │   └── .lint_trigger_counter        # Session counter (gitignored)
-├── scripts/
-│   └── wiki-lint-trigger.sh         # Executable session counter & lint alert
-├── .agents/rules/
-│   └── KARPATHY_RULES.md            # Cardinal principles & wiki rules (auto-symlinked)
-├── .agent/workflows/
-│   ├── wiki-ingest.md               # 8-step decomposition & ingestion workflow
-│   └── wiki-lint.md                 # 10-step graph validation & maintenance workflow
-└── docs/
-    ├── wiki-page.template.md        # Atomic page template with typed relations
-    └── LLM_WIKI.sample.md           # Sample wiki walkthrough
+└── rnex.yaml                        # Plugin configuration
 ```
 
 ---
@@ -110,19 +112,20 @@ rnex plugin enable karpathy-llm
 ```
 
 This command:
-1. Adds `karpathy-llm` to `plugins:` in `rnex.yaml`.
-2. Copies initial templates (`wiki/index.md`, `wiki/_log.md`, `wiki/hot.md`, `raw/.gitkeep`, `docs/wiki-page.template.md`, `docs/LLM_WIKI.sample.md`, `scripts/wiki-lint-trigger.sh`).
-3. Links `KARPATHY_RULES.md` and workflows into workspace root (`.agents/rules/`, `.agent/workflows/`).
-4. Ensures `wiki/.lint_trigger_counter` is added to `.gitignore`.
+1. Adds `karpathy-llm` to `plugins:` in `rnex.yaml` with default configuration (`lint_trigger_enabled: true`).
+2. Copies initial templates (`wiki/index.md`, `wiki/_log.md`, `wiki/hot.md`, `raw/.gitkeep`, `.rnex/templates/wiki-page.template.md`, `.rnex/templates/LLM_WIKI.sample.md`, `.rnex/scripts/wiki-lint-trigger.sh`).
+3. Links `KARPATHY_RULES.md` and workflows into `.rnex/rules/` and `.rnex/workflows/`.
+4. Ensures `.rnex/.lint_trigger_counter` is added to `.gitignore`.
 5. Syncs scope links and AI context files across all registered member repositories via `rnex sync`.
 
 ### Option 2: Declarative in `rnex.yaml`
 
-Add `karpathy-llm` to `plugins:` in `rnex.yaml`:
+Configure `karpathy-llm` under `plugins:` in `rnex.yaml`:
 
 ```yaml
 plugins:
-  - karpathy-llm
+  karpathy-llm:
+    lint_trigger_enabled: true
 ```
 
 Then synchronize:
@@ -137,7 +140,7 @@ rnex sync
 
 1. **Intake:** Drop raw research papers, meeting notes, PRDs, or architecture specs into `/raw/` unmodified.
 2. **Ingest:** Instruct your AI assistant: *"Run wiki-ingest on raw/source-document.md"*.
-3. **Session Cadence:** After sessions where repository files were edited, run `scripts/wiki-lint-trigger.sh`.
+3. **Session Cadence:** After sessions where repository files were edited, run `.rnex/scripts/wiki-lint-trigger.sh`.
 4. **Maintenance:** If prompted by `[WIKI MAINTENANCE DUE]`, instruct the assistant: *"Run wiki-lint"*.
 5. **Toggle Automation:** Edit `lint_trigger: enabled` or `lint_trigger: disabled` in `/wiki/index.md` anytime.
 

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

@@ -4,14 +4,14 @@ description: Andrej Karpathy's agent behavioral principles, context engineering
 author: nu-nenoi
 homepage: https://github.com/nu-nenoi/repo-nexus
 ai_files:
-  - rules/KARPATHY_RULES.md: .agents/rules/KARPATHY_RULES.md
-  - workflows/wiki-ingest.md: .agent/workflows/wiki-ingest.md
-  - workflows/wiki-lint.md: .agent/workflows/wiki-lint.md
+  - rules/KARPATHY_RULES.md: .rnex/rules/KARPATHY_RULES.md
+  - workflows/wiki-ingest.md: .rnex/workflows/wiki-ingest.md
+  - workflows/wiki-lint.md: .rnex/workflows/wiki-lint.md
 templates:
   - templates/index.md: wiki/index.md
   - templates/_log.md: wiki/_log.md
   - templates/hot.md: wiki/hot.md
   - templates/raw.gitkeep: raw/.gitkeep
-  - templates/wiki-page.sample.md: docs/wiki-page.template.md
-  - templates/LLM_WIKI.sample.md: docs/LLM_WIKI.sample.md
-  - scripts/wiki-lint-trigger.sh: scripts/wiki-lint-trigger.sh
+  - templates/wiki-page.sample.md: .rnex/templates/wiki-page.template.md
+  - templates/LLM_WIKI.sample.md: .rnex/templates/LLM_WIKI.sample.md
+  - scripts/wiki-lint-trigger.sh: .rnex/scripts/wiki-lint-trigger.sh

package/toolkit/plugins/karpathy-llm/rules/KARPATHY_RULES.md

@@ -54,10 +54,10 @@ When working in a repository with an active Karpathy LLM Wiki (`/wiki/` and `/ra
 
 - **Intake**: All source material (articles, transcripts, docs, notes) goes to `/raw/` unmodified. Never write directly to `/wiki/` without ingesting.
 - **Orientation**: Before answering domain questions, read `/wiki/index.md` to find relevant pages, then read only those pages. If `hot.md` exists, read it first as a quick-orient step.
-- **Ingestion**: When files appear in `/raw/`, run the `wiki-ingest` workflow (`.agent/workflows/wiki-ingest.md`). One source document typically produces many atomic pages (commonly 5–25 pages) — do not collapse a source into a single file.
-- **Cadence**: After any session where repository files were created, edited, or deleted, run `scripts/wiki-lint-trigger.sh`. If it outputs `[WIKI MAINTENANCE DUE]`, run the `wiki-lint` workflow (`.agent/workflows/wiki-lint.md`) before stopping.
+- **Ingestion**: When files appear in `/raw/`, run the `wiki-ingest` workflow (`.rnex/workflows/wiki-ingest.md`). One source document typically produces many atomic pages (commonly 5–25 pages) — do not collapse a source into a single file.
+- **Cadence**: After any session where repository files were created, edited, or deleted, run `.rnex/scripts/wiki-lint-trigger.sh`. If it outputs `[WIKI MAINTENANCE DUE]`, run the `wiki-lint` workflow (`.rnex/workflows/wiki-lint.md`) before stopping.
 - **No-op sessions**: Do not run the trigger after read-only or purely conversational sessions where no files changed.
-- **Enable/disable**: Wiki automation is controlled by `lint_trigger: enabled|disabled` in `/wiki/index.md` frontmatter. Edit that field to toggle — the change is committed and visible to the whole team.
+- **Enable/disable**: Wiki automation is controlled by `lint_trigger_enabled: true|false` in `rnex.yaml` (and `lint_trigger: enabled|disabled` in `/wiki/index.md` frontmatter). Edit either field to toggle.
 
 ---
 

package/toolkit/plugins/karpathy-llm/scripts/wiki-lint-trigger.sh

@@ -1,13 +1,28 @@
 #!/bin/sh
 # ============================================================================
-# scripts/wiki-lint-trigger.sh — Autonomous Karpathy Wiki Lint Trigger
+# .rnex/scripts/wiki-lint-trigger.sh — Autonomous Karpathy Wiki Lint Trigger
 # ============================================================================
-# Check if wiki/index.md exists and contains lint_trigger: enabled.
-# If not, exit silently with code 0.
+
+# 1. Check rnex.yaml configuration if present
+if [ -f "rnex.yaml" ]; then
+  _disabled=$(awk '
+    /^plugins:/ { in_p=1; next }
+    in_p && /^[^ #]/ { exit }
+    in_p && /^  karpathy-llm:[ ]*$/ { in_k=1; next }
+    in_k && /^    lint_trigger_enabled:[ ]*false/ { print "yes"; exit }
+    in_k && !/^    / && !/^[ ]*#/ { in_k=0 }
+  ' rnex.yaml)
+  if [ "$_disabled" = "yes" ]; then
+    exit 0
+  fi
+fi
+
+# 2. Check if wiki/index.md exists and contains lint_trigger: enabled
 grep -q "lint_trigger: enabled" wiki/index.md 2>/dev/null || exit 0
 
-WIKI_DIR="wiki"
-COUNTER_FILE="$WIKI_DIR/.lint_trigger_counter"
+COUNTER_DIR=".rnex"
+[ -d "$COUNTER_DIR" ] || COUNTER_DIR="wiki"
+COUNTER_FILE="$COUNTER_DIR/.lint_trigger_counter"
 
 # Read and increment session counter
 count=0