repo-nexus 0.7.0 → 0.7.1

package/docs/plugins/index.md

@@ -109,7 +109,7 @@ plugins:
 
   # Functional / Knowledge Plugins
   karpathy-llm:
-    lint_trigger: git-post-merge
+    lint_trigger: manual
     notify_on_changes: true
 ```
 

package/docs/plugins/karpathy-llm.md

@@ -97,7 +97,7 @@ plugins:
 
     # Automated Git hook trigger for wiki verification
     # Options: git-post-merge, git-post-commit, git-pre-commit, git-pre-push, manual
-    lint_trigger: git-post-merge
+    lint_trigger: manual
 
     # Notify developer when changes are committed to ./docs/ or .rnex/wiki/
     notify_on_changes: true
@@ -110,7 +110,7 @@ plugins:
 |:---|:---|:---|:---|
 | `wiki_dir` | string | `.rnex/wiki` | Directory containing curated atomic markdown pages. |
 | `raw_dir` | string | `./docs` | Append-only directory for unmodified source intake documents. |
-| `lint_trigger` | string | `git-post-merge` | Git hook event that triggers wiki change detection (`git-post-merge`, `git-post-commit`, `git-pre-commit`, `git-pre-push`, `manual`). |
+| `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/`. |
 | `enabled` | boolean | `true` | Enable or disable the plugin. Overridable in `.local.rnex.yaml`. |
 

package/docs/rnex.example.yaml

@@ -113,9 +113,9 @@ plugins:
   #   prompts: true        # mirror prompts to .windsurf/prompts/*.md (default: true)
   #   workflows: true      # mirror workflows as prompts (default: true)
   # karpathy-llm:
-  #   wiki_dir: .rnex/wiki        # Directory for curated atomic markdown pages (default: .rnex/wiki)
-  #   raw_dir: ./docs             # Append-only directory for unmodified intake documents (default: ./docs)
-  #   lint_trigger: git-post-merge # Git hook event: git-post-merge, git-post-commit, git-pre-commit, git-pre-push, manual
+  #   raw_dir: "./docs"           # Append-only directory for unmodified intake documents (default: ./docs)
+  #   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

@@ -15,6 +15,7 @@ cmd_init() {
   _cli_gemini=""
   _cli_cursor=""
   _cli_windsurf=""
+  _cli_karpathy=""
 
   while [ $# -gt 0 ]; do
     case "$1" in
@@ -31,6 +32,8 @@ cmd_init() {
       --no-cursor) _cli_cursor="false" ;;
       --windsurf) _cli_windsurf="true" ;;
       --no-windsurf) _cli_windsurf="false" ;;
+      --karpathy|--karpathy-llm) _cli_karpathy="true" ;;
+      --no-karpathy|--no-karpathy-llm) _cli_karpathy="false" ;;
       --ai|--instructions|--ai-instructions)
         shift
         # Legacy flag ignored in favor of plugins
@@ -116,6 +119,9 @@ cmd_init() {
     if [ "$_cli_windsurf" = "true" ]; then
       _init_plugins="${_init_plugins}  windsurf:\n    instructions: true\n    prompts: true\n    workflows: true\n"
     fi
+    if [ "$_cli_karpathy" = "true" ]; then
+      _init_plugins="${_init_plugins}  karpathy-llm:\n    raw_dir: \"./docs\"\n    wiki_dir: \".rnex/wiki\"\n    lint_trigger: \"manual\"\n"
+    fi
 
     cat > "$_target_yaml" <<YAML_EOF
 # Repo Nexus workspace configuration

package/lib/commands/plugin.sh

@@ -87,7 +87,7 @@ cmd_plugin_info() {
     printf '\n%bConfigurable Options (in rnex.yaml or .local.rnex.yaml):%b\n' "$_BOLD" "$_NC"
     printf '  - wiki_dir: <dir>  (directory for curated markdown pages; current: %s)\n' "$(karpathy_wiki_dir)"
     printf '  - raw_dir: <dir>   (directory for unmodified intake documents; current: %s)\n' "$(karpathy_raw_dir)"
-    printf '  - lint_trigger: git-post-merge|git-post-commit|git-pre-commit|git-pre-push|manual  (current: %s)\n' "${_cur_lt:-git-post-merge}"
+    printf '  - lint_trigger: git-post-merge|git-post-commit|git-pre-commit|git-pre-push|manual  (current: %s)\n' "${_cur_lt:-manual}"
     printf '  - notify_on_changes: true|false  (show notification when raw/wiki changes are committed; current: %s)\n' "${_cur_nc:-true}"
   fi
 

package/lib/yaml.sh

@@ -309,6 +309,22 @@ yaml_enable_plugin() {
           }
         ' "$_target_file" > "$_tmp" && mv "$_tmp" "$_target_file"
         ;;
+      karpathy-llm)
+        awk -v name="$_name" '
+          /^plugins:[ ]*$/ || /^plugins:[ ]*#/ {
+            print
+            printf "  %s:\n    raw_dir: \"./docs\"\n    wiki_dir: \".rnex/wiki\"\n    lint_trigger: \"manual\"\n", name
+            added=1
+            next
+          }
+          { print }
+          END {
+            if (!added) {
+              printf "plugins:\n  %s:\n    raw_dir: \"./docs\"\n    wiki_dir: \".rnex/wiki\"\n    lint_trigger: \"manual\"\n", name
+            }
+          }
+        ' "$_target_file" > "$_tmp" && mv "$_tmp" "$_target_file"
+        ;;
       *)
         awk -v name="$_name" '
           /^plugins:[ ]*$/ || /^plugins:[ ]*#/ {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.7.0",
+  "version": "0.7.1",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",
@@ -68,4 +68,4 @@
   "devDependencies": {
     "vitepress": "^1.6.0"
   }
-}
+}

package/templates/rnex.example.yaml

@@ -113,9 +113,9 @@ plugins:
   #   prompts: true        # mirror prompts to .windsurf/prompts/*.md (default: true)
   #   workflows: true      # mirror workflows as prompts (default: true)
   # karpathy-llm:
-  #   wiki_dir: .rnex/wiki        # Directory for curated atomic markdown pages (default: .rnex/wiki)
-  #   raw_dir: ./docs             # Append-only directory for unmodified intake documents (default: ./docs)
-  #   lint_trigger: git-post-merge # Git hook event: git-post-merge, git-post-commit, git-pre-commit, git-pre-push, manual
+  #   raw_dir: "./docs"           # Append-only directory for unmodified intake documents (default: ./docs)
+  #   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/toolkit/plugins/karpathy-llm/hooks/after_sync.sh

@@ -1,8 +1,15 @@
 #!/bin/sh
 set -e
 
+# Exit early if rnex utilities aren't available 
+[ -z "$RNEX_ROOT" ] && { echo "Error: RNEX_ROOT not set"; exit 1; }
+
 # Resolve root workspace
-_root="${RNEX_ROOT:-$PWD}"
+_root="$RNEX_ROOT"
+
+# Target directory inside .rnex/ (the internal wiki's Raw intake state)
+WIKI_RAW_DIR="$RNEX_ROOT/.rnex/wiki/raw"
+mkdir -p "$WIKI_RAW_DIR"
 
 # Helper to read plugin config
 get_cfg() {
@@ -74,3 +81,51 @@ mkdir -p "$_pdir/templates"
 if [ -f "$_tmpl_dir/rnex-wiki-page.sample.md" ] && [ ! -f "$_pdir/templates/rnex-wiki-page.template.md" ]; then
   cp "$_tmpl_dir/rnex-wiki-page.sample.md" "$_pdir/templates/rnex-wiki-page.template.md"
 fi
+
+# 1. Parse 'raw_dir' configuration from rnex.yaml/.local.rnex.yaml (Defaults to './docs')
+# We check if parsed in RNEX_CONFIG_MERGED (YAML) using a standard grep/sed lookup
+RAW_DIR_VAL=$(grep -h -E '^\s*raw_dir:' "$RNEX_ROOT/rnex.yaml" "$RNEX_ROOT/.local.rnex.yaml" 2>/dev/null | tail -n1 | awk -F: '{print $NF}' | awk '{print $1}' | tr -d '"'\''')
+[ -z "$RAW_DIR_VAL" ] && RAW_DIR_VAL="$(get_cfg "raw_dir" "./docs")"
+RAW_DIR="${RAW_DIR_VAL:-./docs}"
+
+# Clear and sync the custom local raw folder files to raw intake (if any exist)
+if [ -d "$RNEX_ROOT/$RAW_DIR" ]; then
+  _raw_abs="$(cd "$RNEX_ROOT/$RAW_DIR" 2>/dev/null && pwd -P || true)"
+  _wiki_raw_abs="$(cd "$WIKI_RAW_DIR" 2>/dev/null && pwd -P || true)"
+  if [ -n "$_raw_abs" ] && [ "$_raw_abs" != "$_wiki_raw_abs" ]; then
+    find "$RNEX_ROOT/$RAW_DIR" -type f \( -name "*.md" -o -name "*.txt" -o -name "*.json" \) 2>/dev/null | while read -r filepath; do
+      filename=$(basename "$filepath")
+      # Prevent overwriting standard operational files
+      if [ "$filename" != "index.md" ] && [ "$filename" != "hot.md" ] && [ "$filename" != "_log.md" ]; then
+        cp "$filepath" "$WIKI_RAW_DIR/$filename"
+      fi
+    done
+  fi
+fi
+
+# 2. Automatically sync README.md from all enabled/cloned member repositories
+# Get list of enabled repositories using a secure cross-repo read or `rnex list`
+REPOS_DIR_VAL=$(grep -h -E '^\s*repos_dir:' "$RNEX_ROOT/rnex.yaml" "$RNEX_ROOT/.local.rnex.yaml" 2>/dev/null | tail -n1 | awk -F: '{print $NF}' | awk '{print $1}' | tr -d '"'\''')
+REPOS_DIR="${REPOS_DIR_VAL:-./repos}"
+
+if [ -d "$RNEX_ROOT/$REPOS_DIR" ]; then
+  for repo_path in "$RNEX_ROOT/$REPOS_DIR"/*; do
+    [ ! -d "$repo_path" ] && continue
+    repo_name=$(basename "$repo_path")
+    
+    # Ignore repos that are disabled locally (checking status state)
+    # Checks if enabled: false exists for this repo in configuration
+    if grep -A5 "  $repo_name:" "$RNEX_ROOT/rnex.yaml" "$RNEX_ROOT/.local.rnex.yaml" 2>/dev/null | grep -q "enabled: false"; then
+      continue
+    fi
+
+    # Read and sync any README file with case-insensitive check
+    for readme_name in README.md readme.md README.markdown README; do
+      if [ -f "$repo_path/$readme_name" ]; then
+        # Namespace the copied file with its repo name to prevent conflicts
+        cp "$repo_path/$readme_name" "$WIKI_RAW_DIR/README_${repo_name}.md"
+        break
+      fi
+    done
+  done
+fi

package/toolkit/plugins/karpathy-llm/hooks/git_post-commit.sh

@@ -40,7 +40,7 @@ _raw="$(get_cfg "raw_dir" "./docs")"
 _wiki="$(printf '%s' "$_wiki" | sed -e 's#^/##' -e 's#/$##')"
 _raw="$(printf '%s' "$_raw" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
-_trigger="$(get_cfg "lint_trigger" "git-post-merge")"
+_trigger="$(get_cfg "lint_trigger" "manual")"
 if [ "$_trigger" = "git-post-commit" ] || [ "$_trigger" = "post-commit" ]; then
   if git -C "$_root" diff-tree -r --name-only HEAD 2>/dev/null | grep -qE "(^|/)($_raw|$_wiki)/"; then
     _notify="$(get_cfg "notify_on_changes" "true")"

package/toolkit/plugins/karpathy-llm/hooks/git_post-merge.sh

@@ -40,7 +40,7 @@ _raw="$(get_cfg "raw_dir" "./docs")"
 _wiki="$(printf '%s' "$_wiki" | sed -e 's#^/##' -e 's#/$##')"
 _raw="$(printf '%s' "$_raw" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
-_trigger="$(get_cfg "lint_trigger" "git-post-merge")"
+_trigger="$(get_cfg "lint_trigger" "manual")"
 if [ "$_trigger" = "git-post-merge" ] || [ "$_trigger" = "post-merge" ]; then
   if git -C "$_root" diff-tree -r --name-only ORIG_HEAD HEAD 2>/dev/null | grep -qE "(^|/)($_raw|$_wiki)/"; then
     _notify="$(get_cfg "notify_on_changes" "true")"

package/toolkit/plugins/karpathy-llm/hooks/git_pre-commit.sh

@@ -40,7 +40,7 @@ _raw="$(get_cfg "raw_dir" "./docs")"
 _wiki="$(printf '%s' "$_wiki" | sed -e 's#^/##' -e 's#/$##')"
 _raw="$(printf '%s' "$_raw" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
-_trigger="$(get_cfg "lint_trigger" "git-post-merge")"
+_trigger="$(get_cfg "lint_trigger" "manual")"
 if [ "$_trigger" = "git-pre-commit" ] || [ "$_trigger" = "pre-commit" ]; then
   if git -C "$_root" diff --cached --name-only 2>/dev/null | grep -qE "(^|/)($_raw|$_wiki)/"; then
     _notify="$(get_cfg "notify_on_changes" "true")"

package/toolkit/plugins/karpathy-llm/hooks/git_pre-push.sh

@@ -40,7 +40,7 @@ _raw="$(get_cfg "raw_dir" "./docs")"
 _wiki="$(printf '%s' "$_wiki" | sed -e 's#^/##' -e 's#/$##')"
 _raw="$(printf '%s' "$_raw" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
 
-_trigger="$(get_cfg "lint_trigger" "git-post-merge")"
+_trigger="$(get_cfg "lint_trigger" "manual")"
 if [ "$_trigger" = "git-pre-push" ] || [ "$_trigger" = "pre-push" ]; then
   _notify="$(get_cfg "notify_on_changes" "true")"
   if [ "$_notify" != "false" ]; then

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

@@ -1,17 +1,28 @@
 name: karpathy-llm
-version: 0.5.1
-description: Andrej Karpathy's agent behavioral principles, context engineering guidelines, and autonomous LLM Wiki knowledge architecture
+version: 1.0.0
+description: Andréj Karpathy's verification frameworks & wiki patterns for AI coding agents.
 author: unoxen
 homepage: https://github.com/unoxen/repo-nexus
+
+config_defaults:
+  raw_dir: "./docs"
+  wiki_dir: ".rnex/wiki"
+  lint_trigger: "manual" # Default changed to manual to avoid unsolicited background trigger tasks
+  notify_on_changes: true
+
 config:
-  wiki_dir: .rnex/wiki
-  raw_dir: ./docs
-  lint_trigger: git-post-merge
+  raw_dir: "./docs"
+  wiki_dir: ".rnex/wiki"
+  lint_trigger: "manual"
   notify_on_changes: true
+
 rules:
   - rules/rnex-behavioral.md: .rnex/plugins/karpathy-llm/rules/rnex-behavioral.md
+  - rules/behavioral.md: .rnex/plugins/karpathy-llm/rules/behavioral.md
   - workflows/rnex-wiki-ingest.md: .rnex/plugins/karpathy-llm/workflows/rnex-wiki-ingest.md
+  - workflows/wiki-ingest.md: .rnex/plugins/karpathy-llm/workflows/wiki-ingest.md
   - workflows/rnex-wiki-lint.md: .rnex/plugins/karpathy-llm/workflows/rnex-wiki-lint.md
+  - workflows/wiki-lint.md: .rnex/plugins/karpathy-llm/workflows/wiki-lint.md
 instructions:
   - instructions/rnex-wiki-architecture.md: .rnex/plugins/karpathy-llm/instructions/rnex-wiki-architecture.md
 templates:

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

@@ -0,0 +1,47 @@
+# Karpathy Coding Agent Behavioral Principles
+
+> "The delicate art and science of context engineering: filling the context window with just the right information for the next step." — Andrej Karpathy
+
+These rules define standing behavioral principles for AI coding assistants (Cursor, Claude Code, GitHub Copilot, Antigravity, Windsurf) working in this workspace.
+
+---
+
+## 1. The Four Cardinal Principles
+
+### Principle 1: Think Before Coding
+* **State Assumptions Explicitly:** Before implementing any non-trivial change, state your understanding of the problem, assumptions made, and proposed solution.
+* **Surface Trade-Offs:** If multiple approaches exist, outline the alternatives with their trade-offs before generating code.
+* **Verify Repository Boundaries:** In multi-repo workspaces, determine which member repositories are affected. Never make silent architectural assumptions that span across repo boundaries.
+
+### Principle 2: Simplicity First
+* **Favor Readable Over Clever:** Write the simplest code that solves the immediate problem. Avoid unnecessary abstractions, speculative generics, and premature optimizations.
+* **Zero Boilerplate Bloat:** Do not introduce extra wrapper layers, helper classes, or framework-heavy patterns unless explicitly requested or required by existing codebase conventions.
+* **Less Code is Better Code:** If an existing utility, POSIX primitive, or library function does the job, reuse it.
+
+### Principle 3: Surgical Changes
+* **Minimal Blast Radius:** Touch *only* the lines and files required to achieve the goal.
+* **Preserve Documentation & Comments:** Never delete or overwrite existing comments, documentation, or code structure unrelated to your changes.
+* **Zero Unintended Reformatting:** Avoid running blanket code formatters across entire files that create massive, unreadable git diffs. Keep diffs tight, focused, and reviewable.
+
+### Principle 4: Goal-Driven Execution & Verification
+* **Define Success Criteria Upfront:** Know how you will prove that your change works before you write the first line of code.
+* **Verify with Automated Checks:** Run linters, unit tests, and build commands before declaring a task complete.
+* **Inspect the Diff:** Review your own git diff before committing or presenting the solution to ensure no extraneous changes were introduced.
+
+---
+
+## 2. Multi-Repo Context Engineering
+
+In a Repo Nexus workspace, independent repositories are organized into `./repos/<name>/` as autonomous Git repositories. Coding agents must follow these rules:
+
+1. **Repository Boundaries:**
+   - Edits made to `repos/<name>/` modify the underlying member repository directly.
+   - Member repositories are autonomous projects. Do not introduce cross-repository source imports or shared runtime dependencies unless an explicit monorepo architecture is configured.
+
+2. **Member .rnex Directory Routing:**
+   - Member repositories may contain an `.rnex/` directory (e.g. `repos/<name>/.rnex/`) containing repository-specific documents, instructions, rules, workflows, and scripts. Coding assistants must inspect this directory for member-specific instructions.
+   - Run git operations (commits, branches, pushes) directly within the respective member repository root (`repos/<name>/`).
+
+3. **Context Economy:**
+   - Do not redundantly read entire files or directory trees when targeted symbol lookups or line ranges suffice.
+   - Rely on active workspace context, indexing, and compiled documentation rather than re-scanning raw files repeatedly.

package/toolkit/plugins/karpathy-llm/workflows/wiki-ingest.md

@@ -0,0 +1,66 @@
+# Wiki Ingestion Workflow (`wiki-ingest`)
+
+Universal workflow for decomposing and ingesting raw source materials into atomic Karpathy LLM Wiki pages.
+
+---
+
+## Ingestion Protocol
+
+1. **Resolve Configuration & Scan Intake:**
+   - Read `rnex.yaml` (and `.local.rnex.yaml` if present) to resolve the active `raw_dir` (default: `./docs`) and `wiki_dir` (default: `.rnex/wiki`) under `plugins.karpathy-llm`.
+   - Scan `<raw_dir>/` (default: `./docs`) for source materials (articles, transcripts, documents, research notes, meeting logs) not yet recorded in `<wiki_dir>/_log.md` (default: `.rnex/wiki/_log.md`).
+   - All source material must reside in `<raw_dir>/` unmodified. Never write directly to `<wiki_dir>/` without ingesting.
+
+2. **Read & Clarify:**
+   - Read each source fully.
+   - If scope, domain boundaries, target audience, or level of detail is unclear, ask one round of clarifying questions before proceeding.
+
+3. **Atomic Decomposition:**
+   - Decompose each source into atomic wiki pages — **one per distinct concept, person, organization, event, or theme** (or architecture decision/contract).
+   - A single source document commonly produces **5–25 pages**. Never collapse an entire source into a single file.
+   - Place pages according to workspace wiki organization:
+     - **Flat:** directly under `<wiki_dir>/` (e.g., `<wiki_dir>/<topic>.md`)
+     - **Structured:** in categorical subfolders within `<wiki_dir>/`:
+       - Research → `concepts/`, `people/`, `organizations/`, `sources/`, `analysis/`
+       - Second brain → `projects/`, `people/`, `decisions/`, `logs/`
+       - Content archive → `sources/`, `people/`, `tools/`, `concepts/`
+       - Codebase → `architecture/`, `decisions/`, `runbooks/`, `people/`
+
+4. **Frontmatter Relations:**
+   - For each page, write the required YAML frontmatter with typed relations:
+   ```yaml
+   ---
+   title: ""
+   tags: []
+   last_updated: YYYY-MM-DD
+   # Typed relation fields — paths relative to <wiki_dir>/ (or workspace root for raw sources)
+   sources: []          # <raw_dir>/ files this page was derived from
+   related: []          # thematically related wiki pages
+   extends: []          # pages this one builds upon or specialises
+   contradicts: []      # pages with conflicting information
+   mentioned_in: []     # pages that link to this one (leave empty; maintained by lint)
+   ---
+   ```
+   - **Crucial:** The relation graph lives in frontmatter, not in prose links. Agents traverse the graph by reading frontmatter fields, not by scanning body text.
+
+5. **Author Concise Body:**
+   - Write a concise body with summary, key facts, and insights.
+   - Add inline standard Markdown links (`[Label](./path.md)`) where contextually useful in prose.
+
+6. **Update Navigation Index (Annotated Links):**
+   - Update `<wiki_dir>/index.md` (default: `.rnex/wiki/index.md`) with links to all new pages in their corresponding categorized sections.
+   - Include a concise 1-line summary next to each link (e.g. `- [Concept Name](path.md): One-line summary of role or contract`) so agents pinpoint target pages in a single read without exploratory scanning.
+
+7. **Update Hot Cache (Bounded ~500-Word Ceiling):**
+   - Update `<wiki_dir>/hot.md` (default: `.rnex/wiki/hot.md`) with the rolling orientation summary across 3 structured sections:
+     1. **Architecture & Member Repo Map**: Active domain ownership per member repo.
+     2. **Current Focus & Recent Ingests**: Active topics from recent ingests.
+     3. **Key Contracts & Boundaries**: Critical cross-repo or subsystem rules.
+   - **Enforce Token Economy**: Keep `<wiki_dir>/hot.md` strictly under ~500 words. Condense or prune older focus items to prevent bloat.
+
+8. **Append Operation Log:**
+   - Append a timestamped entry to `<wiki_dir>/_log.md` (default: `.rnex/wiki/_log.md`) detailing:
+     - Date & time
+     - Raw intake file processed
+     - List of atomic pages generated
+     - Any flagged follow-ups or knowledge gaps

package/toolkit/plugins/karpathy-llm/workflows/wiki-lint.md

@@ -0,0 +1,50 @@
+# Wiki Lint & Maintenance Workflow (`wiki-lint`)
+
+Periodic health check and maintenance workflow to preserve wiki graph integrity, validate typed relations, recompute bidirectional links, resolve knowledge gaps, and rebuild indexes.
+
+---
+
+## Lint & Maintenance Protocol
+
+1. **Resolve Configuration & Verify Paths:**
+   - Read `rnex.yaml` (and `.local.rnex.yaml` if present) to resolve the active `wiki_dir` (default: `.rnex/wiki`) and `raw_dir` (default: `./docs`) under `plugins.karpathy-llm`.
+   - For every page under `<wiki_dir>/`, verify that all paths in frontmatter relation fields (`related`, `extends`, `contradicts`, `sources`) resolve to existing files under `<wiki_dir>/` or `<raw_dir>/`.
+   - Fix or flag broken paths.
+
+2. **Recompute `mentioned_in`:**
+   - Recompute `mentioned_in` for every page under `<wiki_dir>/` by scanning all other pages' relation fields and inline links.
+   - Update the field in frontmatter.
+
+3. **Find Orphaned Pages:**
+   - Detect pages under `<wiki_dir>/` not reachable from `<wiki_dir>/index.md` or any `mentioned_in` field.
+   - Add them to the index in their appropriate category.
+
+4. **Detect Duplicate or Overlapping Pages:**
+   - Detect duplicate or heavily overlapping pages.
+   - Consolidate and update relations across the wiki graph.
+
+5. **Check Factual Inconsistencies:**
+   - Check for factual inconsistencies between pages in `contradicts` relations or covering the same topic.
+   - Clarify or resolve contradictions.
+
+6. **Identify Knowledge Gaps:**
+   - Identify knowledge gaps: concepts referenced in relation fields or prose but lacking their own atomic page.
+   - Create stub pages or flag for future ingest.
+
+7. **Suggest Source Candidates:**
+   - Suggest source candidates from `<raw_dir>/` or external searches to fill identified knowledge gaps.
+
+8. **Rebuild Navigation Index (Annotated Links):**
+   - Rebuild `<wiki_dir>/index.md` (default: `.rnex/wiki/index.md`) to reflect the current set of pages and categories accurately.
+   - Ensure every page entry maintains a concise 1-line descriptive annotation.
+
+9. **Update Hot Cache (Bounded ~500-Word Ceiling):**
+   - Refresh `<wiki_dir>/hot.md` (default: `.rnex/wiki/hot.md`), verifying the 3 structured sections (Architecture & Repo Map, Current Focus, Key Contracts).
+   - Ensure the total length remains strictly under ~500 words by pruning superseded entries.
+
+10. **Append Operation Log:**
+    - Append a lint summary to `<wiki_dir>/_log.md` (default: `.rnex/wiki/_log.md`) detailing:
+      - Broken links fixed or flagged
+      - `mentioned_in` updates
+      - Orphans and duplicates resolved
+      - Gaps identified or stubbed

package/toolkit/prompts/index.md

@@ -13,10 +13,10 @@ When an AI assistant is assigned a cross-repo or workspace-wide task, consult th
    - **Purpose**: Cross-repository health, git status, branch tracking, and configuration validation.
    - **When to use**: Auditing workspace status, verifying uncommitted changes, or syncing member repositories before releases.
 
-3. **[`rnex-wiki-ingest.md`](./rnex-wiki-ingest.md)**
+3. **[`rnex-ingest.md`](./rnex-ingest.md)** (alias: [`rnex-wiki-ingest.md`](./rnex-wiki-ingest.md))
    - **Purpose**: Autonomous ingestion of intake materials from configured raw intake directory into atomic Karpathy LLM Wiki pages.
    - **When to use**: Decomposing research papers, documentation, transcripts, or specifications into the knowledge base.
 
-4. **[`rnex-wiki-lint.md`](./rnex-wiki-lint.md)**
+4. **[`rnex-lint.md`](./rnex-lint.md)** (alias: [`rnex-wiki-lint.md`](./rnex-wiki-lint.md))
    - **Purpose**: Deterministic graph audit, dead link validation, `mentioned_in` backlink reconciliation, and index rebuild.
    - **When to use**: Routine wiki maintenance, pre-commit validation, or after adding/renaming wiki pages.

package/toolkit/prompts/rnex-ingest.md

@@ -0,0 +1,14 @@
+# Operational Task: Ingest New Material
+
+You are tasked with executing the ingestion and atomic break-down workflow.
+
+## Context & Inputs
+- Source files location: `.rnex/wiki/raw/` (inclusive of active member repo `README_*.md` files)
+- Goal: Deconstruct files into individual interlinked pages in `.rnex/wiki/`.
+
+## Workflow & Guidelines Router
+1. Read the strict ingest steps and verification metrics only from `.rnex/plugins/karpathy-llm/workflows/wiki-ingest.md`.
+2. Follow styling, structural, and behavioral constraints inside `.rnex/plugins/karpathy-llm/rules/behavioral.md`.
+3. Adhere to global instruction patterns in `.rnex/ai-instructions.md`.
+
+Transform unmodified raw documents on ingestion following exactly the referenced workflow. Do not use inline logic or generate outside explicit instructions. Run 'wiki-lint' upon completion to review accuracy. Update Operation Log (`.rnex/wiki/_log.md`).

package/toolkit/prompts/rnex-lint.md

@@ -0,0 +1,15 @@
+# Operational Task: Workspace Wiki Lint & Audit
+
+You are tasked with executing the Workspace Wiki Lint workflow.
+
+## Context & Inputs
+- Target Scope: `.rnex/wiki/` (including `.rnex/wiki/raw/` and synchronized member READMEs)
+- Custom Rules & Workflows loaded: `.rnex/plugins/karpathy-llm/`
+- Current Workspace Manifest: `rnex.yaml` and `.local.rnex.yaml`
+
+## Verification Rule Router
+1. Locate and parse your validation instructions exclusively from `.rnex/plugins/karpathy-llm/workflows/wiki-lint.md`.
+2. Evaluate adherence based on the agent behavior standards described in `.rnex/plugins/karpathy-llm/rules/behavioral.md` and compiled rules in `.rnex/ai-instructions.md`.
+3. Do NOT invent new lint checks or execute uncompiled heuristic instructions.
+
+Execute the 10-step protocol defined strictly within the referenced workflow. Audit `raw_dir` items, link paths, index categorization, and relational YAML frontmatter. Provide your structured audit and write feedback output to the Audit trail in `.rnex/wiki/_log.md`.

package/toolkit/prompts/rnex-wiki-ingest.md

@@ -0,0 +1,14 @@
+# Operational Task: Ingest New Material
+
+You are tasked with executing the ingestion and atomic break-down workflow.
+
+## Context & Inputs
+- Source files location: `.rnex/wiki/raw/` (inclusive of active member repo `README_*.md` files)
+- Goal: Deconstruct files into individual interlinked pages in `.rnex/wiki/`.
+
+## Workflow & Guidelines Router
+1. Read the strict ingest steps and verification metrics only from `.rnex/plugins/karpathy-llm/workflows/wiki-ingest.md`.
+2. Follow styling, structural, and behavioral constraints inside `.rnex/plugins/karpathy-llm/rules/behavioral.md`.
+3. Adhere to global instruction patterns in `.rnex/ai-instructions.md`.
+
+Transform unmodified raw documents on ingestion following exactly the referenced workflow. Do not use inline logic or generate outside explicit instructions. Run 'wiki-lint' upon completion to review accuracy. Update Operation Log (`.rnex/wiki/_log.md`).

package/toolkit/prompts/rnex-wiki-lint.md

@@ -0,0 +1,15 @@
+# Operational Task: Workspace Wiki Lint & Audit
+
+You are tasked with executing the Workspace Wiki Lint workflow.
+
+## Context & Inputs
+- Target Scope: `.rnex/wiki/` (including `.rnex/wiki/raw/` and synchronized member READMEs)
+- Custom Rules & Workflows loaded: `.rnex/plugins/karpathy-llm/`
+- Current Workspace Manifest: `rnex.yaml` and `.local.rnex.yaml`
+
+## Verification Rule Router
+1. Locate and parse your validation instructions exclusively from `.rnex/plugins/karpathy-llm/workflows/wiki-lint.md`.
+2. Evaluate adherence based on the agent behavior standards described in `.rnex/plugins/karpathy-llm/rules/behavioral.md` and compiled rules in `.rnex/ai-instructions.md`.
+3. Do NOT invent new lint checks or execute uncompiled heuristic instructions.
+
+Execute the 10-step protocol defined strictly within the referenced workflow. Audit `raw_dir` items, link paths, index categorization, and relational YAML frontmatter. Provide your structured audit and write feedback output to the Audit trail in `.rnex/wiki/_log.md`.