repo-nexus 0.6.3 → 0.6.5

package/CHANGELOG.md

@@ -8,6 +8,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### Added
+- **Dynamic AI Instructions & Complete Plugin Deactivation in `rnex fix`**:
+  - [`get_rnex_instructions()`](file:///Users/admin/Projects/ai/repo-nexus/lib/ai.sh) dynamically evaluates whether `karpathy-llm` is enabled. When disabled or omitted from configuration, the Karpathy LLM Wiki mandatory gate alert, wiki orientation startup step, forbidden wiki actions, and wiki subagent references are omitted from [`AGENTS.md`](file:///Users/admin/Projects/ai/repo-nexus/AGENTS.md) and native provider instructions.
+  - `sync_plugins` automatically prunes scoped directories (`.rnex/plugins/<plugin>/`) from both the workspace root and member repositories whenever a plugin is marked `enabled: false` or omitted from config.
+  - Provider prompt mirrors across all supported assistants (`.github/prompts`, `.claude/commands`, `.claude/prompts`, `.gemini/prompts`, `.cursor/prompts`, `.windsurf/prompts`) are cleaned of prompts and workflows belonging to disabled plugins, while preserving base prompts and active plugin prompts.
+  - Hook dispatchers and `status` reports evaluate active enablement (`yaml_plugin_enabled`) rather than key presence, preventing disabled plugins from registering hook alerts or status indicators.
+  - User-authored content in wiki and intake directories is strictly preserved during plugin deactivation.
 - **Universal `AGENTS.md` & Native Provider Instructions Architecture**:
   - Maintained [`AGENTS.md`](file:///Users/admin/Projects/ai/repo-nexus/AGENTS.md) at the workspace root as the universal, cross-tool standard for workspace routing instructions.
   - Assistants that read `AGENTS.md` unconditionally (such as GitHub Copilot) rely directly on `AGENTS.md`, eliminating redundant instruction files (`.github/copilot-instructions.md`) and diverging contexts.

package/docs/index.md

@@ -6,7 +6,7 @@ hero:
   text: "Virtual Meta-Repo Companion"
   tagline: "Unite independent repositories into a cohesive AI-enabled workspace, without dependencies, Git submodules or monorepo migrations."
   image:
-    src: /logo.jpg
+    src: /logo.png
     alt: Repo Nexus Logo
   actions:
     - theme: brand

package/lib/ai.sh

@@ -61,7 +61,9 @@ AI_MARKER_END="<!-- REPO-NEXUS:END -->"
 
 get_rnex_instructions() {
   _wiki_dir="$(karpathy_wiki_dir)"
-  cat <<AGENTS_EOF
+
+  if yaml_plugin_enabled "karpathy-llm"; then
+    cat <<AGENTS_EOF
 # Multi-Repo AI Workspace Context
 
 This workspace operates as a **Repo Nexus Virtual Meta-Repo** uniting independent repositories.
@@ -119,6 +121,55 @@ When workspace configuration, routing blocks, plugin assets, or member repositor
 ## Git Operations
 Commit and push changes directly within the respective member repository root (\`repos/<name>/\`).
 AGENTS_EOF
+  else
+    cat <<AGENTS_EOF
+# Multi-Repo AI Workspace Context
+
+This workspace operates as a **Repo Nexus Virtual Meta-Repo** uniting independent repositories.
+
+## Routing Protocol for AI Assistants
+
+### Mandatory Session Startup
+
+Before answering the first task or making any task-specific tool call in a new session, execute these steps in strict sequence:
+
+1. **Read Configuration First (Highest Priority)**: Inspect and read \`.local.rnex.yaml\` (if present) and \`rnex.yaml\` to identify workspace structure (\`repos_dir\`), active member repositories (\`repos/\`), and enabled plugins.
+   - \`.local.rnex.yaml\` takes highest priority over \`rnex.yaml\`.
+   - Repositories are enabled by default unless explicitly marked \`enabled: false\`. Disabled repositories are excluded from active tasks.
+2. **Plugin Instructions**: Inspect instructions for every enabled Repo Nexus plugin under \`.rnex/plugins/<plugin-name>/\`.
+3. **Targeted Member Repository Access Only**:
+   - Navigate directly to the specific files in \`repos/<name>/\` relevant to the user request.
+   - Never perform blind repository-wide scans or unbounded searches across \`repos/\`.
+
+This is a hard gate, not optional orientation. Complete it once per session and retain the resulting context; do not repeatedly reload these files.
+
+### Forbidden Startup Actions
+- ❌ **DO NOT** grep or search \`repos/\` as your first step.
+- ❌ **DO NOT** perform recursive tree exploration of member repositories.
+
+## Workspace Skills, Workflows & Rules
+Tools and agents operate on skills, workflows, instructions, and rules located under \`.rnex/\`:
+- **Skills**: Inspect \`.rnex/skills/\` and active plugin skills under \`.rnex/plugins/<plugin-name>/skills/\`.
+- **Workflows**: Inspect \`.rnex/workflows/\` and active plugin workflows under \`.rnex/plugins/<plugin-name>/workflows/\`.
+- **Rules & Instructions**: Inspect \`.rnex/rules/\`, \`.rnex/instructions/\`, and active plugin rules/instructions under \`.rnex/plugins/<plugin-name>/\`.
+
+## Subagents
+Autonomous subagents are defined under \`.rnex/agents/\` and active plugin agents under \`.rnex/plugins/<plugin-name>/agents/\`.
+- Subagents are kept in \`.rnex/\` and are not mirrored to external provider folders.
+- To execute a task requiring a subagent, adopt the role, operational persona, and constraints specified in the corresponding subagent definition file.
+
+## Member Repositories (\`repos/<name>/\`)
+Each member repository is an autonomous Git repository. For repository-specific instructions, inspect \`repos/<name>/.rnex/\`. Inspect only targeted files required for the task.
+
+## Workspace Maintenance
+When workspace configuration, routing blocks, plugin assets, or member repository structures require reconciliation or schema upgrades:
+- Run \`rnex fix\` (or its alias \`rnex update\` / \`rnex upgrade\`, which runs the unified fix reconciliation with upfront version checking).
+- Use \`rnex fix -y\` to non-destructively apply configuration version upgrades automatically.
+
+## Git Operations
+Commit and push changes directly within the respective member repository root (\`repos/<name>/\`).
+AGENTS_EOF
+  fi
 }
 
 merge_rnex_instructions() {
@@ -344,11 +395,18 @@ sync_rnex_base_assets() {
       cp -f "$_sk_dir"/* "$NEXUS_DIR/.rnex/skills/$_sk_name/" 2>/dev/null || true
     done
   fi
+
+  # Purge any legacy plugin assets that shouldn't be in base .rnex/
+  rm -rf "$NEXUS_DIR/.rnex/skills/rnex-setup-karpathy-wiki" "$NEXUS_DIR/.rnex/skills/setup-karpathy-wiki" 2>/dev/null || true
+  rm -rf "$NEXUS_DIR/.rnex/skills/rnex-wiki-ingest" "$NEXUS_DIR/.rnex/skills/rnex-wiki-lint" "$NEXUS_DIR/.rnex/skills/wiki-curator" 2>/dev/null || true
+  rm -f "$NEXUS_DIR/.rnex/workflows/rnex-wiki-ingest.md" "$NEXUS_DIR/.rnex/workflows/rnex-wiki-lint.md" "$NEXUS_DIR/.rnex/workflows/wiki-ingest.md" "$NEXUS_DIR/.rnex/workflows/wiki-lint.md" 2>/dev/null || true
+  rm -f "$NEXUS_DIR/.rnex/agents/rnex-wiki-curator.agent.md" "$NEXUS_DIR/.rnex/agents/wiki-curator.agent.md" 2>/dev/null || true
 }
 
 sync_prompts() {
   sync_rnex_base_assets
   sync_ai_providers
+  clean_disabled_plugins_prompts_all_providers
 }
 
 sync_provider_prompts() {
@@ -380,6 +438,28 @@ sync_provider_prompts() {
   rm -f "$_sp_dir/rnex-setup-karpathy-wiki${_ext}" "$_sp_dir/setup-karpathy-wiki${_ext}" 2>/dev/null || true
   rm -f "$_sp_dir/wiki-ingest${_ext}" "$_sp_dir/wiki-lint${_ext}" 2>/dev/null || true
 
+  # Remove prompts belonging to disabled plugins from this provider directory
+  for _parent in "$SCRIPT_LOCATION/toolkit/plugins" "$(dirname "$SCRIPT_LOCATION")/toolkit/plugins" "$NEXUS_DIR/toolkit/plugins" "$NEXUS_DIR/.rnex/plugins"; do
+    [ -d "$_parent" ] || continue
+    for _pdir in "$_parent"/*; do
+      [ -d "$_pdir" ] || continue
+      _pname="$(basename "$_pdir")"
+      if ! yaml_plugin_enabled "$_pname"; then
+        for _sub in prompts workflows; do
+          [ -d "$_pdir/$_sub" ] || continue
+          for _pfile in "$_pdir/$_sub"/*.md; do
+            [ -f "$_pfile" ] || continue
+            _base="$(basename "$_pfile" .md)"
+            case "$_base" in
+              index|README) continue ;;
+            esac
+            rm -f "$_sp_dir/${_base}${_ext}" 2>/dev/null || true
+          done
+        done
+      fi
+    done
+  done
+
   # Base toolkit prompts (from prompts or workflows)
   if [ -n "$_src_prompts" ]; then
     for _pfile in "$_src_prompts"/rnex-*.md; do
@@ -451,6 +531,53 @@ sync_provider_prompts() {
   done
 }
 
+clean_plugin_prompts_across_providers() {
+  _pdir="$1"
+  [ -d "$_pdir" ] || return 0
+
+  for _sub in prompts workflows; do
+    [ -d "$_pdir/$_sub" ] || continue
+    for _pfile in "$_pdir/$_sub"/*.md; do
+      [ -f "$_pfile" ] || continue
+      _base="$(basename "$_pfile" .md)"
+      case "$_base" in
+        index|README) continue ;;
+      esac
+      rm -f "$NEXUS_DIR/.github/prompts/${_base}.prompt.md" 2>/dev/null || true
+      rm -f "$NEXUS_DIR/.claude/commands/${_base}.md" 2>/dev/null || true
+      rm -f "$NEXUS_DIR/.claude/prompts/${_base}.md" 2>/dev/null || true
+      rm -f "$NEXUS_DIR/.gemini/prompts/${_base}.prompt.md" 2>/dev/null || true
+      rm -f "$NEXUS_DIR/.cursor/prompts/${_base}.md" 2>/dev/null || true
+      rm -f "$NEXUS_DIR/.windsurf/prompts/${_base}.md" 2>/dev/null || true
+    done
+  done
+
+  rmdir "$NEXUS_DIR/.github/prompts" 2>/dev/null || true
+  rmdir "$NEXUS_DIR/.claude/commands" 2>/dev/null || true
+  rmdir "$NEXUS_DIR/.claude/prompts" 2>/dev/null || true
+  rmdir "$NEXUS_DIR/.gemini/prompts" 2>/dev/null || true
+  rmdir "$NEXUS_DIR/.cursor/prompts" 2>/dev/null || true
+  rmdir "$NEXUS_DIR/.windsurf/prompts" 2>/dev/null || true
+}
+
+clean_disabled_plugins_prompts_all_providers() {
+  _seen_plugins=" "
+  for _parent in "$SCRIPT_LOCATION/toolkit/plugins" "$(dirname "$SCRIPT_LOCATION")/toolkit/plugins" "$NEXUS_DIR/toolkit/plugins" "$NEXUS_DIR/.rnex/plugins"; do
+    [ -d "$_parent" ] || continue
+    for _pdir in "$_parent"/*; do
+      [ -d "$_pdir" ] || continue
+      _pname="$(basename "$_pdir")"
+      case "$_seen_plugins" in
+        *" $_pname "*) continue ;;
+      esac
+      _seen_plugins="${_seen_plugins}${_pname} "
+      if ! yaml_plugin_enabled "$_pname"; then
+        clean_plugin_prompts_across_providers "$_pdir"
+      fi
+    done
+  done
+}
+
 clean_provider_prompts() {
   _sp_dir="$1"
   _ext="${2:-.md}"

package/lib/commands/fix.sh

@@ -40,13 +40,16 @@ cmd_fix() {
   # 1. Ensure .gitignore ignores repos/, .rnex/, and local configs, and strips legacy counters
   reconcile_gitignore "$NEXUS_DIR"
 
-  # 2. Reconcile universal workspace instructions in AGENTS.md
+  # 2. Reconcile plugins (scopes, asset pruning for disabled plugins)
+  sync_plugins
+
+  # 3. Reconcile universal workspace instructions in AGENTS.md
   merge_rnex_instructions "$NEXUS_DIR/AGENTS.md"
 
-  # 3. Sync standard skills, workflows, and provider prompts
+  # 4. Sync standard skills, workflows, and provider prompts
   sync_prompts
 
-  # 4. Reconcile Git hooks according to configuration
+  # 5. Reconcile Git hooks according to configuration
   case "$GIT_HOOKS_CONFIG" in
     false|no|0)
       _cur_hp="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
@@ -82,9 +85,6 @@ cmd_fix() {
       ;;
   esac
 
-  # 5. Reconcile plugins
-  sync_plugins
-
   # 6. Reconcile member repos
   yaml_list_repos | while read -r _name; do
     [ -n "$_name" ] || continue

package/lib/commands/plugin.sh

@@ -17,9 +17,12 @@ cmd_plugin_list() {
     _version="$(plugin_get_field "$_pdir" "version")"
     _desc="$(plugin_get_field "$_pdir" "description")"
 
-    if yaml_has_plugin "$_name"; then
+    if yaml_plugin_enabled "$_name"; then
       printf '  %b[enabled]%b   %b%-15s%b %b(v%s)%b - %s\n' \
         "$_G" "$_NC" "$_BOLD" "$_name" "$_NC" "$_DIM" "${_version:-0.1.0}" "$_NC" "$_desc"
+    elif yaml_has_plugin "$_name"; then
+      printf '  %b[disabled]%b  %b%-15s%b %b(v%s)%b - %s\n' \
+        "$_Y" "$_NC" "$_BOLD" "$_name" "$_NC" "$_DIM" "${_version:-0.1.0}" "$_NC" "$_desc"
     else
       printf '  %b[available]%b %b%-15s%b %b(v%s)%b - %s\n' \
         "$_DIM" "$_NC" "$_BOLD" "$_name" "$_NC" "$_DIM" "${_version:-0.1.0}" "$_NC" "$_desc"
@@ -50,7 +53,7 @@ cmd_plugin_info() {
   if yaml_plugin_enabled "$_name"; then
     _status="${_G}enabled${_NC}"
   elif yaml_has_plugin "$_name"; then
-    _status="${_DIM}disabled locally (${WORKSPACE_LOCAL_YAML})${_NC}"
+    _status="${_DIM}disabled in configuration${_NC}"
   else
     _status="${_DIM}available (not enabled)${_NC}"
   fi
@@ -179,24 +182,8 @@ cmd_plugin_disable() {
     log_ok "Plugin '$_name' disabled from workspace"
   fi
 
-  if ! yaml_plugin_enabled "$_name"; then
-    if [ -d "$NEXUS_DIR/.rnex/plugins/$_name" ]; then
-      rm -rf "$NEXUS_DIR/.rnex/plugins/$_name"
-      log_ok "Removed workspace plugin scope: .rnex/plugins/$_name"
-    fi
-
-    yaml_list_repos | while read -r _rname; do
-      _rpath="$(resolve_repo_path "$_rname")"
-      if [ -d "$_rpath/.rnex/plugins/$_name" ]; then
-        rm -rf "$_rpath/.rnex/plugins/$_name"
-      fi
-    done
-  fi
-
-  sync_prompts
-  if [ ! -f "$NEXUS_DIR/AGENTS.md" ]; then
-    merge_rnex_instructions "$NEXUS_DIR/AGENTS.md"
-  fi
+  sync_plugins
+  cmd_fix -q
   log_ok "Plugin '$_name' disabled from workspace"
 }
 

package/lib/commands/status.sh

@@ -64,7 +64,7 @@ cmd_status() {
     true|yes|1)
       if [ "$_gh_active" -eq 1 ]; then
         _active_trigger=""
-        if yaml_has_plugin "karpathy-llm"; then
+        if yaml_plugin_enabled "karpathy-llm"; then
           _active_trigger="$(yaml_plugin_get "karpathy-llm" "lint_trigger")"
         fi
         if [ -n "$_active_trigger" ]; then
@@ -79,7 +79,7 @@ cmd_status() {
     *)
       if [ "$_gh_active" -eq 1 ]; then
         _active_trigger=""
-        if yaml_has_plugin "karpathy-llm"; then
+        if yaml_plugin_enabled "karpathy-llm"; then
           _active_trigger="$(yaml_plugin_get "karpathy-llm" "lint_trigger")"
         fi
         if [ -n "$_active_trigger" ]; then

package/lib/hooks.sh

@@ -138,16 +138,16 @@ cmd_hooks() {
       done
 
       _active_trigger=""
-      if yaml_has_plugin "karpathy-llm"; then
+      if yaml_plugin_enabled "karpathy-llm"; then
         _active_trigger="$(yaml_plugin_get "karpathy-llm" "lint_trigger")"
+        printf '\n%bActive Plugin Triggers:%b\n' "$_BOLD" "$_NC"
+        if [ -n "$_active_trigger" ]; then
+          printf '  %b●%b karpathy-llm: %s\n' "$_G" "$_NC" "$_active_trigger"
+        else
+          printf '  %b○%b karpathy-llm: (manual only / no trigger set in rnex.yaml)\n' "$_DIM" "$_NC"
+        fi
+        printf '\n'
       fi
-      printf '\n%bActive Plugin Triggers:%b\n' "$_BOLD" "$_NC"
-      if [ -n "$_active_trigger" ]; then
-        printf '  %b●%b karpathy-llm: %s\n' "$_G" "$_NC" "$_active_trigger"
-      else
-        printf '  %b○%b karpathy-llm: (manual only / no trigger set in rnex.yaml)\n' "$_DIM" "$_NC"
-      fi
-      printf '\n'
       ;;
     run)
       shift
@@ -158,7 +158,7 @@ cmd_hooks() {
       case "$_hook_name" in
         post-merge)
           cmd_fix -y --quiet || true
-          if yaml_has_plugin "karpathy-llm"; then
+          if yaml_plugin_enabled "karpathy-llm"; then
             _trigger="$(yaml_plugin_get "karpathy-llm" "lint_trigger")"
             if [ "$_trigger" = "git-post-merge" ] || [ "$_trigger" = "post-merge" ]; then
               _wiki_dir="$(karpathy_wiki_dir)"
@@ -175,7 +175,7 @@ cmd_hooks() {
           return 0
           ;;
         post-commit)
-          if yaml_has_plugin "karpathy-llm"; then
+          if yaml_plugin_enabled "karpathy-llm"; then
             _trigger="$(yaml_plugin_get "karpathy-llm" "lint_trigger")"
             if [ "$_trigger" = "git-post-commit" ] || [ "$_trigger" = "post-commit" ]; then
               _wiki_dir="$(karpathy_wiki_dir)"
@@ -193,7 +193,7 @@ cmd_hooks() {
           return 0
           ;;
         pre-commit)
-          if yaml_has_plugin "karpathy-llm"; then
+          if yaml_plugin_enabled "karpathy-llm"; then
             _trigger="$(yaml_plugin_get "karpathy-llm" "lint_trigger")"
             if [ "$_trigger" = "git-pre-commit" ] || [ "$_trigger" = "pre-commit" ]; then
               _wiki_dir="$(karpathy_wiki_dir)"
@@ -211,7 +211,7 @@ cmd_hooks() {
           return 0
           ;;
         pre-push)
-          if yaml_has_plugin "karpathy-llm"; then
+          if yaml_plugin_enabled "karpathy-llm"; then
             _trigger="$(yaml_plugin_get "karpathy-llm" "lint_trigger")"
             if [ "$_trigger" = "git-pre-push" ] || [ "$_trigger" = "pre-push" ]; then
               _wiki_dir="$(karpathy_wiki_dir)"

package/lib/plugins.sh

@@ -115,8 +115,24 @@ sync_plugins() {
   _wiki_dir="$(karpathy_wiki_dir)"
   _raw_dir="$(karpathy_raw_dir)"
 
+  # 1. Prune plugins that are disabled or no longer enabled in config
+  if [ -d "$NEXUS_DIR/.rnex/plugins" ]; then
+    for _existing in "$NEXUS_DIR/.rnex/plugins"/*; do
+      [ -d "$_existing" ] || continue
+      _pname="$(basename "$_existing")"
+      if ! yaml_plugin_enabled "$_pname"; then
+        clean_plugin_prompts_across_providers "$_existing"
+        rm -rf "$_existing"
+        log_ok "Removed disabled plugin scope: .rnex/plugins/$_pname"
+      fi
+    done
+    rmdir "$NEXUS_DIR/.rnex/plugins" 2>/dev/null || true
+  fi
+
+  # 2. Sync enabled plugins
   yaml_list_plugins | while read -r _pname; do
     [ -n "$_pname" ] || continue
+    yaml_plugin_enabled "$_pname" || continue
     _pdir="$(find_plugin_dir "$_pname" 2>/dev/null || true)"
     if [ -z "$_pdir" ]; then
       log_warn "Plugin '$_pname' declared in config but not found on disk"

package/lib/repos.sh

@@ -86,17 +86,31 @@ EOF
     log_ok "Initialized .rnex in $(basename "$_repo_path")"
   fi
 
+  # Prune disabled plugins from member repo
+  if [ -d "$_r_rnex/plugins" ]; then
+    for _existing in "$_r_rnex/plugins"/*; do
+      [ -d "$_existing" ] || continue
+      _pname="$(basename "$_existing")"
+      if ! yaml_plugin_enabled "$_pname"; then
+        rm -rf "$_existing"
+      fi
+    done
+    rmdir "$_r_rnex/plugins" 2>/dev/null || true
+  fi
+
   # Sync scoped active plugins into member repo under .rnex/plugins/<plugin-name>/
   yaml_list_plugins | while read -r _pname; do
     [ -n "$_pname" ] || continue
+    yaml_plugin_enabled "$_pname" || continue
     _pdir="$(find_plugin_dir "$_pname" 2>/dev/null || true)"
     [ -n "$_pdir" ] || continue
 
     _dest_pdir="$_r_rnex/plugins/$_pname"
     mkdir -p "$_dest_pdir"
 
-    # Deterministically sync plugin asset directories into member repo
-    for _sub in rules workflows instructions prompts skills agents templates; do
+    # Deterministically sync plugin asset directories into member repo (no prompts in plugins)
+    rm -rf "${_dest_pdir:?}/prompts" 2>/dev/null || true
+    for _sub in rules workflows instructions skills agents templates; do
       if [ -d "$_pdir/$_sub" ]; then
         rm -rf "${_dest_pdir:?}/$_sub"
         mkdir -p "$_dest_pdir/$_sub"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.6.3",
+  "version": "0.6.5",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",