repo-nexus 0.7.22 → 0.7.24

package/docs/CLI.md

@@ -37,11 +37,11 @@ rnex sync [-y|--yes] [-q|--quiet]
 2. **Git Ignore & Search Indexing**: Reconciles `.gitignore` (ignoring `repos/*` and `.local.rnex.yaml`) and `.ignore` (un-ignoring `repos/*` for search tools).
 3. **Plugin Sync**: Prunes disabled plugins and deterministically copies enabled plugin assets, rules, skills, templates, and executable lifecycle hooks into `.rnex/plugins/<plugin-name>/`.
 4. **Compiled AI Instructions**: Compiles `.rnex/ai-instructions.md` by combining the base template with active configuration and all enabled plugin `instructions.md` fragments. Top-level provider files (`AGENTS.md`, `CLAUDE.md`, etc.) receive only a single strict directive pointing to `.rnex/ai-instructions.md`.
-5. **Skill Reconciliation & User Skill Generation**: Copies core agentic skills from `toolkit/skills/` to `.rnex/skills/`, and generates lightweight, zero-logic User Skills (prefixed with `rnex-`) in configured AI assistant directories (`.cursor/rules/`, `.claude/skills/`, `.gemini/skills/`, `.windsurf/rules/`) pointing directly to `.rnex/skills/` or plugin skill directories.
+5. **Skill Reconciliation & User Skill Generation**: Copies core agentic skills from `toolkit/skills/` to `.rnex/skills/`, and generates lightweight, zero-logic User Skills (prefixed with `rnex-`) in configured AI assistant directories (`.cursor/rules/`, `.claude/skills/`, `.agents/skills/`, `.windsurf/rules/`) pointing directly to `.rnex/skills/` or plugin skill directories.
 6. **Harness Sync**: Reconciles root `.rnex/` and member repository harnesses (`repos/<name>/.rnex/`) for all enabled member repositories where `rnex_dir: true`.
 7. **Git Hooks**: Installs or reconciles workspace Git hooks in `.rnex/hooks` when `git_hooks: true`.
 8. **Multi-Root Workspace**: Synchronizes `.code-workspace` folder mappings when `code_workspace: true`.
-9. **Event-Driven Auto-Sync Scripts & Stamp**: Generates `.rnex/bin/auto-sync.sh` and updates `.rnex/.sync_stamp`.
+9. **Event-Driven Auto-Sync Scripts & Stamp**: Generates `.rnex/bin/auto-sync.sh` and updates `.rnex/sync_stamp`.
 
 ---
 

package/docs/cli/workspace.md

@@ -28,7 +28,7 @@ rnex init [options] [directory]
 | `--no-hooks` | | boolean | `false` | Skip Git hooks configuration during initialization. |
 | `--claude` | | boolean | `false` | Enable Claude Code plugin (maintains `CLAUDE.md`, generates skills in `.claude/skills/`). |
 | `--cursor` | | boolean | `false` | Enable Cursor plugin (maintains `.cursorrules`, generates skills in `.cursor/rules/`). |
-| `--gemini` | | boolean | `false` | Enable Google Gemini plugin (maintains `GEMINI.md`, generates skills in `.gemini/skills/`). |
+| `--gemini` | | boolean | `false` | Enable Google Gemini plugin (maintains `GEMINI.md`, generates skills in `.agents/skills/`). |
 | `--windsurf` | | boolean | `false` | Enable Windsurf plugin (maintains `.windsurfrules`, generates skills in `.windsurf/rules/`). |
 
 ### Examples
@@ -71,7 +71,7 @@ rnex sync [options]
 7. Reconciles automated Git hooks in `.rnex/hooks/` against `git_hooks` config.
 8. Re-creates member `.rnex/` scaffolding in active repositories (`rnex_dir: true`).
 9. Updates multi-root `.code-workspace` folder mappings if configured.
-10. Generates `.rnex/bin/auto-sync.sh` and updates the checksum stamp in `.rnex/.sync_stamp`.
+10. Generates `.rnex/bin/auto-sync.sh` and updates the checksum stamp in `.rnex/sync_stamp`.
 
 ---
 
@@ -86,7 +86,7 @@ rnex status
 
 ### Execution
 * **Strictly Read-Only**: Inspects workspace health, active repos, loaded config files (`rnex.yaml` and `.local.rnex.yaml`), git hooks, and plugins.
-* **Sync Diagnostics**: Compares current config checksums against `.rnex/.sync_stamp` and suggests running `rnex sync` if configuration drift is detected.
+* **Sync Diagnostics**: Compares current config checksums against `.rnex/sync_stamp` and suggests running `rnex sync` if configuration drift is detected.
 
 ---
 

package/docs/examples/ai-workflows.md

@@ -23,7 +23,7 @@ When a workspace is initialized, Repo Nexus maintains core agentic skills in `.r
 | `wiki-ingest` | Plugin (`karpathy-llm`) | Ingest raw intake documents into atomic Karpathy LLM Wiki pages. | `.rnex/plugins/karpathy-llm/skills/wiki-ingest.md` |
 | `wiki-lint` | Plugin (`karpathy-llm`) | Validate markdown links, compute backlinks, and update the master index. | `.rnex/plugins/karpathy-llm/skills/wiki-lint.md` |
 
-When provider plugins (such as `claude`, `gemini`, `cursor`, or `windsurf`) are enabled with `skills: true`, zero-logic User Skill pointers (`rnex-<skill-name>.md`) are generated directly into the respective native provider directories (`.cursor/rules/`, `.claude/skills/`, `.gemini/skills/`, `.windsurf/rules/`).
+When provider plugins (such as `claude`, `gemini`, `cursor`, or `windsurf`) are enabled with `skills: true`, zero-logic User Skill pointers (`rnex-<skill-name>.md`) are generated directly into the respective native provider directories (`.cursor/rules/`, `.claude/skills/`, `.agents/skills/`, `.windsurf/rules/`).
 
 ---
 

package/docs/guide/configuration.md

@@ -126,5 +126,5 @@ rnex sync
 ```
 
 ::: tip Status & Auto-Sync
-Running `rnex status` inspects workspace health and checks if configuration is in sync with `.rnex/.sync_stamp`. Running `rnex sync` applies full reconciliation and updates the sync stamp. Workspace commands (like `rnex list`) also automatically trigger auto-sync whenever configuration changes.
+Running `rnex status` inspects workspace health and checks if configuration is in sync with `.rnex/sync_stamp`. Running `rnex sync` applies full reconciliation and updates the sync stamp. Workspace commands (like `rnex list`) also automatically trigger auto-sync whenever configuration changes.
 :::

package/docs/plugins/gemini.md

@@ -1,13 +1,13 @@
 ---
 title: Google Gemini & Antigravity Plugin
-description: Integrate Google Gemini and Antigravity IDE with Repo Nexus, generating zero-logic user skill pointers in .gemini/skills/.
+description: Integrate Google Gemini and Antigravity IDE with Repo Nexus, generating zero-logic user skill pointers in .agents/skills/.
 ---
 
 # Google Gemini & Antigravity Plugin
 
 The **`gemini`** plugin integrates Google Gemini CLI and Google Antigravity IDE into a Repo Nexus Virtual Meta-Repo.
 
-All AI assistants in Repo Nexus share [`AGENTS.md`](file:///Users/admin/Projects/ai/repo-nexus/AGENTS.md) at the workspace root as the single universal source of truth for routing. When enabled, the `gemini` plugin generates zero-logic User Skill pointers into `.gemini/skills/` (e.g. `rnex-clone-sync.md`, `rnex-batch-exec.md`, `rnex-karpathy-llm-wiki-ingest`).
+All AI assistants in Repo Nexus share [`AGENTS.md`](file:///Users/admin/Projects/ai/repo-nexus/AGENTS.md) at the workspace root as the single universal source of truth for routing. When enabled, the `gemini` plugin generates zero-logic User Skill pointers into `.agents/skills/` (e.g. `rnex-clone-sync/SKILL.md`, `rnex-batch-exec/SKILL.md`, `rnex-karpathy-llm-wiki-ingest/SKILL.md`).
 
 Operational skills, rules, and subagents remain cleanly encapsulated within `.rnex/skills/` and active plugin directories (`.rnex/plugins/<plugin-name>/`).
 
@@ -15,8 +15,8 @@ Operational skills, rules, and subagents remain cleanly encapsulated within `.rn
 
 ## Capabilities
 
-1. **Zero-Logic User Skills (`.gemini/skills/rnex-*/SKILL.md`)**:
-   - Generates native `SKILL.md` bundles prefixed with `rnex-` in `.gemini/skills/` with YAML frontmatter for Gemini and Antigravity skill discovery.
+1. **Zero-Logic User Skills (`.agents/skills/rnex-*/SKILL.md`)**:
+   - Generates native `SKILL.md` bundles prefixed with `rnex-` in `.agents/skills/` with YAML frontmatter for Gemini and Antigravity skill discovery.
    - Contains zero inline heuristics—redirects Gemini/Antigravity directly to the underlying agentic skill protocols inside `.rnex/`.
 
 2. **Native Instructions Support via `GEMINI.md`**:
@@ -58,14 +58,14 @@ Configure options under `plugins.gemini` in `rnex.yaml` or `.local.rnex.yaml`:
 plugins:
   gemini:
     instructions: true   # Sync routing instructions to GEMINI.md (default: true)
-    skills: true         # Generate user skills in .gemini/skills/ (default: true)
+    skills: true         # Generate user skills in .agents/skills/ (default: true)
     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 `.gemini/skills/rnex-*.md`. |
+| `skills` | boolean | `true` | Generate user skill pointers in `.agents/skills/rnex-*/SKILL.md`. |
 | `enabled` | boolean | `true` | Enable or disable the plugin. Overridable in `.local.rnex.yaml`. |
 
 ---
@@ -76,15 +76,19 @@ When `gemini` is enabled with functional plugins like `karpathy-llm`, it generat
 
 ```text
 my-workspace/
-├── AGENTS.md                          # Universal workspace instructions & routing
 ├── GEMINI.md                          # Gemini-specific instructions (if instructions: true)
-├── .gemini/
+├── .agents/
 │   └── skills/                        # Zero-logic User Skill pointers
-│       ├── rnex-clone-sync.md
-│       ├── rnex-batch-exec.md
-│       ├── rnex-workspace-status.md
+│       ├── rnex-clone-sync/
+│       │   └── SKILL.md
+│       ├── rnex-batch-exec/
+│       │   └── SKILL.md
+│       ├── rnex-workspace-status/
+│       │   └── SKILL.md
 │       ├── rnex-karpathy-llm-wiki-ingest/
+│       │   └── SKILL.md
 │       └── rnex-karpathy-llm-wiki-lint/
+│           └── SKILL.md
 ├── .rnex/
 │   ├── skills/                        # Core workspace agentic skills
 │   └── plugins/
@@ -103,6 +107,6 @@ rnex plugin disable gemini
 ```
 
 Repo Nexus automatically performs surgical cleanup:
-- Removes auto-generated user skills under `.gemini/skills/rnex-*.md`.
+- Removes auto-generated user skills under `.agents/skills/rnex-*`.
 - Cleans up managed routing instructions in `GEMINI.md`.
-- Developer-created files under `.gemini/` that do not originate from Repo Nexus are preserved.
+- Developer-created files under `.agents/` or `.gemini/` that do not originate from Repo Nexus are preserved.

package/docs/plugins/index.md

@@ -23,7 +23,7 @@ Active plugins are mirrored into each active member repository under `repos/<nam
 Repo Nexus decouples functional plugins from AI provider plugins:
 - **Core Skills (`toolkit/skills/` $\rightarrow$ `.rnex/skills/`)**: Workspace-level capabilities owned by Repo Nexus core.
 - **Plugin Skills (`toolkit/plugins/<plugin>/skills/` $\rightarrow$ `.rnex/plugins/<plugin>/skills/`)**: Scoped domain skills owned exclusively by individual plugins.
-- **User Skills**: Provider plugins (`copilot`, `claude`, `gemini`, `cursor`, and `windsurf`) project zero-logic user skill pointers into active provider directories using native `SKILL.md` bundles with YAML frontmatter in skill directories (`.github/skills/`, `.claude/skills/`, `.gemini/skills/`) and flat files in rule directories (`.cursor/rules/`, `.windsurf/rules/`), redirecting AI assistants directly to the underlying agentic skills in `.rnex/`.
+- **User Skills**: Provider plugins (`copilot`, `claude`, `gemini`, `cursor`, and `windsurf`) project zero-logic user skill pointers into active provider directories using native `SKILL.md` bundles with YAML frontmatter in skill directories (`.github/skills/`, `.claude/skills/`, `.agents/skills/`) and flat files in rule directories (`.cursor/rules/`, `.windsurf/rules/`), redirecting AI assistants directly to the underlying agentic skills in `.rnex/`.
 
 ### 4. Non-Destructive Delimited Merging
 When plugins update root instruction files (`AGENTS.md`, `CLAUDE.md`, `GEMINI.md`, `.cursorrules`, `.windsurfrules`), Repo Nexus isolates auto-managed routing between explicit delimiters:
@@ -48,7 +48,7 @@ Developer-authored instructions outside of these delimiters are strictly preserv
 |:---|:---|:---|:---|
 | [`claude`](claude.md) | AI Provider | Anthropic Claude Code & Desktop integration: maintains `CLAUDE.md` and generates user skills in `.claude/skills/`. | [Read Guide](claude.md) |
 | [`cursor`](cursor.md) | AI Provider | Cursor IDE integration: maintains `.cursorrules`, `.cursorignore`, and generates user skills in `.cursor/rules/`. | [Read Guide](cursor.md) |
-| [`gemini`](gemini.md) | AI Provider | Google Gemini CLI & Antigravity IDE integration: maintains `GEMINI.md`, `.geminiignore`, and generates user skills in `.gemini/skills/`. | [Read Guide](gemini.md) |
+| [`gemini`](gemini.md) | AI Provider | Google Gemini CLI & Antigravity IDE integration: maintains `GEMINI.md`, `.geminiignore`, and generates user skills in `.agents/skills/`. | [Read Guide](gemini.md) |
 | [`windsurf`](windsurf.md) | AI Provider | Windsurf IDE integration: maintains `.windsurfrules` and generates user skills in `.windsurf/rules/`. | [Read Guide](windsurf.md) |
 | [`karpathy-llm`](karpathy-llm.md) | Knowledge & Rules | Andrej Karpathy's 4 cardinal principles for coding agents, multi-repo context engineering standards, and autonomous zero-dependency LLM Wiki architecture (`./docs`, `.rnex/wiki`). | [Read Guide](karpathy-llm.md) |
 

package/docs/plugins/karpathy-llm.md

@@ -169,7 +169,7 @@ The `karpathy-llm` plugin encapsulates its agentic skills in `.rnex/plugins/karp
 - `wiki-ingest.md`
 - `wiki-lint.md`
 
-During `rnex sync`, its `after_sync.sh` lifecycle hook automatically registers zero-logic User Skill pointers (`rnex-karpathy-llm-wiki-ingest` and `rnex-karpathy-llm-wiki-lint`) across all enabled AI provider directories (`.cursor/rules/`, `.claude/skills/`, `.gemini/skills/`, `.windsurf/rules/`).
+During `rnex sync`, its `after_sync.sh` lifecycle hook automatically registers zero-logic User Skill pointers (`rnex-karpathy-llm-wiki-ingest` and `rnex-karpathy-llm-wiki-lint`) across all enabled AI provider directories (`.cursor/rules/`, `.claude/skills/`, `.agents/skills/`, `.windsurf/rules/`).
 
 When running `rnex plugin disable karpathy-llm`, its `before_plugin_disable.sh` lifecycle hook automatically unregisters the User Skills from all provider directories, while keeping core workspace skills intact.
 

package/docs/rnex.example.yaml

@@ -74,7 +74,7 @@ git_hooks: true
 #
 # Built-in plugins:
 #   claude         — Anthropic Claude Code integration: manages CLAUDE.md; generates user skills in .claude/skills/
-#   gemini         — Google Gemini / Antigravity integration: manages GEMINI.md; generates user skills in .gemini/skills/
+#   gemini         — Google Gemini / Antigravity integration: manages GEMINI.md; generates user skills in .agents/skills/
 #   cursor         — Cursor IDE integration: manages .cursorrules & .cursor/rules/; generates user skills in .cursor/rules/
 #   windsurf       — Windsurf IDE integration: manages .windsurfrules; generates user skills in .windsurf/rules/
 #   karpathy-llm   — Andrej Karpathy's agent behavioral principles,
@@ -95,7 +95,7 @@ plugins:
   #   skills: true         # generate user skills in .claude/skills/ (default: true)
   # gemini:
   #   instructions: true   # sync routing instructions to GEMINI.md (default: true)
-  #   skills: true         # generate user skills in .gemini/skills/ (default: true)
+  #   skills: true         # generate user skills in .agents/skills/ (default: true)
   # cursor:
   #   instructions: true   # sync routing instructions to .cursorrules (default: true)
   #   skills: true         # generate user skills in .cursor/rules/ (default: true)

package/lib/ai.sh

@@ -405,7 +405,7 @@ get_active_provider_skill_dirs() {
           cursor)   _sdir=".cursor/rules" ;;
           claude)   _sdir=".claude/skills" ;;
           windsurf) _sdir=".windsurf/rules" ;;
-          gemini)   _sdir=".gemini/skills" ;;
+          gemini)   _sdir=".agents/skills" ;;
         esac
       fi
       if [ -n "$_sdir" ]; then

package/lib/commands/init.sh

@@ -162,8 +162,18 @@ YAML_EOF
     log_ok "Created $RNEX_CONFIG_FILE"
   fi
 
+  # Set active workspace context for initialization
+  _orig_nexus="$NEXUS_DIR"
+  _orig_yaml="$WORKSPACE_YAML"
+  _orig_local_yaml="$WORKSPACE_LOCAL_YAML"
+  NEXUS_DIR="$_init_dir"
+  WORKSPACE_YAML="$_target_yaml"
+  WORKSPACE_LOCAL_YAML="$_init_dir/$RNEX_LOCAL_CONFIG_FILE"
+
   # ---- 2. Merge routing instructions into AI instructions files ------------
-  merge_rnex_instructions "$_init_dir/AGENTS.md"
+  if ! has_active_provider_instructions "$_init_dir"; then
+    merge_rnex_instructions "$_init_dir/AGENTS.md"
+  fi
   [ -f "$_init_dir/CLAUDE.md" ] && merge_rnex_instructions "$_init_dir/CLAUDE.md"
   [ -f "$_init_dir/GEMINI.md" ] && merge_rnex_instructions "$_init_dir/GEMINI.md"
   [ -f "$_init_dir/.cursorrules" ] && merge_rnex_instructions "$_init_dir/.cursorrules"
@@ -178,12 +188,6 @@ YAML_EOF
   # ---- 4. Create internal .rnex directory and sync base assets -------------
   mkdir -p "$_init_dir/.rnex"
   mkdir -p "$_init_dir/.rnex/plugins"
-  _orig_nexus="$NEXUS_DIR"
-  _orig_yaml="$WORKSPACE_YAML"
-  _orig_local_yaml="$WORKSPACE_LOCAL_YAML"
-  NEXUS_DIR="$_init_dir"
-  WORKSPACE_YAML="$_target_yaml"
-  WORKSPACE_LOCAL_YAML="$_init_dir/$RNEX_LOCAL_CONFIG_FILE"
   sync_plugins
   build_ai_instructions "$_init_dir"
   sync_skills

package/lib/commands/plugin.sh

@@ -70,7 +70,7 @@ cmd_plugin_info() {
   [ -z "$_skill_target" ] && case "$_name" in
     copilot)  _skill_target=".github/skills/" ;;
     claude)   _skill_target=".claude/skills/" ;;
-    gemini)   _skill_target=".gemini/skills/" ;;
+    gemini)   _skill_target=".agents/skills/" ;;
     cursor)   _skill_target=".cursor/rules/" ;;
     windsurf) _skill_target=".windsurf/rules/" ;;
   esac

package/lib/commands/status.sh

@@ -50,8 +50,8 @@ cmd_status() {
     printf '  %b●%b Workspace:   %s\n' "$_DIM" "$_NC" "$CODE_WORKSPACE_FILE"
   fi
 
-  _stamp_file="$NEXUS_DIR/.rnex/.sync_stamp"
-  [ -f "$_stamp_file" ] || _stamp_file="$NEXUS_DIR/.rnex/sync_stamp"
+  _stamp_file="$NEXUS_DIR/.rnex/sync_stamp"
+  [ -f "$_stamp_file" ] || _stamp_file="$NEXUS_DIR/.rnex/.sync_stamp"
   _cur_sum="$(get_config_sum "$NEXUS_DIR")"
   if [ ! -f "$_stamp_file" ] || [ "$_cur_sum" != "$(cat "$_stamp_file" 2>/dev/null)" ]; then
     printf '  %b!%b Sync Stamp:    workspace out of sync with configuration (run "rnex sync")\n' "$_Y" "$_NC"
@@ -142,7 +142,7 @@ cmd_status() {
   fi
   if [ -f "$NEXUS_DIR/AGENTS.md" ]; then
     printf '  %b✓%b %s %b(standard instructions directive)%b\n' "$_G" "$_NC" "AGENTS.md" "$_DIM" "$_NC"
-  else
+  elif ! has_active_provider_instructions "$NEXUS_DIR"; then
     printf '  %b✗%b %s %b(standard instructions directive — MISSING; run "rnex sync" to create)%b\n' "$_R" "$_NC" "AGENTS.md" "$_R" "$_NC"
   fi
   if [ -f "$NEXUS_DIR/CLAUDE.md" ]; then
@@ -187,7 +187,9 @@ cmd_status() {
   if [ -d "$NEXUS_DIR/.windsurf/rules" ] && ls "$NEXUS_DIR/.windsurf/rules"/rnex-*.md >/dev/null 2>&1; then
     printf '  %b✓%b %s %b(Windsurf user skills)%b\n' "$_G" "$_NC" ".windsurf/rules/" "$_DIM" "$_NC"
   fi
-  if [ -d "$NEXUS_DIR/.gemini/skills" ] && { ls "$NEXUS_DIR/.gemini/skills"/rnex-*.md >/dev/null 2>&1 || ls -d "$NEXUS_DIR/.gemini/skills"/rnex-* >/dev/null 2>&1; }; then
+  if [ -d "$NEXUS_DIR/.agents/skills" ] && { ls "$NEXUS_DIR/.agents/skills"/rnex-*.md >/dev/null 2>&1 || ls -d "$NEXUS_DIR/.agents/skills"/rnex-* >/dev/null 2>&1; }; then
+    printf '  %b✓%b %s %b(Gemini user skills)%b\n' "$_G" "$_NC" ".agents/skills/" "$_DIM" "$_NC"
+  elif [ -d "$NEXUS_DIR/.gemini/skills" ] && { ls "$NEXUS_DIR/.gemini/skills"/rnex-*.md >/dev/null 2>&1 || ls -d "$NEXUS_DIR/.gemini/skills"/rnex-* >/dev/null 2>&1; }; then
     printf '  %b✓%b %s %b(Gemini user skills)%b\n' "$_G" "$_NC" ".gemini/skills/" "$_DIM" "$_NC"
   fi
   if [ -d "$NEXUS_DIR/.github/skills" ] && { ls "$NEXUS_DIR/.github/skills"/rnex-*.md >/dev/null 2>&1 || ls -d "$NEXUS_DIR/.github/skills"/rnex-* >/dev/null 2>&1; }; then

package/lib/commands/sync.sh

@@ -15,8 +15,8 @@ set -e
 _ws="$(cd "$(dirname "$0")/../.." 2>/dev/null && pwd -P)"
 [ -f "$_ws/rnex.yaml" ] || exit 0
 
-_stamp="$_ws/.rnex/.sync_stamp"
-[ -f "$_stamp" ] || _stamp="$_ws/.rnex/sync_stamp"
+_stamp="$_ws/.rnex/sync_stamp"
+[ -f "$_stamp" ] || _stamp="$_ws/.rnex/.sync_stamp"
 _cur_sum="$(cd "$_ws" 2>/dev/null && cksum rnex.yaml .local.rnex.yaml 2>/dev/null | cksum | awk '{print $1, $2}')"
 _saved_sum=""
 [ -f "$_stamp" ] && _saved_sum="$(cat "$_stamp" 2>/dev/null)"
@@ -78,7 +78,11 @@ cmd_sync() {
   reconcile_gitignore "$NEXUS_DIR"
 
   # 1.2. Reconcile universal workspace instructions in AGENTS.md
-  merge_rnex_instructions "$NEXUS_DIR/AGENTS.md"
+  if has_active_provider_instructions; then
+    clean_rnex_instructions "$NEXUS_DIR/AGENTS.md"
+  else
+    merge_rnex_instructions "$NEXUS_DIR/AGENTS.md"
+  fi
 
   # 1.3. Generate auto-sync script and AI session-start hooks (hardcoded harness)
   _write_auto_sync_script "$NEXUS_DIR"
@@ -93,7 +97,7 @@ cmd_sync() {
   # 2.1. Compile .rnex/ai-instructions.md
   build_ai_instructions "$NEXUS_DIR"
 
-  # 2.2. Update sync stamp (.rnex/.sync_stamp and .rnex/sync_stamp)
+  # 2.2. Update sync stamp (.rnex/sync_stamp)
   update_sync_stamp "$NEXUS_DIR"
 
   # --------------------------------------------------------------------------

package/lib/workspace.sh

@@ -52,8 +52,8 @@ update_sync_stamp() {
     fi
   fi
   _csum="$(get_config_sum "$_dir")"
-  printf '%s\n' "$_csum" > "$_dir/.rnex/.sync_stamp"
   printf '%s\n' "$_csum" > "$_dir/.rnex/sync_stamp"
+  rm -f "$_dir/.rnex/.sync_stamp"
 }
 
 check_auto_sync() {
@@ -76,8 +76,8 @@ check_auto_sync() {
     _cfg_file="$(resolve_path "$CUSTOM_CONFIG" 2>/dev/null || true)"
   fi
   [ -f "$_cfg_file" ] || return 0
-  _stamp="$_ws/.rnex/.sync_stamp"
-  [ -f "$_stamp" ] || _stamp="$_ws/.rnex/sync_stamp"
+  _stamp="$_ws/.rnex/sync_stamp"
+  [ -f "$_stamp" ] || _stamp="$_ws/.rnex/.sync_stamp"
   if [ ! -f "$_stamp" ] || [ "$(get_config_sum "$_ws")" != "$(cat "$_stamp" 2>/dev/null)" ]; then
     cmd_sync -y --quiet
   fi

package/lib/yaml.sh

@@ -177,6 +177,29 @@ windsurf_plugin_enabled() { provider_plugin_enabled "windsurf"; }
 windsurf_instructions_enabled() { provider_option_enabled "windsurf" "instructions"; }
 windsurf_skills_enabled() { provider_option_enabled "windsurf" "skills"; }
 
+has_active_provider_instructions() {
+  _dir="${1:-${NEXUS_DIR:-$PWD}}"
+  _saved_ws_yaml="${WORKSPACE_YAML:-}"
+  _saved_local_yaml="${WORKSPACE_LOCAL_YAML:-}"
+  if [ -n "$1" ] && [ -d "$1" ]; then
+    WORKSPACE_YAML="$1/rnex.yaml"
+    WORKSPACE_LOCAL_YAML="$1/.local.rnex.yaml"
+  fi
+  _res=1
+  if copilot_instructions_enabled || \
+     claude_instructions_enabled || \
+     gemini_instructions_enabled || \
+     cursor_instructions_enabled || \
+     windsurf_instructions_enabled; then
+    _res=0
+  fi
+  if [ -n "$1" ] && [ -d "$1" ]; then
+    WORKSPACE_YAML="$_saved_ws_yaml"
+    WORKSPACE_LOCAL_YAML="$_saved_local_yaml"
+  fi
+  return $_res
+}
+
 _yaml_plugin_set_in_file() {
   _file="$1"; _plugin="$2"; _field="$3"; _value="$4"
   if [ ! -f "$_file" ]; then

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.7.22",
+  "version": "0.7.24",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",

package/templates/rnex-env.sh

@@ -8,7 +8,8 @@ if [ -z "$RNEX_PROVIDER_SKILL_DIRS" ]; then
   [ -d "$RNEX_ROOT/.cursor" ] && _dirs="${_dirs:+$_dirs }.cursor/rules"
   [ -d "$RNEX_ROOT/.claude" ] && _dirs="${_dirs:+$_dirs }.claude/skills"
   [ -d "$RNEX_ROOT/.windsurf" ] && _dirs="${_dirs:+$_dirs }.windsurf/rules"
-  [ -d "$RNEX_ROOT/.gemini" ] && _dirs="${_dirs:+$_dirs }.gemini/skills"
+  [ -d "$RNEX_ROOT/.agents" ] && _dirs="${_dirs:+$_dirs }.agents/skills"
+  [ -d "$RNEX_ROOT/.gemini" ] && _dirs="${_dirs:+$_dirs }.agents/skills"
   export RNEX_PROVIDER_SKILL_DIRS="$_dirs"
 fi
 
@@ -148,6 +149,17 @@ if ! command -v provider_option_enabled >/dev/null 2>&1; then
   }
 fi
 
+if ! command -v has_active_provider_instructions >/dev/null 2>&1; then
+  has_active_provider_instructions() {
+    provider_option_enabled "copilot" "instructions" 2>/dev/null && return 0
+    provider_option_enabled "claude" "instructions" 2>/dev/null && return 0
+    provider_option_enabled "gemini" "instructions" 2>/dev/null && return 0
+    provider_option_enabled "cursor" "instructions" 2>/dev/null && return 0
+    provider_option_enabled "windsurf" "instructions" 2>/dev/null && return 0
+    return 1
+  }
+fi
+
 # Instructions routing helpers
 if ! command -v merge_rnex_instructions >/dev/null 2>&1; then
   merge_rnex_instructions() {

package/templates/rnex.example.yaml

@@ -74,7 +74,7 @@ git_hooks: true
 #
 # Built-in plugins:
 #   claude         — Anthropic Claude Code integration: manages CLAUDE.md; generates user skills in .claude/skills/
-#   gemini         — Google Gemini / Antigravity integration: manages GEMINI.md; generates user skills in .gemini/skills/
+#   gemini         — Google Gemini / Antigravity integration: manages GEMINI.md; generates user skills in .agents/skills/
 #   cursor         — Cursor IDE integration: manages .cursorrules & .cursor/rules/; generates user skills in .cursor/rules/
 #   windsurf       — Windsurf IDE integration: manages .windsurfrules; generates user skills in .windsurf/rules/
 #   karpathy-llm   — Andrej Karpathy's agent behavioral principles,
@@ -95,7 +95,7 @@ plugins:
   #   skills: true         # generate user skills in .claude/skills/ (default: true)
   # gemini:
   #   instructions: true   # sync routing instructions to GEMINI.md (default: true)
-  #   skills: true         # generate user skills in .gemini/skills/ (default: true)
+  #   skills: true         # generate user skills in .agents/skills/ (default: true)
   # cursor:
   #   instructions: true   # sync routing instructions to .cursorrules (default: true)
   #   skills: true         # generate user skills in .cursor/rules/ (default: true)

package/toolkit/plugins/gemini/README.md

@@ -5,7 +5,7 @@ A built-in Repo Nexus plugin providing bidirectional alignment and operational p
 ## Capabilities
 
 1. **Instructions Integration**: Generates and maintains `GEMINI.md` with Repo Nexus routing instructions while preserving custom instructions outside delimiters.
-2. **User Skills Generation**: Standardized Repo Nexus core skills and active plugins' skills are mirrored as zero-logic User Skill pointers (`rnex-<name>.md`) in `.gemini/skills/`.
+2. **User Skills Generation**: Standardized Repo Nexus core skills and active plugins' skills are mirrored as zero-logic User Skill pointers (`rnex-<name>.md`) in `.agents/skills/`.
 3. **File Discovery Un-Ignore**: Maintains `.geminiignore` (`!repos/*`) so Gemini CLI and Google Antigravity can discover and access member repository files.
 
 ## Usage
@@ -28,5 +28,5 @@ plugins:
 | Option | Type | Default | Description |
 |--------|------|---------|-------------|
 | `instructions` | boolean | `true` | Maintain routing in `GEMINI.md` |
-| `skills` | boolean | `true` | Generate user skills in `.gemini/skills/` |
+| `skills` | boolean | `true` | Generate user skills in `.agents/skills/` |
 | `enabled` | boolean | `true` | Set to `false` in `.local.rnex.yaml` to override team config |

package/toolkit/plugins/gemini/hooks/after_sync.sh

@@ -29,5 +29,12 @@ fi
 
 _sk="$(provider_option_enabled "gemini" "skills" 2>/dev/null && echo "true" || echo "false")"
 if [ "$_sk" != "true" ]; then
+  clean_provider_user_skills "$_root/.agents/skills"
+fi
+
+# Clean legacy .gemini/skills if it exists
+if [ -d "$_root/.gemini/skills" ]; then
   clean_provider_user_skills "$_root/.gemini/skills"
+  rmdir "$_root/.gemini/skills" 2>/dev/null || true
+  rmdir "$_root/.gemini" 2>/dev/null || true
 fi

package/toolkit/plugins/gemini/hooks/before_plugin_disable.sh

@@ -10,6 +10,8 @@ fi
 
 clean_provider_ignore "$_root/.geminiignore"
 clean_rnex_instructions "$_root/GEMINI.md"
+clean_provider_user_skills "$_root/.agents/skills"
 clean_provider_user_skills "$_root/.gemini/skills"
 rm -rf "$_root/.gemini/prompts" 2>/dev/null || true
 rmdir "$_root/.gemini" 2>/dev/null || true
+rmdir "$_root/.agents" 2>/dev/null || true

package/toolkit/plugins/gemini/instructions/rnex-gemini-integration.md

@@ -4,7 +4,7 @@ This workspace has the Repo Nexus `gemini` plugin enabled.
 
 ## Operating Principles
 - **Gemini Instructions (`GEMINI.md`)**: Synthesizes workspace routing protocol between `<!-- REPO-NEXUS:START -->` and `<!-- REPO-NEXUS:END -->`, preserving any manual user instructions outside those markers. This serves as the primary instructions file for Google Gemini CLI and Google Antigravity.
-- **User Skills (`.gemini/skills/rnex-*.md`)**: Zero-logic user skill pointers linking directly to core skills (`.rnex/skills/`) and active plugins' skills (`.rnex/plugins/<name>/skills/`).
+- **User Skills (`.agents/skills/rnex-*/SKILL.md`)**: Zero-logic user skill pointers linking directly to core skills (`.rnex/skills/`) and active plugins' skills (`.rnex/plugins/<name>/skills/`).
 - **File Discovery Un-Ignore (`.geminiignore`)**: Un-ignores member repositories (`!repos/*`) so Gemini CLI and Google Antigravity can discover and access member repository files, while workspace Git continues to ignore them.
 - **Decoupled Cross-Plugin Discovery**: The `gemini` provider discovers and registers user skills from whatever Repo Nexus plugins are currently active.
 
@@ -15,7 +15,7 @@ Configure plugin options in `rnex.yaml` or override them per developer in `.loca
 plugins:
   gemini:
     instructions: true   # Maintain routing in GEMINI.md (default: true)
-    skills: true         # Generate user skills in .gemini/skills/ (default: true)
+    skills: true         # Generate user skills in .agents/skills/ (default: true)
 ```
 
 To disable locally without altering team configuration, add to `.local.rnex.yaml`:

package/toolkit/plugins/gemini/plugin.yaml

@@ -1,9 +1,9 @@
 name: gemini
 version: 0.5.1
-description: Google Gemini and Antigravity integration (maintains GEMINI.md instructions and generates user skills in .gemini/skills/)
+description: Google Gemini and Antigravity integration (maintains GEMINI.md instructions and generates user skills in .agents/skills/)
 author: unoxen
 homepage: https://github.com/unoxen/repo-nexus
-skill_dir: .gemini/skills
+skill_dir: .agents/skills
 
 config_defaults:
   instructions: true