repo-nexus 0.6.4 → 0.6.6

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/README.md

@@ -12,34 +12,28 @@ A **simple, lightweight Virtual Meta-Repo companion** for multi-repo workspaces
 - **No Git Submodules or Nested Git Collisions**: Member repositories are physically cloned into `./repos/` and strictly ignored by workspace Git. Each repository maintains its own standalone history, remotes, branches, and commits with zero submodule friction.
 - **Unified Workspace for AI Coding Assistants**: Open one root folder to give Cursor, Claude Code, GitHub Copilot, Codex, or Antigravity complete cross-service visibility.
 - **Two-Level Configuration as Source of Truth**: Shared team manifest in `rnex.yaml` with machine-specific overrides in `.local.rnex.yaml` (highest priority).
-- **1-Command Team Onboarding**: Teammates clone the meta-repo and run `rnex clone` to clone and configure all member repos in seconds.
+- **OneCommand Team Onboarding**: Teammates clone the meta-repo and run `rnex clone` to clone and configure all member repos in seconds.
 - **Cross-Repo Batch Operations**: Run arbitrary commands across all active repositories with `rnex exec <command>`.
 - **Scoped Plugins & Context Packs**: Modular plugin packages scoped under `.rnex/plugins/<plugin-name>/` with support for domain directories (e.g. `raw/` and `wiki/` for `karpathy-llm`).
 - **Zero Dependencies**: Pure POSIX shell CLI (`rnex`). Works out of the box across macOS, Linux, and Windows (WSL/Git Bash).
 
-> 💡 **Documentation & Guides:**
-> - Check out the **[Documentation Site](https://unoxen.github.io/repo-nexus/)** or local **[CLI Reference](docs/cli/)** for complete command syntax, flags, Git hooks, plugins, and prompts.
-> - Check out the **[Plugins Guide](docs/plugins/)** for detailed documentation on all built-in AI provider and domain plugins.
-> - Check out the **[Frequently Asked Questions (FAQ)](docs/faq/)** for architecture deep dives, Git workflows, and AI context strategies.
+> 💡 **Documentation:** Full documentation lives on the **[Documentation Site](https://unoxen.github.io/repo-nexus/)** (sources in [`docs/`](docs/)):
+> - **[Architecture](docs/guide/architecture.md)** and **[Why Repo Nexus?](docs/guide/why-repo-nexus.md)** — workspace layout and rationale
+> - **[CLI Reference](docs/cli/)** — all commands, flags, everyday usage, Git hooks, and shell completion
+> - **[Plugins Guide](docs/plugins/)** — built-in AI provider and domain plugins
+> - **[Configuration](docs/guide/configuration.md)** — `rnex.yaml` and `.local.rnex.yaml` schema
+> - **[FAQ](docs/faq/)** — architecture deep dives, Git workflows, and AI context strategies
 
 ---
 
 ## Table of Contents
 
 - [What Repo Nexus Is (and What It Isn't)](#what-repo-nexus-is-and-what-it-isnt)
-- [How It Works: Virtual Meta-Repo Architecture](#how-it-works-virtual-meta-repo-architecture)
 - [Key Principles](#key-principles)
 - [Installation](#installation)
 - [Quick Start](#quick-start)
-- [Everyday Usage](#everyday-usage)
-- [Plugins & Scoped Context Packs](#plugins--scoped-context-packs)
-- [Two-Level Configuration (`rnex.yaml` & `.local.rnex.yaml`)](#two-level-configuration)
-- [CLI Command Reference](#cli-command-reference)
-- [Full CLI Reference Manual (docs/cli/)](docs/cli/)
-- [Shell Auto-Completion](#shell-auto-completion)
 - [Project Structure](#project-structure)
 - [Running Tests](#running-tests)
-- [Frequently Asked Questions (FAQ)](docs/faq/)
 - [License](#license)
 
 ---
@@ -55,34 +49,6 @@ A **simple, lightweight Virtual Meta-Repo companion** for multi-repo workspaces
 
 ---
 
-## How It Works: Virtual Meta-Repo Architecture
-
-```
-┌─────────────────────────────────────────────────────────────┐
-│  Repo Nexus Workspace Root (Virtual Meta-Repo)              │
-│                                                             │
-│  my-workspace/                                              │
-│    .local.rnex.yaml  (Highest Priority: local overrides)    │
-│    rnex.yaml         (Team Manifest: repos & plugins)       │
-│    AGENTS.md         (Routing-only AI agent instructions)   │
-│    .gitignore        (Strictly ignores repos/ & local yaml) │
-│    .rnex/            (Strictly encapsulated internal state) │
-│      plugins/        (Scoped plugin directories)            │
-│        karpathy-llm/ (Isolated rules, workflows, templates) │
-│    repos/            (Autonomous Physical Git Clones)       │
-│      backend/        (Own .git, branches, PRs)              │
-│        .rnex/        (Quarantined member-specific context)  │
-│      frontend/       (Own .git, branches, PRs)              │
-│        .rnex/        (Quarantined member-specific context)  │
-│                                                             │
-│  • Agent opens workspace → reads config first → sees stack. │
-│  • Repos are 100% normal Git clones (zero submodules).      │
-│  • Work across repos seamlessly using rnex exec.            │
-└─────────────────────────────────────────────────────────────┘
-```
-
----
-
 ## Key Principles
 
 1. **Configuration as Single Source of Truth**:
@@ -159,262 +125,6 @@ All declared member repositories are cloned and wired up automatically!
 
 ---
 
-## Everyday Usage
-
-```bash
-# Register and clone a repository
-rnex add backend git@github.com:myorg/backend.git
-
-# Register a repository in local config only (.local.rnex.yaml)
-rnex add --local analytics git@github.com:myorg/analytics.git
-
-# Clone all missing member repositories
-rnex clone
-
-# Run a command across all active repositories
-rnex exec git status -s
-rnex exec npm test
-
-# Disable a repository (skipped by clone, exec, and agents)
-rnex disable analytics
-rnex disable --local analytics    # disable locally without modifying team rnex.yaml
-
-# Re-enable a repository
-rnex enable analytics
-
-# List all registered repositories with clone status and active branch
-rnex list
-
-# Inspect workspace health, active repos, and plugin status
-rnex status
-
-# Reconcile workspace, sync plugins, and upgrade config in a single pass (aliases: sync, update, upgrade)
-rnex fix
-
-# Unregister and delete a repository
-rnex remove analytics
-```
-
----
-
-## Plugins & Scoped Context Packs
-
-Repo Nexus features a scoped plugin architecture. Plugins package curated AI instructions, agent behavioral rules, and architecture templates that are synchronized into dedicated directories under `.rnex/plugins/<plugin-name>/`.
-
-```bash
-# List available and active plugins
-rnex plugin list
-
-# Inspect plugin details and provided files
-rnex plugin info karpathy-llm
-
-# Enable a plugin in your workspace
-rnex plugin enable karpathy-llm
-
-# Disable a plugin and clean up scoped assets
-rnex plugin disable karpathy-llm
-```
-
-### Built-in Plugins
-
-> For dedicated guides, configuration options, and directory layouts for each plugin, see the [**Repo Nexus Plugins Guide**](docs/plugins/).
-
-#### 1. `copilot`
-The `copilot` plugin provides GitHub Copilot integration, automatically mirroring workspace and active plugin assets:
-* **Prompts (`.github/prompts/*.prompt.md`)**: Formatted with YAML frontmatter (`name`, `description`) for the VS Code Copilot Chat prompt picker and slash commands.
-* **Agent Skills (`.github/skills/<name>/SKILL.md`)**: Configured for GitHub Copilot Agent mode and `gh skill`.
-* **Custom Agents (`.github/agents/*.agent.md`)**: Active plugins' agent definitions mirrored for Copilot workspace custom agents.
-* **Instructions (`.github/copilot-instructions.md`)**: Synthesized workspace routing and active plugin guidelines, preserving manual user instructions.
-* **Configurable Options**:
-  ```yaml
-  plugins:
-    copilot:
-      prompts: true        # mirror prompts to .github/prompts/*.prompt.md (default: true)
-      skills: true         # mirror skills to .github/skills/<name>/SKILL.md (default: true)
-      instructions: true   # mirror guidelines to .github/copilot-instructions.md (default: true)
-      agents: true         # mirror custom agents to .github/agents/*.agent.md (default: true)
-  ```
-
-#### 2. `claude`
-The `claude` plugin integrates Anthropic's Claude Code and Claude CLI:
-* **Instructions (`CLAUDE.md`)**: Manages the root `CLAUDE.md` routing context, replacing `AGENTS.md`.
-* **Slash Commands (`.claude/commands/*.md`)**: Standardized commands (`/rnex-cross-repo-feature`, etc.) for Claude Code.
-* **Agent Skills (`.claude/skills/<name>/SKILL.md`)**: Mirrored tool skills and workflows.
-* **Configurable Options**:
-  ```yaml
-  plugins:
-    claude:
-      instructions: true   # maintain CLAUDE.md (default: true)
-      prompts: true        # mirror slash commands to .claude/commands/ (default: true)
-      skills: true         # mirror skills to .claude/skills/ (default: true)
-  ```
-
-#### 3. `gemini`
-The `gemini` plugin integrates Google Gemini CLI and Gemini Code Assist:
-* **Instructions (`GEMINI.md`)**: Manages root `GEMINI.md` context, replacing `AGENTS.md`.
-* **Prompts (`.gemini/prompts/*.prompt.md`)**: Standardized prompts formatted with YAML frontmatter.
-* **Skills (`.gemini/skills/<name>/SKILL.md`)**: Mirrored tool skills for Gemini agents.
-* **Configurable Options**:
-  ```yaml
-  plugins:
-    gemini:
-      instructions: true   # maintain GEMINI.md (default: true)
-      prompts: true        # mirror prompts to .gemini/prompts/ (default: true)
-      skills: true         # mirror skills to .gemini/skills/ (default: true)
-  ```
-
-#### 4. `cursor`
-The `cursor` plugin integrates the Cursor IDE:
-* **Instructions (`.cursorrules` & `.cursor/rules/repo-nexus.mdc`)**: Synchronizes project routing rules.
-* **Prompts (`.cursor/prompts/*.md`)**: Mirrored prompt files.
-* **Skills (`.cursor/skills/<name>/SKILL.md`)**: Mirrored agent skills.
-* **Configurable Options**:
-  ```yaml
-  plugins:
-    cursor:
-      instructions: true   # maintain .cursorrules and MDC rule (default: true)
-      prompts: true        # mirror prompts to .cursor/prompts/ (default: true)
-      skills: true         # mirror skills to .cursor/skills/ (default: true)
-  ```
-
-#### 5. `windsurf`
-The `windsurf` plugin integrates the Codeium Windsurf IDE:
-* **Instructions (`.windsurfrules`)**: Synchronizes project routing rules.
-* **Prompts (`.windsurf/prompts/*.md`)**: Mirrored prompt files.
-* **Skills (`.windsurf/skills/<name>/SKILL.md`)**: Mirrored agent skills.
-* **Configurable Options**:
-  ```yaml
-  plugins:
-    windsurf:
-      instructions: true   # maintain .windsurfrules (default: true)
-      prompts: true        # mirror prompts to .windsurf/prompts/ (default: true)
-      skills: true         # mirror skills to .windsurf/skills/ (default: true)
-  ```
-
-#### 6. `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:
-* **The 4 Cardinal Agent Rules** (`.rnex/plugins/karpathy-llm/rules/behavioral.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.
-  4. *Goal-Driven Execution:* Upfront verification criteria, automated tests, and diff inspection.
-* **Autonomous Karpathy LLM Wiki Architecture:**
-  * **Intake (`/raw/`):** Append-only intake for unmodified source documents.
-  * **Curated Knowledge Base (`/wiki/`):** Interlinked atomic markdown pages with typed YAML frontmatter relations.
-  * **Navigation Index (`/wiki/index.md`):** Master categorized navigation index.
-  * **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.
-* **Standardized Workflows (`.rnex/plugins/karpathy-llm/workflows/`):**
-  * `wiki-ingest.md`: 8-step protocol decomposing raw source documents into atomic wiki pages.
-  * `wiki-lint.md`: 10-step protocol validating paths, relations, contradictions, and indexing.
-
----
-
-## Two-Level Configuration
-
-1. **Repo Config (`rnex.yaml`):** Shared manifest committed to Git. Declares member repos, Git URLs, default enabled states, and active plugins.
-2. **Local Config (`.local.rnex.yaml`):** Machine-specific file ignored in `.gitignore`. Takes **highest priority** and overrides repo settings.
-
-### Repo Configuration (`rnex.yaml`)
-
-```yaml
-# Directory for member repository clones
-repos_dir: ./repos
-
-# Automated workspace Git hooks (default: true)
-git_hooks: true
-
-# Workspace plugins and tool integrations
-plugins:
-  copilot:
-    prompts: true
-    skills: true
-    instructions: true
-    agents: true
-  karpathy-llm: {}
-
-# Member repositories (enabled by default)
-repos:
-  backend:
-    url: git@github.com:myorg/backend-api.git
-    rnex_dir: true      # default: true (creates repos/backend/.rnex/)
-  frontend:
-    url: https://github.com/myorg/web-app.git
-    rnex_dir: true
-  analytics:
-    url: git@github.com:myorg/analytics.git
-    enabled: false       # disabled: skipped by clone and exec
-    rnex_dir: false
-```
-
-### Local Configuration (`.local.rnex.yaml`)
-
-```yaml
-# Highest priority local overrides
-repos:
-  analytics:
-    enabled: true        # locally enable analytics on this workstation
-```
-
----
-
-## CLI Command Reference
-
-> 📖 **Full Manual Available:** See the comprehensive **[CLI Reference Manual](docs/cli/)** for exhaustive details, deep dives into every command and flag, lifecycle behaviors, automated Git hooks, scoped plugins, standardized prompts catalog, and shell completion recipes.
-
-### Global Options
-| Option | Description |
-|:---|:---|
-| `-c, --config <file>` | Explicit path to `rnex.yaml` (executes in that workspace directory) |
-| `-h, --help` | Display command help and usage instructions |
-| `-v, --version` | Display version |
-
-### Commands
-| Command | Description |
-|:---|:---|
-| `rnex init [-y] [--ai <file>] [--code-workspace [file]] [--hooks\|--no-hooks] [dir]` | Initialize a new Virtual Meta-Repo workspace in current (or target) directory |
-| `rnex install [dir]` | Install `rnex` & `repo-nexus` globally into `~/.local/bin` (or custom dir) |
-| `rnex add [--local] [--disabled] <name> <git-url>` | Register and clone repo into `./repos/<name>` |
-| `rnex clone` | Clone all missing enabled repositories declared in `rnex.yaml` |
-| `rnex exec <command...>` | Execute a shell command across all active member repositories |
-| `rnex remove <name>` | Unregister repo and delete `./repos/<name>` |
-| `rnex enable [--local] <name>` | Enable a repository in active workspace |
-| `rnex disable [--local] <name>` | Disable a repository from active workspace |
-| `rnex list` | List all member repositories with clone state, active branch, and `.rnex` status |
-| `rnex status` | Inspect workspace health, active repos, config loaded, git hooks, and plugins |
-| `rnex rnex-dir <enable\|disable> <name>` | Toggle `.rnex/` directory integration for a member repository |
-| `rnex fix [-y] [--quiet]` (or `sync`) | Reconcile workspace repositories, plugins, prompts, and member `.rnex/` directories |
-| `rnex update [-y]` (or `upgrade`) | Safely upgrade workspace configuration schema and routing instructions |
-| `rnex hooks <install\|uninstall\|status> [--local]` | Manage automated Git hooks (`.rnex/hooks` and `git_hooks: true\|false`) |
-| `rnex plugin <list\|info\|enable\|disable>` | Manage workspace plugins |
-| `rnex completion <bash\|zsh\|fish>` | Generate shell auto-completion script |
-
----
-
-## Shell Auto-Completion
-
-Generate auto-completions for your shell:
-
-### Zsh
-```bash
-# Add to ~/.zshrc
-source <(rnex completion zsh)
-```
-
-### Bash
-```bash
-# Add to ~/.bashrc
-source <(rnex completion bash)
-```
-
-### Fish
-```bash
-# Add to ~/.config/fish/config.fish
-rnex completion fish | source
-```
-
----
-
 ## Project Structure
 
 ```

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": "0.6.4",
+  "version": "0.6.6",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",
@@ -30,26 +30,29 @@
   "bugs": {
     "url": "https://github.com/unoxen/repo-nexus/issues"
   },
-  "homepage": "https://github.com/unoxen/repo-nexus#readme",
+  "homepage": "https://unoxen.github.io/repo-nexus/",
   "keywords": [
     "rnex",
     "repo-nexus",
-    "multi-repo",
-    "monorepo",
+    "nexus-repository",
+    "nexus",
+    "repo",
+    "repository",
     "meta-repo",
+    "meta-repository",
+    "virtual-meta-repo",
+    "multi-repo",
+    "context-repository",
+    "ai-first-repository",
     "harness",
+    "ai-harness",
+    "wiki-llm",
     "workspace",
     "toolkit",
-    "ai-agents",
-    "agents.md",
-    "cursor-rules",
-    "claude-code",
-    "copilot",
+    "context-engineering",
     "cursor",
     "plugins",
     "karpathy",
-    "context-engineering",
-    "developer-tools",
     "cli"
   ],
   "license": "MIT",