repo-nexus 0.2.11 → 0.3.0

package/README.md

@@ -50,32 +50,23 @@ A **simple, lightweight companion tool** for multi-repo workflows. It links mult
 
 ---
 
-## How It Works: The Two Symlink Flows
+## How It Works: Zero-Touch Multi-Repo Architecture
 
 ```
 ┌─────────────────────────────────────────────────────────────┐
-│  1. SCOPE IN — Bring member repos INTO Repo Nexus           │
+│  Repo Nexus Workspace Root                                 │
 │                                                             │
 │  my-workspace/                                              │
 │    repos/                                                   │
 │      backend/   ──(symlink)──>  ~/code/backend-api          │
 │      frontend/  ──(symlink)──>  ~/code/web-app              │
-│    AGENTS.md         (universal AI instructions)            │
-│    rnex.yaml         (manifest: AI files + repos)           │
+│    AGENTS.md         (root universal AI instructions)       │
+│    .rnex/            (plugins, rules, and workflows)        │
+│    rnex.yaml         (manifest: repos_dir, plugins, repos)  │
 │                                                             │
-│  Agent opens workspace → sees all repos in one place.       │
-│  Edits through symlinks modify the original files directly. │
-└─────────────────────────────────────────────────────────────┘
-
-┌─────────────────────────────────────────────────────────────┐
-│  2. INJECT OUT — Auto-sync AI context INTO member repos     │
-│                                                             │
-│  ~/code/backend-api/                                        │
-│    AGENTS.md     ──(symlink)──>  my-workspace/AGENTS.md     │
-│    src/              (real codebase)                        │
-│                                                             │
-│  Open backend-api standalone → AI tools automatically see   │
-│  shared instructions as if they were local files.           │
+│  • Agent opens workspace → sees all repos in one tree.      │
+│  • Edits through symlinks modify original files directly.   │
+│  • Member repositories remain 100% clean and untouched.     │
 └─────────────────────────────────────────────────────────────┘
 ```
 
@@ -89,10 +80,13 @@ A **simple, lightweight companion tool** for multi-repo workflows. It links mult
 2. **Symlink Write-Through**:
    Symlinks are transparent pointers resolved by your OS. When you or an AI agent edit `repos/backend/src/index.ts`, the OS resolves the link and writes directly to the source repository on disk.
 
-3. **Single Source of Truth for AI Context**:
-   Edit `AGENTS.md` once in Repo Nexus, and changes immediately reflect across all member repositories.
+3. **Clean Member Repositories & Dedicated `.rnex/` Scope**:
+   Member repository roots remain clean and unpolluted. By default, `rnex` creates a dedicated `.rnex/` directory in each member repo (`repos/<name>/.rnex/`) to isolate all Repo Nexus documents, instructions, rules, workflows, and scripts. This setting is configurable per repository (`rnex_dir: true|false`) and can be disabled to leave a member repo 100% untouched.
+
+4. **Multi-Repo AI Context Discovery**:
+   Root `AGENTS.md` and `.rnex/` govern workspace-wide AI assistant behavior, while AI tools operating at the workspace level inspect `repos/<name>/.rnex/` for member-specific instructions without cluttering root codebases.
 
-4. **Dynamic Workspace Scope**:
+5. **Dynamic Workspace Scope**:
    Easily show or hide member repos from the active workspace without modifying disk contents.
 
 ---
@@ -157,25 +151,32 @@ During `rnex init`, the CLI automatically scans for existing AI configuration fi
 ## Everyday Usage
 
 ```bash
-# Register a repository (links into scope & auto-injects AI context)
+# Register a repository (links into scope & initializes member .rnex/ directory)
 rnex add my-app ~/code/my-app
 
-# Inspect workspace status & linked AI files
+# Register a repository with .rnex/ disabled (100% untouched)
+rnex add --no-rnex-dir my-app ~/code/my-app
+
+# Inspect workspace health, active repos, and .rnex status
 rnex status
 
-# List all registered repositories
+# List all registered repositories with scope and .rnex status
 rnex list
 
+# Toggle .rnex directory integration for a member repo
+rnex rnex-dir disable my-app
+rnex rnex-dir enable my-app
+
 # Temporarily hide a repo from active indexing/agent scope
 rnex hide my-app
 
 # Restore a hidden repo back to active scope
 rnex show my-app
 
-# Reconcile/repair all symlinks across all repos (idempotent)
+# Reconcile all scope links, plugins, and member .rnex/ directories
 rnex sync
 
-# Unregister a repository (removes scope link & cleans up injected AI files)
+# Unregister a repository (removes scope link & member .rnex assets)
 rnex remove my-app
 ```
 
@@ -223,19 +224,12 @@ The `karpathy-llm` plugin packages Andrej Karpathy's verified LLM agent design p
 
 ## Workspace Configuration (`rnex.yaml`)
 
-The configuration file defines repo symlink directory, AI context files to sync, enabled plugins, and registered repositories:
+The configuration file defines repo symlink directory, enabled plugins, and registered repositories:
 
 ```yaml
 # Directory for repository symlinks (relative or absolute)
 repos_dir: ./repos
 
-# AI context files to automatically sync into every member repo
-ai_files:
-  - AGENTS.md
-  - .github/copilot-instructions.md
-  # - .cursorrules
-  # - CLAUDE.md
-
 # Workspace plugins
 plugins:
   karpathy-llm:
@@ -246,15 +240,18 @@ repos:
   backend:
     path: /Users/dev/code/backend-api
     scope: visible
+    rnex_dir: true      # default: true (creates repos/backend/.rnex/)
   frontend:
     path: ../web-app
     scope: visible
+    rnex_dir: true
   analytics:
     path: /Users/dev/code/analytics
     scope: hidden
+    rnex_dir: false     # disabled: leaves analytics repo 100% untouched
 ```
 
-> See [`docs/rnex.example.yaml`](docs/rnex.example.yaml) for a comprehensive example with all options and supported AI tool configs.
+> See [`docs/rnex.example.yaml`](docs/rnex.example.yaml) for a comprehensive example with all options.
 > For common questions and architecture details, see the [Frequently Asked Questions (FAQ)](docs/FAQ.md).
 
 ---
@@ -273,15 +270,14 @@ repos:
 |:---|:---|
 | `rnex init [dir]` | Initialize a new workspace in current (or target) directory |
 | `rnex install [dir]` | Install `rnex` & `repo-nexus` globally into `~/.local/bin` (or custom dir) |
-| `rnex add [-y] <name> <path>` | Register repo, create scope symlink, and sync AI context (prompts to extend existing files) |
-| `rnex remove <name>` | Unregister repo, unlink from scope, and clean up injected AI files |
-| `rnex list` | List all registered repos and visibility scopes |
-| `rnex status` | Display status of AI context files, active member repos, and paths |
+| `rnex add [--no-rnex-dir] <name> <path>` | Register repo, create scope link, and configure member `.rnex/` |
+| `rnex remove <name>` | Unregister repo, unlink scope, and clean up member `.rnex/` assets |
+| `rnex list` | List all registered repos, visibility scopes, and `.rnex` status |
+| `rnex status` | Display status of workspace AI context, active plugins, and member repos |
+| `rnex rnex-dir <enable\|disable> <name>` | Toggle `.rnex/` directory integration for a member repository |
 | `rnex show <name>` | Make a hidden repo visible in workspace |
 | `rnex hide <name>` | Hide a repo from active workspace indexing |
-| `rnex sync` | Reconcile all scope symlinks and AI context files from config |
-
-> **Note on Existing AI Files**: Pre-existing files in member repositories are never overwritten. When adding a new repo, `rnex` prompts whether to update existing files and safely extends them with workspace context between managed markers. Pass `-y` / `--yes` to auto-confirm.
+| `rnex sync` | Reconcile all scope symlinks, plugins, and member `.rnex/` directories |
 
 ---
 
@@ -301,28 +297,6 @@ Any command executed with an explicit config file operates within the directory
 
 ---
 
-## Supported AI Configuration Files
-
-`rnex init` auto-detects these files and includes them in your workspace config:
-
-| File / Directory | AI Tool |
-|:---|:---|
-| `AGENTS.md` | Universal AI agent instructions |
-| `CLAUDE.md` | Claude Code |
-| `.cursorrules` | Cursor |
-| `.cursor/rules/` | Cursor (directory) |
-| `.windsurfrules` | Windsurf / Codeium |
-| `.windsurf/rules/` | Windsurf (directory) |
-| `.github/copilot-instructions.md` | GitHub Copilot |
-| `.aider.conf.yml` | Aider |
-| `CONVENTIONS.md` | Coding conventions |
-| `.clinerules` | Cline / Roo Code |
-| `CODEX.md` | Codex |
-| `.continue/` | Continue.dev |
-| `SKILL.md` | Skills (emerging standard) |
-
----
-
 ## Project Structure
 
 ```
@@ -338,7 +312,7 @@ repo-nexus/
 │   ├── workflows/ci.yml            # GitHub Actions CI workflow
 │   └── ISSUE_TEMPLATE/             # Bug report and feature request templates
 ├── tests/
-│   └── test_cli.sh                 # Automated CLI test suite (21 tests)
+│   └── test_cli.sh                 # Automated CLI test suite (20 tests)
 ├── toolkit/                        # Shared prompts, scripts, templates
 ├── package.json                    # npm package manifest
 ├── LICENSE                         # MIT License

package/docs/AGENTS.sample.md

@@ -6,5 +6,6 @@ This workspace operates as a **Repo Nexus** linking multiple independent reposit
 
 1. **Symlink Write-Through**: Files edited under `repos/<name>/` directly modify the target repository.
 2. **Repo Boundaries**: Each repository is isolated. Do not introduce cross-repo imports unless explicitly architected.
-3. **Shared Context**: This file is symlinked across member repositories. Keep instructions universal. Use local instructions for repo-specific rules.
-4. **Git Operations**: Commit and push changes directly within the respective member repository root.
+3. **Shared Context**: This file governs AI assistant behavior across all member repositories. Keep instructions universal. Use local instructions for repo-specific rules.
+4. **Member Repo RNEX Context**: Member repositories may contain an `.rnex/` directory (accessible via `repos/<name>/.rnex/`) containing repository-specific documents, instructions, rules, workflows, and scripts managed by Repo Nexus. AI assistants operating at the workspace level MUST inspect `repos/<name>/.rnex/` for member-specific context, guidelines, and commands.
+5. **Git Operations**: Commit and push changes directly within the respective member repository root.

package/docs/FAQ.md

@@ -15,7 +15,7 @@ This document answers common questions about **Repo Nexus (`rnex`)**, why it exi
   - [Why not just use a monorepo or Git submodules?](#why-not-just-use-a-monorepo-or-git-submodules)
 - [Architecture & Mechanics](#architecture--mechanics)
   - [How does rnex work without copying files?](#how-does-rnex-work-without-copying-files)
-  - [What is "Scope In" vs. "Inject Out"?](#what-is-scope-in-vs-inject-out)
+  - [How does rnex connect repositories? (Zero-Touch Architecture)](#how-does-rnex-connect-repositories-zero-touch-architecture)
   - [Can I use Git commands (pull, push, commit) on symlinked repos?](#can-i-use-git-commands-pull-push-commit-on-symlinked-repos)
   - [Can AI agents create and modify files inside member repos via symlinks?](#can-ai-agents-create-and-modify-files-inside-member-repos-via-symlinks)
   - [Will rnex interfere with Git branches, remotes, or commit histories?](#will-rnex-interfere-with-git-branches-remotes-or-commit-histories)
@@ -23,10 +23,11 @@ This document answers common questions about **Repo Nexus (`rnex`)**, why it exi
   - [How does it optimize workspaces for IDEs?](#how-does-it-optimize-workspaces-for-ides)
   - [How does it support accurate AI context?](#how-does-it-support-accurate-ai-context)
   - [What is the risk of tool lock-in?](#what-is-the-risk-of-tool-lock-in)
-  - [Do I need rnex to inject symlinks into my member repos?](#do-i-need-rnex-to-inject-symlinks-into-my-member-repos)
-  - [How should AI instructions be structured across repos? (Committed files vs. symlinks)](#how-should-ai-instructions-be-structured-across-repos-committed-files-vs-symlinks)
-  - [What happens if a member repository already has an existing AI configuration file?](#what-happens-if-a-member-repository-already-has-an-existing-ai-configuration-file)
-  - [Which AI assistants and configuration files are supported?](#which-ai-assistants-and-configuration-files-are-supported)
+  - [Does rnex modify or inject loose files into member repositories?](#does-rnex-modify-or-inject-loose-files-into-member-repositories)
+  - [What is the member repository .rnex/ directory and how do AI tools use it?](#what-is-the-member-repository-rnex-directory-and-how-do-ai-tools-use-it)
+  - [How should AI instructions be structured across repos? (Committed files vs. workspace context)](#how-should-ai-instructions-be-structured-across-repos-committed-files-vs-workspace-context)
+  - [Can member repositories maintain their own AI configuration files?](#can-member-repositories-maintain-their-own-ai-configuration-files)
+  - [Which AI assistants are supported?](#which-ai-assistants-are-supported)
   - [How do I prevent AI agents from running out of context or token bloat?](#how-do-i-prevent-ai-agents-from-running-out-of-context-or-token-bloat)
 - [Platforms & Setup](#platforms--setup)
   - [What are the system requirements? Does it work on Windows?](#what-are-the-system-requirements-does-it-work-on-windows)
@@ -85,7 +86,7 @@ This creates two major frictions:
 | :--- | :--- | :--- |
 | **Git Monorepo** | Heavy migration effort, combined CI/CD pipelines, complex permission management, slow Git checkouts. | **Zero migration**: Repositories remain completely independent with their own remotes, histories, and deployment pipelines. |
 | **Git Submodules** | Detached HEAD states, tricky merge conflicts, complex multi-step commits, rigid parent-child coupling. | **No Git friction**: Member repositories are linked via filesystem symlinks. Git never tracks other repos as submodules. |
-| **Manual Copy-Paste** | AI configuration files rapidly drift out of sync across repositories. | **Auto-synced**: Edit `AGENTS.md` once in the workspace; changes immediately reflect across all member repositories. |
+| **Manual Copy-Paste** | AI configuration files and rules rapidly drift out of sync across repositories. | **Centralized AI Context**: Define instructions once in workspace `AGENTS.md` and `.rnex/`; coding assistants apply them across all linked projects. |
 
 ---
 
@@ -97,14 +98,16 @@ This creates two major frictions:
 
 ---
 
-### What is "Scope In" vs. "Inject Out"?
+### How does rnex connect repositories? (Zero-Touch Architecture)
 
-`rnex` offers two complementary symlink flows:
+`rnex` uses a clean **Zero-Touch** symlink architecture:
 
-1. **Scope In (Repos into Workspace)**:
-   When you run `rnex add <name> <path>`, a symlink is created at `repos/<name>` pointing to the source project directory. Opening the workspace directory in your editor gives you (and your AI assistant) full access to all linked repositories in a single file tree.
-2. **Inject Out (AI Context into Member Repos)**:
-   Shared configuration files defined in `rnex.yaml` (such as `AGENTS.md`) can be symlinked from the workspace into the root of every member repository. Opening a repository standalone allows standalone IDE windows to discover the shared rules as local files.
+1. **Workspace Root**:
+   When you run `rnex add <name> <path>`, a single symlink is created at `repos/<name>` inside the workspace, pointing directly to the target project directory on disk.
+2. **Zero Pollution in Member Repos**:
+   `rnex` never injects symlinks, modifies existing files, or alters `.gitignore` in your member repositories. Member repositories remain 100% clean and pristine.
+3. **Unified AI Context**:
+   When opening the Repo Nexus workspace in your editor, your AI assistant sees all member repositories under `repos/` in a single file tree, guided by the workspace-level `AGENTS.md` and `.rnex/` configuration.
 
 ---
 
@@ -142,7 +145,7 @@ By defining your multi-repo structure through repo-nexus, it bridges the gap acr
 
 ### How does it support accurate AI context?
 
-It serves as an informational metadata layer across repositories. It allows you to synchronize and propagate AI rule parameters, prompt setups, and documentation frameworks (like `.cursorrules`, `AGENTS.md`, or `CLAUDE.md`) globally so that coding assistants see the entire multi-repo architecture as one coherent context.
+It serves as an informational metadata layer across repositories. It allows you to define shared AI rule parameters, guidelines, and documentation frameworks (like `AGENTS.md`, plugin packs, and `.rnex/` instructions) at the workspace level so that coding assistants see the entire multi-repo architecture as one coherent context.
 
 ---
 
@@ -152,61 +155,66 @@ Zero. Because repo-nexus only overlays structural configuration metadata rather
 
 ---
 
-### Do I need rnex to inject symlinks into my member repos?
+### Does rnex modify or inject loose files into member repositories?
 
-**Not necessarily.** If your primary workflow is opening the Nexus workspace root (or relying on global workstation AI configs), you do **not** need `rnex` to inject symlinks into member repos.
+**No.** Member repository roots remain clean and unpolluted:
+- No loose symlinks, wrapper scripts, or markers are injected into member repository roots.
+- Existing repository files (such as `AGENTS.md` or `.cursorrules`) are never overwritten or altered.
+- No `.gitignore` files inside member repos are touched or modified.
+- All workspace-related documents, rules, workflows, and scripts are strictly encapsulated within a dedicated `.rnex/` directory inside the member repo.
 
-Running in **Zero-Touch Mode** (`ai_files: []` in `rnex.yaml`):
-- Keeps member repositories 100% pristine.
-- Prevents temporary symlinks or `.gitignore` modifications inside member repos.
-- The AI agent will read `AGENTS.md` directly from the workspace root and apply it across all linked projects.
+---
+
+### What is the member repository .rnex/ directory and how do AI tools use it?
 
-"Inject Out" is only needed if you frequently open individual member repositories standalone in an editor without opening the Nexus workspace, yet still want that standalone window to pick up shared rules.
+By default, Repo Nexus initializes an `.rnex/` folder inside each member repository (`repos/<name>/.rnex/`):
+- **Encapsulated Workspace Data**: Stores documents, instructions, rules, workflows, and scripts related to Repo Nexus for this member repository, preventing any root pollution.
+- **AI Tool Awareness**: AI coding assistants (such as Antigravity, Claude Code, Cursor, Copilot) operating at the Repo Nexus workspace level are instructed via root `AGENTS.md` to inspect `repos/<name>/.rnex/` for repository-specific context, guidelines, and commands.
+- **Enabled by Default**: If `rnex_dir` is omitted for a repository, it evaluates to `true` (enabled by default).
+- **Configurable per repo**: You can enable or disable this setting at any time using `rnex_dir: true|false` in `rnex.yaml`, or via the CLI:
+  ```bash
+  rnex add --no-rnex-dir <name> <path>   # Register repo without .rnex/
+  rnex rnex-dir disable <name>          # Disable and clean .rnex/
+  rnex rnex-dir enable <name>           # Re-enable and sync .rnex/
+  ```
+  When disabled, the member repository is left 100% untouched.
 
 ---
 
-### How should AI instructions be structured across repos? (Committed files vs. symlinks)
+### How should AI instructions be structured across repos? (Committed files vs. workspace context)
 
 The cleanest architecture separates concerns into two distinct layers:
 
 1. **Workspace Level (Nexus Root)**:
-   Contains multi-repo context, cross-service orchestrations, and workspace-wide rules in `AGENTS.md`.
+   Contains multi-repo context, cross-service orchestrations, and workspace-wide rules in `AGENTS.md` and `.rnex/`.
 2. **Member Repo Level (Committed Files)**:
-   Individual repositories can maintain their own domain-specific AI instructions (e.g., repository `.cursorrules`, `CLAUDE.md`, or component conventions) as **real, first-class files committed to Git**.
+   Individual repositories maintain their own domain-specific AI instructions (e.g., repository `.cursorrules`, `CLAUDE.md`, or component conventions) as **real, first-class files committed to Git**.
 
-**Why real committed files are better than injected symlinks for member repos**:
+**Why real committed files are best for member repos**:
 - **Shared with the Team**: Anyone on the team who clones the repo immediately gets the rules without needing `rnex` or symlinks.
 - **No Path Fragility**: Symlinks pointing back to an external workspace break if cloned on another computer or Windows. Committed files never break.
 - **Repository Autonomy**: Each project remains self-documenting and independent.
 
 ---
 
-### What happens if a member repository already has an existing AI configuration file?
+### Can member repositories maintain their own AI configuration files?
 
-`rnex` will **never replace or overwrite** existing AI files in a member repository.
+**Yes.** Individual repositories can maintain their own domain-specific AI instructions (such as `.cursorrules`, `CLAUDE.md`, or repository-level `AGENTS.md`) as standard, first-class files committed to their own Git history.
 
-When you run `rnex add <name> <path>`, `rnex` detects any pre-existing AI context files (such as `AGENTS.md` or `.cursorrules`) and prompts you whether to update them. If confirmed, `rnex` **extends** the existing file by appending the workspace context enclosed within clearly demarcated markers (`# --- REPO-NEXUS AI CONTEXT ---`).
-
-This preserves all repository-specific rules while layering universal workspace guidelines on top. Subsequent `rnex sync` calls keep the extended block synchronized without duplicating content or modifying the repository's custom instructions. Pass `-y` / `--yes` to `rnex add` to auto-confirm updating existing files.
+`rnex` never overwrites, modifies, or touches these files. When you add a repository to Repo Nexus, its local configuration remains completely intact.
 
 ---
 
-### Which AI assistants and configuration files are supported?
-
-`rnex` is tool-agnostic and auto-detects or syncs standard configuration files for:
+### Which AI assistants are supported?
 
-- **Universal Agents**: `AGENTS.md`
-- **Claude Code**: `CLAUDE.md`
-- **Cursor**: `.cursorrules`, `.cursor/rules/`
-- **Windsurf / Codeium**: `.windsurfrules`, `.windsurf/rules/`
-- **GitHub Copilot**: `.github/copilot-instructions.md`
-- **Aider**: `.aider.conf.yml`, `CONVENTIONS.md`
-- **Cline / Roo Code**: `.clinerules`
-- **Codex**: `CODEX.md`
-- **Continue.dev**: `.continue/`
-- **Skills Standards**: `SKILL.md`
+`rnex` is tool-agnostic. Any AI coding assistant that can open a workspace folder will work seamlessly with Repo Nexus, including:
 
-You can add any custom file or prompt template to the `ai_files` list in `rnex.yaml`.
+- **Universal Agents & Antigravity**: reads root `AGENTS.md`
+- **Claude Code**: reads workspace instructions
+- **Cursor**: indexes all member repositories under `repos/`
+- **Windsurf / Codeium**: indexes active repository symlinks
+- **GitHub Copilot**: provides multi-file completions across linked repositories
+- **Cline / Roo Code / Aider / Codex**: navigates across member repos via `repos/<name>/`
 
 ---
 
@@ -254,7 +262,7 @@ If you move a repository, clone a workspace on a new machine, or notice missing
 rnex sync
 ```
 
-This command reconciles all symlinks for member repositories and AI context files defined in `rnex.yaml`, repairing broken links and ensuring your workspace is healthy. To inspect the current status, run:
+This command reconciles all scope symlinks, active plugins, and member `.rnex/` directories defined in `rnex.yaml`, repairing broken links and ensuring your workspace is healthy. To inspect the current status, run:
 
 ```bash
 rnex status

package/docs/rnex.example.yaml

@@ -19,53 +19,16 @@
 
 repos_dir: ./repos
 
-# ------------------------------------------------------------------------------
-# ai_files — AI context files to auto-sync into member repositories
-# ------------------------------------------------------------------------------
-# Each file listed here is synced from the workspace root into every
-# registered member repository. If a member repository already contains an
-# existing file, it is extended (never replaced) with workspace context.
-# When adding a new repository, rnex prompts whether to update existing files.
-# This keeps AI instructions consistent across all your projects.
-#
-# Paths are relative to the workspace root (where this config file lives).
-# Both files and directories are supported.
-#
-# Well-known AI configuration files by tool:
-#   AGENTS.md                         — Universal AI agent instructions
-#   CLAUDE.md                         — Claude Code project instructions
-#   .cursorrules                      — Cursor editor rules
-#   .cursor/rules/                    — Cursor rules directory
-#   .windsurfrules                    — Windsurf / Codeium rules
-#   .windsurf/rules/                  — Windsurf rules directory
-#   .github/copilot-instructions.md   — GitHub Copilot custom instructions
-#   .aider.conf.yml                   — Aider configuration
-#   CONVENTIONS.md                    — Coding conventions (Aider / general)
-#   .clinerules                       — Cline / Roo Code rules
-#   CODEX.md                          — Codex project instructions
-#   .continue/                        — Continue.dev configuration directory
-#   SKILL.md                          — Skills definition (emerging standard)
-
-ai_files:
-  - AGENTS.md
-  - .github/copilot-instructions.md
-  # - .cursorrules
-  # - CLAUDE.md
-  # - .windsurfrules
-  # - CONVENTIONS.md
-  # - toolkit/prompts/review-checklist.md
-
 # ------------------------------------------------------------------------------
 # plugins — Workspace plugins and AI instruction packs
 # ------------------------------------------------------------------------------
 # Plugins extend your workspace with curated AI guidelines, context rules,
-# and scaffolding templates. When enabled, plugin context files are automatically
-# synchronized into all registered member repositories during `rnex sync`.
+# and scaffolding templates within the `.rnex/` workspace root directory.
 #
 # Manage plugins with:
 #   rnex plugin list              # View available and active plugins
-#   rnex plugin enable <name>     # Enable and sync into member repos
-#   rnex plugin disable <name>    # Disable and clean up
+#   rnex plugin enable <name>     # Enable plugin in workspace
+#   rnex plugin disable <name>    # Disable plugin from workspace
 #
 # Built-in plugins:
 #   karpathy-llm   — Andrej Karpathy's agent behavioral principles,
@@ -81,34 +44,43 @@ plugins:
 # repos — Member repositories managed by Repo Nexus
 # ------------------------------------------------------------------------------
 # Each repo has:
-#   path:   Absolute or relative path to the repository on disk.
-#           Relative paths are resolved relative to this config file.
-#   scope:  "visible" (default) creates a symlink in repos_dir.
-#           "hidden" removes the symlink but keeps the registration.
+#   path:     Absolute or relative path to the repository on disk.
+#             Relative paths are resolved relative to this config file.
+#   scope:    "visible" (default) creates a symlink in repos_dir.
+#             "hidden" removes the symlink but keeps the registration.
+#   rnex_dir: true (default) creates an .rnex/ directory inside the member repo
+#             for storing rnex-related documents, rules, workflows, and scripts.
+#             Set to false to disable and leave the repository completely untouched.
 #
 # Examples with absolute paths:
 #   backend-api:
 #     path: /Users/dev/projects/backend-api
 #     scope: visible
+#     rnex_dir: true
 #
 # Examples with relative paths:
 #   frontend:
 #     path: ../frontend-app
 #     scope: visible
+#     rnex_dir: true
 #
 #   shared-lib:
 #     path: ../../libs/shared
 #     scope: hidden
+#     rnex_dir: false
 
 repos:
   # backend-api:
   #   path: /Users/dev/projects/backend-api
   #   scope: visible
+  #   rnex_dir: true
   #
   # frontend-app:
   #   path: ../frontend-app
   #   scope: visible
+  #   rnex_dir: true
   #
   # analytics:
   #   path: /Users/dev/projects/analytics-service
   #   scope: hidden
+  #   rnex_dir: false

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.2.11",
+  "version": "0.3.0",
   "description": "Lightweight, zero-dependency companion tool for multi-repo workspaces and shared AI context via symlinks (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",