repo-nexus 0.7.39 → 0.8.2

package/LICENSE

@@ -1,21 +1,201 @@
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-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
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package/README.md

@@ -2,7 +2,7 @@
 
 [![CI](https://github.com/unoxen/repo-nexus/actions/workflows/ci.yml/badge.svg)](https://github.com/unoxen/repo-nexus/actions/workflows/ci.yml)
 [![npm version](https://img.shields.io/npm/v/repo-nexus.svg)](https://www.npmjs.com/package/repo-nexus)
-[![License: MIT](https://img.shields.io/github/license/unoxen/repo-nexus)](LICENSE)
+[![License: Apache 2.0](https://img.shields.io/github/license/unoxen/repo-nexus)](LICENSE)
 [![POSIX Compatible](https://img.shields.io/badge/POSIX-compatible-success)](#)
 [![Platform](https://img.shields.io/badge/Platform-macOS%20%7C%20Linux%20%7C%20Windows-lightgrey)](#)
 [![Documentation Site](https://img.shields.io/badge/docs-site-blue.svg)](https://unoxen.github.io/repo-nexus/)
@@ -16,19 +16,19 @@ A **Virtual Meta-Repo** companion for multi-repo workspaces and shared AI contex
 - **Two-Level Configuration as Source of Truth**: Shared team manifest in `rnex.yaml` with machine-specific overrides in `.local.rnex.yaml` (highest priority).
 - **One Command 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. `.rnex/wiki` and `./docs` for `karpathy-llm`).
+- **Scoped Plugins & Context Packs**: Modular plugin packages scoped under `.rnex/plugins/<plugin-name>/` with support for domain directories (e.g. `wiki/` and `./docs` 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**
 >
 > Explore the comprehensive documentation, architecture guides, and interactive references on the **[Documentation Site](https://unoxen.github.io/repo-nexus/)**:
 >
-> - 🚀 **[Getting Started](https://unoxen.github.io/repo-nexus/guide/getting-started)** — Step-by-step onboarding walkthrough and workspace setup
-> - 📐 **[Architecture](https://unoxen.github.io/repo-nexus/guide/architecture)** & **[Why Repo Nexus?](https://unoxen.github.io/repo-nexus/guide/why-repo-nexus)** — Virtual Meta-Repo model, directory layout, and design rationale
-> - 💻 **[CLI Reference](https://unoxen.github.io/repo-nexus/cli/)** — Complete command syntax, global flags, batch execution (`rnex exec`), and Git hooks
-> - 🧩 **[Plugins Guide](https://unoxen.github.io/repo-nexus/plugins/)** — AI provider integrations (Claude, Copilot, Cursor, Gemini, Windsurf) and Karpathy LLM Wiki
-> - ⚙️ **[Configuration Schema](https://unoxen.github.io/repo-nexus/guide/configuration)** — Two-level `rnex.yaml` and `.local.rnex.yaml` specification
-> - ❓ **[Frequently Asked Questions (FAQ)](https://unoxen.github.io/repo-nexus/faq/)** — Common questions, Git submodule differences, and context strategies
+> - 🚀 **[Getting Started](https://unoxen.github.io/repo-nexus/introduction/quick-start)** — Step-by-step onboarding walkthrough and workspace setup
+> - 📐 **[Architecture](https://unoxen.github.io/repo-nexus/documentation/architecture)** & **[Why Repo Nexus?](https://unoxen.github.io/repo-nexus/introduction/why-rnex)** — Virtual Meta-Repo model, directory layout, and design rationale
+> - 💻 **[CLI Reference](https://unoxen.github.io/repo-nexus/reference/cli)** — Complete command syntax, global flags, batch execution (`rnex exec`), and Git hooks
+> - 🧩 **[Plugins Guide](https://unoxen.github.io/repo-nexus/documentation/plugin-ecosystem)** — AI provider integrations (Claude, Codex, Copilot, Cursor, Gemini, Windsurf) and Karpathy LLM Wiki
+> - ⚙️ **[Configuration Schema](https://unoxen.github.io/repo-nexus/documentation/configuration)** — Two-level `rnex.yaml` and `.local.rnex.yaml` specification
+> - ❓ **[Frequently Asked Questions (FAQ)](https://unoxen.github.io/repo-nexus/faq/general)** — Common questions, Git submodule differences, and context strategies
 
 ---
 
@@ -114,8 +114,8 @@ mkdir my-workspace && cd my-workspace
 rnex init
 
 # 2. Register and clone repositories
-rnex add backend git@github.com:myorg/backend-api.git
-rnex add frontend https://github.com/myorg/web-app.git
+rnex repo add git@github.com:myorg/backend-api.git --name backend
+rnex repo add https://github.com/myorg/web-app.git --name frontend
 
 # 3. Check workspace health
 rnex status
@@ -145,11 +145,11 @@ repo-nexus/
 │   ├── ai-instructions.sample.md   # Base template for .rnex/ai-instructions.md
 │   └── rnex.example.yaml           # Full config reference with examples
 ├── docs/
-│   ├── guide/                      # Architecture, workflows, and getting started
-│   ├── cli/                        # Comprehensive CLI reference manual
+│   ├── introduction/               # Welcome, Why rnex?, Quick Start, and Pure Examples
+│   ├── documentation/              # Architecture, Configuration, Workflows, Lifecycle, Plugins
+│   ├── reference/                  # CLI Reference, RNEX Hooks, Git Hooks, and Environment
 │   ├── plugins/                    # Scoped plugin guides and specifications
-│   ├── examples/                   # Multi-repo patterns and case studies
-│   └── faq/                        # Frequently Asked Questions
+│   └── faq/                        # Frequently Asked Questions & Troubleshooting
 ├── .github/
 │   └── workflows/ci.yml            # GitHub Actions CI workflow
 ├── scripts/
@@ -183,4 +183,4 @@ Contributions are welcome! Please read [CONTRIBUTION.md](CONTRIBUTION.md) for co
 
 ## License
 
-[MIT](LICENSE)
+[Apache 2.0](LICENSE)

package/lib/ai.sh

@@ -20,11 +20,17 @@ reconcile_gitignore() {
 repos/*
 !repos/.gitkeep
 
+# Recursive Repo Nexus directories (trailing slashes prevent ignoring rnex executable or rnex.yaml)
+**/.rnex*/
+**/rnex*/
+.rnex*/
+rnex*/
+
 # Local machine-specific configuration
 $RNEX_LOCAL_CONFIG_FILE
 .rnex.local.yaml
 GI_EOF
-    log_ok "Created .gitignore (ignoring repos/ and $RNEX_LOCAL_CONFIG_FILE)"
+    log_ok "Created .gitignore (ignoring repos/, recursive .rnex directories, and $RNEX_LOCAL_CONFIG_FILE)"
   else
     # 1. Strip any legacy lint_trigger_counter entries if present
     if grep -q "lint_trigger_counter" "$_gi" 2>/dev/null; then
@@ -33,11 +39,10 @@ GI_EOF
       log_ok "Removed legacy lint trigger counter entries from .gitignore"
     fi
 
-    # 2. Strip legacy .rnex/ entries if present (.rnex/ contains tracked plugins, skills, and hooks)
-    if grep -qE '^[ ]*#?[ ]*Repo Nexus internal state' "$_gi" 2>/dev/null || grep -qE '^\.rnex/?$' "$_gi" 2>/dev/null; then
+    # 2. Strip any legacy un-slashed .rnex or rnex rules that might match files
+    if grep -qE '^[ ]*#?[ ]*Repo Nexus internal state' "$_gi" 2>/dev/null || grep -qE '^(\.rnex|rnex)$' "$_gi" 2>/dev/null; then
       _tmp="$(mktemp)"
-      grep -vE '(^[ ]*#?[ ]*Repo Nexus internal state|^\.rnex/?$)' "$_gi" > "$_tmp" && mv "$_tmp" "$_gi"
-      log_ok "Removed .rnex/ from .gitignore (.rnex should be tracked in git)"
+      grep -vE '(^[ ]*#?[ ]*Repo Nexus internal state|^(\.rnex|rnex)$)' "$_gi" > "$_tmp" && mv "$_tmp" "$_gi"
     fi
 
     # 3. Ensure repos/* is ignored
@@ -46,7 +51,19 @@ GI_EOF
       log_dim "Added repos/* to .gitignore"
     fi
 
-    # 4. Ensure local config files are ignored
+    # 4. Ensure recursive directory-only rnex rules are present
+    _added_rnex_rules=0
+    for _pat in "**/.rnex*/" "**/rnex*/" ".rnex*/" "rnex*/"; do
+      if ! grep -qFx -- "$_pat" "$_gi" 2>/dev/null; then
+        if [ "$_added_rnex_rules" -eq 0 ]; then
+          printf '\n# Recursive Repo Nexus directories (trailing slashes prevent ignoring rnex binary or rnex.yaml)\n' >> "$_gi"
+          _added_rnex_rules=1
+        fi
+        printf '%s\n' "$_pat" >> "$_gi"
+      fi
+    done
+
+    # 5. Ensure local config files are ignored
     if ! grep -qF "$RNEX_LOCAL_CONFIG_FILE" "$_gi" 2>/dev/null; then
       printf '\n# Local machine-specific configuration\n%s\n' "$RNEX_LOCAL_CONFIG_FILE" >> "$_gi"
       log_dim "Added $RNEX_LOCAL_CONFIG_FILE to .gitignore"
@@ -56,6 +73,30 @@ GI_EOF
     fi
   fi
 
+  # 6. Append any custom file and directory patterns from git.ignore
+  _custom_ignores="$(yaml_get_git_ignore 2>/dev/null || true)"
+  if [ -n "$_custom_ignores" ]; then
+    _added_custom_header=0
+    _old_ifs="$IFS"
+    IFS='
+'
+    for _ci in $_custom_ignores; do
+      IFS="$_old_ifs"
+      [ -n "$_ci" ] || continue
+      if [ "$_ci" = "repos/" ] && grep -qFx -- "repos/*" "$_gi" 2>/dev/null; then
+        continue
+      fi
+      if ! grep -qFx -- "$_ci" "$_gi" 2>/dev/null; then
+        if [ "$_added_custom_header" -eq 0 ]; then
+          printf '\n# Custom entries from git.ignore in workspace configuration\n' >> "$_gi"
+          _added_custom_header=1
+        fi
+        printf '%s\n' "$_ci" >> "$_gi"
+      fi
+    done
+    IFS="$_old_ifs"
+  fi
+
   # Universal search tool ignore file (ripgrep, Claude Code, VS Code, Zed)
   ensure_provider_ignore "$_dir/.ignore" \
     "Member repos (un-ignored for ripgrep, Claude Code, VS Code, and search tools)" \

package/lib/commands/completion.sh

@@ -14,17 +14,22 @@ cmd_completion() {
     bash)
       cat <<'EOF'
 _rnex_completions() {
-  local cur prev commands
+  local cur prev commands repo_subcommands
   COMPREPLY=()
   cur="${COMP_WORDS[COMP_CWORD]}"
   prev="${COMP_WORDS[COMP_CWORD-1]}"
-  commands="init install add clone exec remove enable disable readonly list sync status rnex-dir update upgrade hooks plugin completion version help"
+  commands="init install repo clone exec list sync status plugin completion version help"
+  repo_subcommands="add remove set clone status exec list"
 
   case "$prev" in
     rnex)
       COMPREPLY=( $(compgen -W "$commands" -- "$cur") )
       return 0
       ;;
+    repo)
+      COMPREPLY=( $(compgen -W "$repo_subcommands" -- "$cur") )
+      return 0
+      ;;
     sync)
       COMPREPLY=( $(compgen -W "-y --yes -q --quiet --upgrade" -- "$cur") )
       return 0
@@ -34,14 +39,12 @@ _rnex_completions() {
       return 0
       ;;
     plugin)
-      COMPREPLY=( $(compgen -W "list info enable install update disable" -- "$cur") )
-      return 0
-      ;;
-    hooks)
-      COMPREPLY=( $(compgen -W "install uninstall status" -- "$cur") )
+      local plugins
+      plugins=$(rnex plugin list 2>/dev/null | awk 'NR>3 && $2 ~ /^\[/ {print $3}')
+      COMPREPLY=( $(compgen -W "list info enable install update disable help $plugins" -- "$cur") )
       return 0
       ;;
-    enable|disable|readonly|remove|show|hide|rnex-dir)
+    remove|clone|status|exec|set)
       local repos
       repos=$(rnex list 2>/dev/null | awk 'NR>2 {print $1}')
       COMPREPLY=( $(compgen -W "$repos" -- "$cur") )
@@ -79,20 +82,12 @@ _rnex() {
   commands=(
     'init:Initialize a new Repo Nexus workspace'
     'install:Install rnex globally into ~/.local/bin'
-    'add:Register and clone a member repository'
+    'repo:Single-repository management (add, remove, set, clone, status, exec, list)'
     'clone:Clone missing member repositories'
     'exec:Execute a command across all member repositories'
-    'remove:Unregister and delete a repository'
-    'enable:Enable a repository in active workspace'
-    'disable:Disable a repository in workspace'
-    'readonly:Toggle read-only (information-only) status for a repo'
     'list:List member repositories'
     'sync:Reconcile workspace, plugins, skills, and member .rnex directories'
     'status:Inspect workspace health and status (read-only)'
-    'rnex-dir:Toggle .rnex directory integration for a repo'
-    'update:Upgrade workspace configuration and routing instructions'
-    'upgrade:Alias for update'
-    'hooks:Manage automated Git hooks'
     'plugin:Manage plugins'
     'completion:Generate shell completions'
     'version:Display version'
@@ -112,6 +107,21 @@ _rnex() {
       ;;
     args)
       case "$words[1]" in
+        repo)
+          if [ "$CURRENT" -eq 2 ]; then
+            local -a repo_cmds
+            repo_cmds=('add:Add and optionally clone a member repository' 'remove:Remove a repository from configuration' 'set:Update repository configuration flags' 'clone:Clone a single repository' 'status:Show status of a repository' 'exec:Execute command in repository directory' 'list:List member repositories')
+            _describe -t repo_cmds 'repo subcommand' repo_cmds
+          elif [ "$words[2]" = "set" ]; then
+            local -a set_opts
+            set_opts=('--enable[Enable repository]' '--disable[Disable repository]' '--readonly[Mark repository read-only]' '--readwrite[Allow writing to repository]' '--global[Update team rnex.yaml]' '--local[Update workstation .local.rnex.yaml]')
+            _describe -t set_opts 'repo set option' set_opts
+          else
+            local -a repos
+            repos=($(rnex list 2>/dev/null | awk 'NR>2 {print $1}'))
+            _describe -t repos 'repository' repos
+          fi
+          ;;
         sync)
           local -a sync_opts
           sync_opts=('(-y --yes)'{-y,--yes}'[Automatically answer yes to prompts]' '(-q --quiet)'{-q,--quiet}'[Suppress non-error output]' '--upgrade[Upgrade workspace configuration schema]')
@@ -121,19 +131,9 @@ _rnex() {
           ;;
         plugin)
           local -a plugin_cmds
-          plugin_cmds=('list:List plugins' 'info:Show plugin details' 'enable:Enable plugin' 'install:Install/enable plugin' 'update:Update enabled plugin(s)' 'disable:Disable plugin')
+          plugin_cmds=('list:List plugins' 'info:Show plugin details' 'enable:Enable plugin' 'install:Install/enable plugin' 'update:Update enabled plugin(s)' 'disable:Disable plugin' 'help:Display plugin help')
           _describe -t plugin_cmds 'plugin command' plugin_cmds
           ;;
-        hooks)
-          local -a hook_cmds
-          hook_cmds=('install:Install Git hooks' 'uninstall:Uninstall Git hooks' 'status:Show Git hooks status')
-          _describe -t hook_cmds 'hooks command' hook_cmds
-          ;;
-        enable|disable|readonly|remove|show|hide|rnex-dir)
-          local -a repos
-          repos=($(rnex list 2>/dev/null | awk 'NR>2 {print $1}'))
-          _describe -t repos 'repository' repos
-          ;;
         completion)
           local -a shells
           shells=('bash:Bash completion' 'zsh:Zsh completion' 'fish:Fish completion')
@@ -162,27 +162,22 @@ EOF
       cat <<'EOF'
 complete -c rnex -n "__fish_use_subcommand" -a init -d "Initialize a new workspace"
 complete -c rnex -n "__fish_use_subcommand" -a install -d "Install rnex globally"
-complete -c rnex -n "__fish_use_subcommand" -a add -d "Register and clone a repository"
+complete -c rnex -n "__fish_use_subcommand" -a repo -d "Member repository management"
+complete -c rnex -n "__fish_seen_subcommand_from repo" -a "add remove set clone status exec list"
+complete -c rnex -n "__fish_seen_subcommand_from set" -l readonly -d "Mark repository read-only"
+complete -c rnex -n "__fish_seen_subcommand_from set" -l readwrite -d "Allow writing to repository"
+complete -c rnex -n "__fish_seen_subcommand_from set" -l enable -d "Enable repository"
+complete -c rnex -n "__fish_seen_subcommand_from set" -l disable -d "Disable repository"
+complete -c rnex -n "__fish_seen_subcommand_from set" -l global -d "Apply in team configuration"
+complete -c rnex -n "__fish_seen_subcommand_from set" -l local -d "Apply in local configuration"
 complete -c rnex -n "__fish_use_subcommand" -a clone -d "Clone missing repositories"
 complete -c rnex -n "__fish_use_subcommand" -a exec -d "Execute command across member repos"
-complete -c rnex -n "__fish_use_subcommand" -a remove -d "Remove a repository"
-complete -c rnex -n "__fish_use_subcommand" -a enable -d "Enable a repository"
-complete -c rnex -n "__fish_use_subcommand" -a disable -d "Disable a repository"
-complete -c rnex -n "__fish_use_subcommand" -a readonly -d "Toggle read-only status for a repo"
-complete -c rnex -n "__fish_seen_subcommand_from readonly" -a "enable disable"
-complete -c rnex -n "__fish_seen_subcommand_from readonly" -l local -d "Apply locally"
 complete -c rnex -n "__fish_use_subcommand" -a list -d "List repositories"
-complete -c rnex -n "__fish_use_subcommand" -a rnex-dir -d "Toggle .rnex directory integration for a repo"
-complete -c rnex -n "__fish_seen_subcommand_from rnex-dir" -a "enable disable"
-complete -c rnex -n "__fish_seen_subcommand_from rnex-dir" -l local -d "Apply locally"
 complete -c rnex -n "__fish_use_subcommand" -a sync -d "Reconcile workspace, plugins, skills, and repos"
 complete -c rnex -n "__fish_seen_subcommand_from sync" -l yes -s y -d "Automatically answer yes to prompts"
 complete -c rnex -n "__fish_seen_subcommand_from sync" -l quiet -s q -d "Suppress non-error output"
 complete -c rnex -n "__fish_seen_subcommand_from sync" -l upgrade -d "Upgrade workspace configuration schema"
 complete -c rnex -n "__fish_use_subcommand" -a status -d "Inspect workspace status (read-only)"
-complete -c rnex -n "__fish_use_subcommand" -a update -d "Upgrade workspace configuration"
-complete -c rnex -n "__fish_use_subcommand" -a upgrade -d "Upgrade workspace configuration"
-complete -c rnex -n "__fish_use_subcommand" -a hooks -d "Manage Git hooks"
 complete -c rnex -n "__fish_use_subcommand" -a plugin -d "Manage plugins"
 complete -c rnex -n "__fish_use_subcommand" -a completion -d "Generate completions"
 complete -c rnex -n "__fish_use_subcommand" -a version -d "Show version"

package/lib/commands/init.sh

@@ -135,6 +135,20 @@ cmd_init() {
       done
     fi
 
+    if [ "$_init_git_hooks" = "false" ]; then
+      _hooks_block='    post-merge: []
+    post-checkout: []
+    pre-commit: []
+    pre-push: []'
+    else
+      _hooks_block='    post-merge:
+      - "rnex sync --quiet"
+    post-checkout:
+      - "rnex sync --quiet"
+    pre-commit: []
+    pre-push: []'
+    fi
+
     cat > "$_target_yaml" <<YAML_EOF
 # Repo Nexus workspace configuration
 # See templates/rnex.example.yaml for a comprehensive example with all options.
@@ -147,8 +161,21 @@ repos_dir: ./repos
 # VS Code / Cursor multi-root workspace file (default: false; e.g. true or workspace.code-workspace)
 code_workspace: ${_cli_code_workspace:-false}
 
-# Automated workspace Git hooks (default: true; e.g. post-merge auto-sync, plugin triggers)
-git_hooks: $_init_git_hooks
+# Git Integration (Ignore rules & Git hooks)
+git:
+  ignore:
+    - "repos/"
+    - "**/.rnex*/"
+    - "**/rnex*/"
+  hooks:
+$_hooks_block
+
+# RNEX Lifecycle Hooks
+rnex_hooks:
+  before_sync: []
+  after_sync: []
+  before_clone: []
+  after_clone: []
 
 # Workspace plugins
 plugins:
@@ -167,9 +194,7 @@ YAML_EOF
   WORKSPACE_LOCAL_YAML="$_init_dir/$RNEX_LOCAL_CONFIG_FILE"
 
   # ---- 2. Merge routing instructions into AI instructions files ------------
-  if ! has_active_provider_instructions "$_init_dir"; then
-    merge_rnex_instructions "$_init_dir/AGENTS.md"
-  fi
+  merge_rnex_instructions "$_init_dir/AGENTS.md"
   for _if in CLAUDE.md GEMINI.md CODEX.md .cursorrules .windsurfrules .github/copilot-instructions.md; do
     [ -f "$_init_dir/$_if" ] && merge_rnex_instructions "$_init_dir/$_if"
   done
@@ -203,11 +228,7 @@ YAML_EOF
 
   # ---- 7. Setup automated Git hooks if inside a Git repository ------------
   if [ "$_is_git_ws" -eq 1 ]; then
-    if [ "$_init_git_hooks" = "true" ]; then
-      cmd_hooks_install_dir "$_init_dir"
-    else
-      log_dim "Skipping Git hooks setup (run 'rnex hooks install' later to enable)"
-    fi
+    install_git_hooks "$_init_dir"
   fi
 
   _write_auto_sync_script "$_init_dir"
@@ -221,7 +242,7 @@ YAML_EOF
     log_dim "Created $_created_items"
     printf '\n'
     log_info "Next steps:"
-    log_dim "1. Add repositories with: rnex add [<name>] <git-url>"
+    log_dim "1. Add repositories with: rnex repo add <git-url> [--name <name>]"
     log_dim "2. Clone team repositories: rnex clone"
     log_dim "3. Run commands across all repos: rnex exec <command>"
   fi