repo-nexus 0.5.3 → 0.5.5

package/CHANGELOG.md

@@ -17,6 +17,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
   - Workspace schema migration in `rnex update` and `rnex fix -y` non-destructively inserts `git_hooks` into older configurations.
   - `rnex status` and `rnex hooks status` display configuration state alongside runtime Git hooks status.
 
+### Fixed
+- **Git Hooks Self-Rewrite & Wrapper Preservation**:
+  - Resolved self-rewrite bug where `rnex hooks run post-merge` invoked `cmd_fix`, which truncated and replaced `.rnex/hooks/post-merge` while the shell interpreter was actively executing it.
+  - Added in-hook execution guard (`_RNEX_INSIDE_HOOK=1`) preventing hook script regeneration during active hook dispatch.
+  - Preserved custom / repository-owned wrappers in `.rnex/hooks/` that are not auto-managed by `rnex`.
+  - Added `cmp -s` check before writing hook files to eliminate unnecessary file churn and in-place overwrites.
+  - Automatically chain to existing repository-owned `.githooks/` scripts if present.
+- **Track Workspace `.rnex/` in Version Control**:
+  - Removed `.rnex/` from `.gitignore` templates and generation.
+  - `reconcile_gitignore` and `rnex fix` actively strip legacy `.rnex/` ignore rules from `.gitignore` so that team prompts (`.rnex/prompts/`), plugins (`.rnex/plugins/`), and hooks (`.rnex/hooks/`) are tracked in git.
+  - Updated `rnex status` to expect `.rnex/` to remain tracked by git.
+
 ## [0.5.1] - 2026-10-08
 
 ### Added

package/docs/CLI.md

@@ -78,7 +78,7 @@ rnex init [options] [directory]
 2. Merges Repo Nexus routing instructions (`<!-- REPO-NEXUS:START -->` ... `<!-- REPO-NEXUS:END -->`) into the target AI instructions file.
 3. Creates `./repos/` directory with a tracked `.gitkeep`.
 4. Creates `.rnex/`, `.rnex/plugins/`, and copies standardized prompts to `.rnex/prompts/`.
-5. Reconciles `.gitignore` to ensure `repos/`, `.rnex/`, and `.local.rnex.yaml` are never tracked by the meta-repo.
+5. Reconciles `.gitignore` to ensure `repos/` and `.local.rnex.yaml` are never tracked by the meta-repo (while keeping `.rnex/` tracked).
 6. Generates a multi-root `.code-workspace` file if configured.
 7. Prompts to configure automated workspace Git hooks (`core.hooksPath = .rnex/hooks`) if inside a Git repository.
 
@@ -110,7 +110,7 @@ rnex status
 #### What it reports:
 - **Configuration & Versions**: Path, version tag, and load status of `rnex.yaml` and `.local.rnex.yaml`.
 - **Paths**: Clones directory (`repos_dir`) and primary AI instructions file.
-- **Git Integration**: Validation that `.gitignore` ignores `repos/`, `.rnex/`, and local files, and whether `core.hooksPath` points to `.rnex/hooks`.
+- **Git Integration**: Validation that `.gitignore` ignores `repos/` and local files (while keeping `.rnex/` tracked), and whether `core.hooksPath` points to `.rnex/hooks`.
 - **AI Routing Context**: Existence and routing block markers in `AGENTS.md`, `CLAUDE.md`, `.code-workspace`, and prompts catalog (`.rnex/prompts/index.md`).
 - **Active Plugins**: List of enabled plugins, scoped versions, and asset directories.
 - **Member Repositories**: Every registered repository, enabled/disabled state, clone health, and active Git branch.

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.5.3",
+  "version": "0.5.5",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",

package/rnex

@@ -890,14 +890,11 @@ reconcile_gitignore() {
 repos/*
 !repos/.gitkeep
 
-# Repo Nexus internal state & cache
-.rnex/
-
 # Local machine-specific configuration
 $RNEX_LOCAL_CONFIG_FILE
 .rnex.local.yaml
 GI_EOF
-    log_ok "Created .gitignore (ignoring repos/, .rnex/, and $RNEX_LOCAL_CONFIG_FILE)"
+    log_ok "Created .gitignore (ignoring repos/ and $RNEX_LOCAL_CONFIG_FILE)"
     return 0
   fi
 
@@ -908,18 +905,19 @@ GI_EOF
     log_ok "Removed legacy lint trigger counter entries from .gitignore"
   fi
 
-  # 2. Ensure repos/* is ignored
+  # 2. Strip legacy .rnex/ entries if present (.rnex/ contains tracked prompts, plugins, and hooks)
+  if grep -qE '^[ ]*#?[ ]*Repo Nexus internal state' "$_gi" 2>/dev/null || grep -qE '^\.rnex/?$' "$_gi" 2>/dev/null; then
+    _tmp="$(mktemp)"
+    grep -vE '(^[ ]*#?[ ]*Repo Nexus internal state|^\.rnex/?$)' "$_gi" > "$_tmp" && mv "$_tmp" "$_gi"
+    log_ok "Removed .rnex/ from .gitignore (.rnex should be tracked in git)"
+  fi
+
+  # 3. Ensure repos/* is ignored
   if ! grep -q "^repos" "$_gi" 2>/dev/null; then
     printf '\n# Member repos (managed by rnex)\nrepos/*\n!repos/.gitkeep\n' >> "$_gi"
     log_dim "Added repos/* to .gitignore"
   fi
 
-  # 3. Ensure .rnex/ is ignored
-  if ! grep -q '^\.rnex/' "$_gi" 2>/dev/null && ! grep -q '^\.rnex$' "$_gi" 2>/dev/null; then
-    printf '\n# Repo Nexus internal state & cache\n.rnex/\n' >> "$_gi"
-    log_dim "Added .rnex/ to .gitignore"
-  fi
-
   # 4. 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"
@@ -1258,22 +1256,35 @@ upgrade_workspace_config() {
 _create_hook_script() {
   _dst="$1"
   _hook_type="$2"
-  cat > "$_dst" <<'HOOK_EOF'
+
+  # Preserve custom / repository-owned wrappers that are not auto-managed by rnex
+  if [ -f "$_dst" ] && ! grep -q "Managed automatically by rnex" "$_dst" 2>/dev/null; then
+    return 0
+  fi
+
+  _sub_tmp="$(mktemp)"
+  cat > "$_sub_tmp" <<HOOK_EOF
 #!/bin/sh
-# Repo Nexus Git Hook: __HOOK_TYPE__
+# Repo Nexus Git Hook: $_hook_type
 # Managed automatically by rnex. Do not edit manually.
 
-_dir="$(cd "$(dirname "$0")/../.." 2>/dev/null && pwd -P)"
+_dir="\$(cd "\$(dirname "\$0")/../.." 2>/dev/null && pwd -P)"
 if command -v rnex >/dev/null 2>&1; then
-  rnex hooks run __HOOK_TYPE__ "$@"
-elif [ -f "$_dir/rnex" ]; then
-  "$_dir/rnex" hooks run __HOOK_TYPE__ "$@"
+  rnex hooks run $_hook_type "\$@"
+elif [ -f "\$_dir/rnex" ]; then
+  "\$_dir/rnex" hooks run $_hook_type "\$@"
 fi
 HOOK_EOF
-  _sub_tmp="$(mktemp)"
-  sed "s/__HOOK_TYPE__/$_hook_type/g" "$_dst" > "$_sub_tmp" && mv "$_sub_tmp" "$_dst"
-  rm -f "$_sub_tmp"
-  chmod +x "$_dst"
+
+  chmod +x "$_sub_tmp"
+
+  # Avoid rewriting / modifying file if already identical (prevents inode churn & self-rewrite)
+  if [ -f "$_dst" ] && cmp -s "$_sub_tmp" "$_dst"; then
+    rm -f "$_sub_tmp"
+    return 0
+  fi
+
+  mv "$_sub_tmp" "$_dst"
 }
 
 cmd_hooks_install_dir() {
@@ -1390,6 +1401,7 @@ cmd_hooks() {
       shift
       _hook_name="$1"
       shift || true
+      export _RNEX_INSIDE_HOOK=1
       require_workspace
       case "$_hook_name" in
         post-merge)
@@ -1403,6 +1415,9 @@ cmd_hooks() {
               fi
             fi
           fi
+          if [ -x "$NEXUS_DIR/.githooks/post-merge" ]; then
+            "$NEXUS_DIR/.githooks/post-merge" "$@" || true
+          fi
           return 0
           ;;
         post-commit)
@@ -1416,6 +1431,9 @@ cmd_hooks() {
               fi
             fi
           fi
+          if [ -x "$NEXUS_DIR/.githooks/post-commit" ]; then
+            "$NEXUS_DIR/.githooks/post-commit" "$@" || true
+          fi
           return 0
           ;;
         pre-commit)
@@ -1429,6 +1447,9 @@ cmd_hooks() {
               fi
             fi
           fi
+          if [ -x "$NEXUS_DIR/.githooks/pre-commit" ]; then
+            "$NEXUS_DIR/.githooks/pre-commit" "$@" || return $?
+          fi
           return 0
           ;;
         pre-push)
@@ -1438,6 +1459,9 @@ cmd_hooks() {
               printf '%b[WIKI]%b Pre-push trigger: verifying wiki changes.\n' "$_C" "$_NC"
             fi
           fi
+          if [ -x "$NEXUS_DIR/.githooks/pre-push" ]; then
+            "$NEXUS_DIR/.githooks/pre-push" "$@" || return $?
+          fi
           return 0
           ;;
       esac
@@ -1595,7 +1619,7 @@ YAML_EOF
   sync_prompts
   NEXUS_DIR="$_orig_nexus"
 
-  # ---- 5. Ensure repos/, .rnex/, and local configs are gitignored ---------
+  # ---- 5. Ensure repos/ and local configs are gitignored ---------
   reconcile_gitignore "$_target_dir"
 
   # ---- 6. Generate VS Code / Cursor workspace if configured ----------------
@@ -1952,18 +1976,18 @@ cmd_status() {
   fi
 
   _gi="$NEXUS_DIR/.gitignore"
-  _gi_repos=0; _gi_rnex=0; _gi_local=0; _gi_has_counter=0
+  _gi_repos=0; _gi_local=0; _gi_has_counter=0; _gi_has_rnex=0
   if [ -f "$_gi" ]; then
     grep -q '^repos' "$_gi" 2>/dev/null && _gi_repos=1
-    (grep -q '^\.rnex/' "$_gi" 2>/dev/null || grep -q '^\.rnex$' "$_gi" 2>/dev/null) && _gi_rnex=1
     grep -qF "$RNEX_LOCAL_CONFIG_FILE" "$_gi" 2>/dev/null && _gi_local=1
     grep -q "lint_trigger_counter" "$_gi" 2>/dev/null && _gi_has_counter=1
+    (grep -q '^\.rnex/' "$_gi" 2>/dev/null || grep -q '^\.rnex$' "$_gi" 2>/dev/null) && _gi_has_rnex=1
   fi
 
-  if [ "$_gi_repos" -eq 1 ] && [ "$_gi_rnex" -eq 1 ] && [ "$_gi_local" -eq 1 ] && [ "$_gi_has_counter" -eq 0 ]; then
-    printf '  %b✓%b Git Ignore:    repos/, .rnex/, and %s ignored in .gitignore\n' "$_G" "$_NC" "$RNEX_LOCAL_CONFIG_FILE"
+  if [ "$_gi_repos" -eq 1 ] && [ "$_gi_local" -eq 1 ] && [ "$_gi_has_counter" -eq 0 ] && [ "$_gi_has_rnex" -eq 0 ]; then
+    printf '  %b✓%b Git Ignore:    repos/ and %s ignored in .gitignore\n' "$_G" "$_NC" "$RNEX_LOCAL_CONFIG_FILE"
   else
-    printf '  %b!%b Git Ignore:    recommend running "rnex fix" to update .gitignore (repos/, .rnex/, local configs)\n' "$_Y" "$_NC"
+    printf '  %b!%b Git Ignore:    recommend running "rnex fix" to update .gitignore (repos/, local configs)\n' "$_Y" "$_NC"
   fi
 
   _hooks_path="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
@@ -2177,7 +2201,7 @@ cmd_fix() {
         _cur_hp="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
         if [ "$_cur_hp" != ".rnex/hooks" ] && [ "$_cur_hp" != "$NEXUS_DIR/.rnex/hooks" ]; then
           cmd_hooks_install_dir "$NEXUS_DIR"
-        else
+        elif [ "${_RNEX_INSIDE_HOOK:-0}" -ne 1 ]; then
           _hooks_dir="$NEXUS_DIR/.rnex/hooks"
           _create_hook_script "$_hooks_dir/post-merge" "post-merge"
           _create_hook_script "$_hooks_dir/post-commit" "post-commit"
@@ -2189,11 +2213,13 @@ cmd_fix() {
     *)
       _cur_hp="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
       if [ "$_cur_hp" = ".rnex/hooks" ] || [ "$_cur_hp" = "$NEXUS_DIR/.rnex/hooks" ]; then
-        _hooks_dir="$NEXUS_DIR/.rnex/hooks"
-        _create_hook_script "$_hooks_dir/post-merge" "post-merge"
-        _create_hook_script "$_hooks_dir/post-commit" "post-commit"
-        _create_hook_script "$_hooks_dir/pre-commit" "pre-commit"
-        _create_hook_script "$_hooks_dir/pre-push" "pre-push"
+        if [ "${_RNEX_INSIDE_HOOK:-0}" -ne 1 ]; then
+          _hooks_dir="$NEXUS_DIR/.rnex/hooks"
+          _create_hook_script "$_hooks_dir/post-merge" "post-merge"
+          _create_hook_script "$_hooks_dir/post-commit" "post-commit"
+          _create_hook_script "$_hooks_dir/pre-commit" "pre-commit"
+          _create_hook_script "$_hooks_dir/pre-push" "pre-push"
+        fi
       fi
       ;;
   esac