repo-nexus 0.7.32 → 0.7.34

package/lib/commands/init.sh

@@ -17,18 +17,8 @@ cmd_init() {
       -y|--yes) _non_interactive=1 ;;
       --hooks) _cli_hooks="true" ;;
       --no-hooks) _cli_no_hooks=1; _cli_hooks="false" ;;
-      --copilot) _cli_plugins="${_cli_plugins:+$_cli_plugins }copilot" ;;
-      --no-copilot) _cli_plugins="$(printf '%s' " $_cli_plugins " | sed -e 's/ copilot / /g' -e 's/^ *//;s/ *$//')" ;;
-      --claude) _cli_plugins="${_cli_plugins:+$_cli_plugins }claude" ;;
-      --no-claude) _cli_plugins="$(printf '%s' " $_cli_plugins " | sed -e 's/ claude / /g' -e 's/^ *//;s/ *$//')" ;;
-      --gemini) _cli_plugins="${_cli_plugins:+$_cli_plugins }gemini" ;;
-      --no-gemini) _cli_plugins="$(printf '%s' " $_cli_plugins " | sed -e 's/ gemini / /g' -e 's/^ *//;s/ *$//')" ;;
-      --cursor) _cli_plugins="${_cli_plugins:+$_cli_plugins }cursor" ;;
-      --no-cursor) _cli_plugins="$(printf '%s' " $_cli_plugins " | sed -e 's/ cursor / /g' -e 's/^ *//;s/ *$//')" ;;
-      --windsurf) _cli_plugins="${_cli_plugins:+$_cli_plugins }windsurf" ;;
-      --no-windsurf) _cli_plugins="$(printf '%s' " $_cli_plugins " | sed -e 's/ windsurf / /g' -e 's/^ *//;s/ *$//')" ;;
-      --karpathy|--karpathy-llm) _cli_plugins="${_cli_plugins:+$_cli_plugins }karpathy-llm" ;;
-      --no-karpathy|--no-karpathy-llm) _cli_plugins="$(printf '%s' " $_cli_plugins " | sed -e 's/ karpathy-llm / /g' -e 's/^ *//;s/ *$//')" ;;
+      --karpathy) _cli_plugins="${_cli_plugins:+$_cli_plugins }karpathy-llm" ;;
+      --no-karpathy) _cli_plugins="$(printf '%s' " $_cli_plugins " | sed -e 's/ karpathy-llm / /g' -e 's/^ *//;s/ *$//')" ;;
       --plugin|--enable-plugin)
         shift
         [ -n "$1" ] && _cli_plugins="${_cli_plugins:+$_cli_plugins }$1"
@@ -53,6 +43,18 @@ cmd_init() {
           esac
         fi
         ;;
+      --no-*)
+        _pflag="${1#--no-}"
+        if find_plugin_dir "$_pflag" >/dev/null 2>&1; then
+          _cli_plugins="$(printf '%s' " $_cli_plugins " | sed -e "s/ $_pflag / /g" -e 's/^ *//;s/ *$//')"
+        fi
+        ;;
+      --*)
+        _pflag="${1#--}"
+        if find_plugin_dir "$_pflag" >/dev/null 2>&1; then
+          _cli_plugins="${_cli_plugins:+$_cli_plugins }$_pflag"
+        fi
+        ;;
       *)
         if [ -z "$_init_dir" ]; then
           _init_dir="$1"
@@ -155,9 +157,6 @@ YAML_EOF
   fi
 
   # Set active workspace context for initialization
-  _orig_nexus="$NEXUS_DIR"
-  _orig_yaml="$WORKSPACE_YAML"
-  _orig_local_yaml="$WORKSPACE_LOCAL_YAML"
   NEXUS_DIR="$_init_dir"
   WORKSPACE_YAML="$_target_yaml"
   WORKSPACE_LOCAL_YAML="$_init_dir/$RNEX_LOCAL_CONFIG_FILE"
@@ -166,11 +165,9 @@ YAML_EOF
   if ! has_active_provider_instructions "$_init_dir"; then
     merge_rnex_instructions "$_init_dir/AGENTS.md"
   fi
-  [ -f "$_init_dir/CLAUDE.md" ] && merge_rnex_instructions "$_init_dir/CLAUDE.md"
-  [ -f "$_init_dir/GEMINI.md" ] && merge_rnex_instructions "$_init_dir/GEMINI.md"
-  [ -f "$_init_dir/.cursorrules" ] && merge_rnex_instructions "$_init_dir/.cursorrules"
-  [ -f "$_init_dir/.windsurfrules" ] && merge_rnex_instructions "$_init_dir/.windsurfrules"
-  [ -f "$_init_dir/.github/copilot-instructions.md" ] && merge_rnex_instructions "$_init_dir/.github/copilot-instructions.md"
+  for _if in CLAUDE.md GEMINI.md .cursorrules .windsurfrules .github/copilot-instructions.md; do
+    [ -f "$_init_dir/$_if" ] && merge_rnex_instructions "$_init_dir/$_if"
+  done
 
   # ---- 3. Create repos directory with .gitkeep -----------------------------
   _repos_dir="$_init_dir/repos"
@@ -183,50 +180,21 @@ YAML_EOF
   sync_plugins
   build_ai_instructions "$_init_dir"
   sync_skills
-  WORKSPACE_LOCAL_YAML="$_orig_local_yaml"
-  WORKSPACE_YAML="$_orig_yaml"
-  NEXUS_DIR="$_orig_nexus"
 
   # ---- 5. Ensure repos/ and local configs are gitignored ---------
   reconcile_gitignore "$_init_dir"
 
   # ---- 6. Generate VS Code / Cursor workspace if configured ----------------
-  _target_cw="$_cli_code_workspace"
-  if [ -z "$_target_cw" ] && [ -f "$_init_dir/$RNEX_LOCAL_CONFIG_FILE" ]; then
-    _target_cw="$(awk '/^(code_workspace|vscode_workspace):/ { sub(/^[a-zA-Z0-9_]+:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$_init_dir/$RNEX_LOCAL_CONFIG_FILE")"
-  fi
-  if [ -z "$_target_cw" ] && [ -f "$_target_yaml" ]; then
-    _target_cw="$(awk '/^(code_workspace|vscode_workspace):/ { sub(/^[a-zA-Z0-9_]+:[ ]*/, ""); sub(/[ ]*#.*/, ""); val=$0 } END { if (val) print val }' "$_target_yaml")"
-  fi
-  _target_cw="$(echo "$_target_cw" | tr -d " \t\r\n'\"")"
-  case "$_target_cw" in
-    true|yes|1)
-      _cw_name="$(basename "$_init_dir").code-workspace"
-      ;;
-    false|no|0|none|"")
-      _cw_name=""
-      ;;
-    *)
-      case "$_target_cw" in
-        *.code-workspace) _cw_name="$_target_cw" ;;
-        *) _cw_name="$_target_cw.code-workspace" ;;
-      esac
-      ;;
-  esac
-
+  _orig_repos="$REPOS_DIR"
+  _orig_cw="$CODE_WORKSPACE_FILE"
+  _load_code_workspace "$_cli_code_workspace"
+  _cw_name="$CODE_WORKSPACE_FILE"
   if [ -n "$_cw_name" ]; then
-    _orig_nexus="$NEXUS_DIR"
-    _orig_repos="$REPOS_DIR"
-    _orig_cw="$CODE_WORKSPACE_FILE"
-    CODE_WORKSPACE_FILE="$_cw_name"
-    NEXUS_DIR="$_init_dir"
-    _repos_rel="repos"
-    REPOS_DIR="$_init_dir/$_repos_rel"
+    REPOS_DIR="$_init_dir/repos"
     sync_code_workspace
-    NEXUS_DIR="$_orig_nexus"
-    REPOS_DIR="$_orig_repos"
-    CODE_WORKSPACE_FILE="$_orig_cw"
   fi
+  REPOS_DIR="$_orig_repos"
+  CODE_WORKSPACE_FILE="$_orig_cw"
 
   # ---- 7. Setup automated Git hooks if inside a Git repository ------------
   if [ "$_is_git_ws" -eq 1 ]; then
@@ -240,10 +208,6 @@ YAML_EOF
   _write_auto_sync_script "$_init_dir"
   update_sync_stamp "$_init_dir"
 
-  NEXUS_DIR="$_init_dir"
-  WORKSPACE_YAML="$_target_yaml"
-  WORKSPACE_LOCAL_YAML="$_init_dir/$RNEX_LOCAL_CONFIG_FILE"
-
   if [ "$_config_created" -eq 1 ]; then
     printf '\n'
     log_ok "Initialized Repo Nexus workspace at ${_BOLD}$_init_dir${_NC}"

package/lib/commands/plugin.sh

@@ -245,29 +245,16 @@ cmd_rnex_dir() {
   done
 
   case "$_action" in
-    enable)
+    enable|disable)
       [ -n "$_name" ] || die "Usage: rnex rnex-dir <enable|disable> <name> [--local]"
       yaml_has_repo "$_name" || die "Repo '$_name' is not registered"
-      if [ "$_is_local" -eq 1 ]; then
-        yaml_set_local "$_name" "rnex_dir" "true"
-        log_ok "Enabled member .rnex directory for '$_name' locally in $(basename "$WORKSPACE_LOCAL_YAML")"
+      if [ "$_action" = "enable" ]; then
+        _repo_set_config_and_log "$_name" "rnex_dir" "true" "$_is_local" "Enabled member .rnex directory for"
+        sync_repo_rnex "$_name"
       else
-        yaml_set "$_name" "rnex_dir" "true"
-        log_ok "Enabled member .rnex directory for '$_name' in $(basename "$WORKSPACE_YAML")"
+        _repo_set_config_and_log "$_name" "rnex_dir" "false" "$_is_local" "Disabled member .rnex directory for"
+        clean_repo_rnex "$_name"
       fi
-      sync_repo_rnex "$_name"
-      ;;
-    disable)
-      [ -n "$_name" ] || die "Usage: rnex rnex-dir <enable|disable> <name> [--local]"
-      yaml_has_repo "$_name" || die "Repo '$_name' is not registered"
-      if [ "$_is_local" -eq 1 ]; then
-        yaml_set_local "$_name" "rnex_dir" "false"
-        log_ok "Disabled member .rnex directory for '$_name' locally in $(basename "$WORKSPACE_LOCAL_YAML")"
-      else
-        yaml_set "$_name" "rnex_dir" "false"
-        log_ok "Disabled member .rnex directory for '$_name' in $(basename "$WORKSPACE_YAML")"
-      fi
-      clean_repo_rnex "$_name"
       ;;
     *)
       die "Usage: rnex rnex-dir <enable|disable> <name> [--local]"

package/lib/commands/repo.sh

@@ -168,10 +168,22 @@ cmd_exec() {
   return 0
 }
 
-cmd_enable() {
+_repo_set_config_and_log() {
+  _rname="$1"; _key="$2"; _val="$3"; _local_flag="$4"; _verb="$5"
+  if [ "$_local_flag" -eq 1 ]; then
+    yaml_set_local "$_rname" "$_key" "$_val"
+    log_ok "$_verb '$_rname' locally in $(basename "$WORKSPACE_LOCAL_YAML")"
+  else
+    yaml_set "$_rname" "$_key" "$_val"
+    log_ok "$_verb '$_rname' in $(basename "$WORKSPACE_YAML")"
+  fi
+}
+
+_repo_toggle_state() {
   require_workspace
-  _is_local=0
-  _name=""
+  _target_val="$1"; _verb="$2"
+  shift 2
+  _is_local=0; _name=""
   while [ $# -gt 0 ]; do
     case "$1" in
       --local) _is_local=1 ;;
@@ -179,42 +191,22 @@ cmd_enable() {
     esac
     shift
   done
-  [ -n "$_name" ] || die "Usage: rnex enable [--local] <name>"
+  _cmd_lbl="enable"
+  [ "$_target_val" = "false" ] && _cmd_lbl="disable"
+  [ -n "$_name" ] || die "Usage: rnex $_cmd_lbl [--local] <name>"
   yaml_has_repo "$_name" || die "Repo '$_name' is not registered"
+  _repo_set_config_and_log "$_name" "enabled" "$_target_val" "$_is_local" "$_verb"
+}
 
-  if [ "$_is_local" -eq 1 ]; then
-    yaml_set_local "$_name" "enabled" "true"
-    log_ok "Enabled repo '$_name' locally in $(basename "$WORKSPACE_LOCAL_YAML")"
-  else
-    yaml_set "$_name" "enabled" "true"
-    log_ok "Enabled repo '$_name' in $(basename "$WORKSPACE_YAML")"
-  fi
+cmd_enable() {
+  _repo_toggle_state "true" "Enabled repo" "$@"
   sync_repo_rnex "$_name"
   sync_code_workspace
   run_hook "after_sync" "$@"
 }
 
 cmd_disable() {
-  require_workspace
-  _is_local=0
-  _name=""
-  while [ $# -gt 0 ]; do
-    case "$1" in
-      --local) _is_local=1 ;;
-      *) _name="$1" ;;
-    esac
-    shift
-  done
-  [ -n "$_name" ] || die "Usage: rnex disable [--local] <name>"
-  yaml_has_repo "$_name" || die "Repo '$_name' is not registered"
-
-  if [ "$_is_local" -eq 1 ]; then
-    yaml_set_local "$_name" "enabled" "false"
-    log_ok "Disabled repo '$_name' locally in $(basename "$WORKSPACE_LOCAL_YAML")"
-  else
-    yaml_set "$_name" "enabled" "false"
-    log_ok "Disabled repo '$_name' in $(basename "$WORKSPACE_YAML")"
-  fi
+  _repo_toggle_state "false" "Disabled repo" "$@"
   sync_code_workspace
 }
 

package/lib/commands/status.sh

@@ -4,6 +4,23 @@
 # lib/commands/status.sh — Workspace health and status diagnostics
 # ============================================================================
 
+_status_active_plugin_trigger() {
+  for _p in $(yaml_list_plugins 2>/dev/null || true); do
+    yaml_plugin_enabled "$_p" 2>/dev/null || continue
+    _trig="$(yaml_plugin_get "$_p" "lint_trigger" 2>/dev/null || true)"
+    [ -z "$_trig" ] && _trig="$(yaml_plugin_get "$_p" "trigger" 2>/dev/null || true)"
+    if [ -n "$_trig" ] && [ "$_trig" != "manual" ]; then
+      printf '%s' "$_trig"
+      return 0
+    fi
+  done
+  return 0
+}
+
+_status_has_rnex_skills() {
+  [ -d "$1" ] && { ls "$1"/rnex-*.md >/dev/null 2>&1 || ls -d "$1"/rnex-* >/dev/null 2>&1; }
+}
+
 cmd_status() {
   require_workspace
   ensure_repos_dir
@@ -90,16 +107,7 @@ cmd_status() {
       ;;
     true|yes|1)
       if [ "$_gh_active" -eq 1 ]; then
-        _active_trigger=""
-        for _p in $(yaml_list_plugins 2>/dev/null || true); do
-          yaml_plugin_enabled "$_p" 2>/dev/null || continue
-          _trig="$(yaml_plugin_get "$_p" "lint_trigger" 2>/dev/null || true)"
-          [ -z "$_trig" ] && _trig="$(yaml_plugin_get "$_p" "trigger" 2>/dev/null || true)"
-          if [ -n "$_trig" ] && [ "$_trig" != "manual" ]; then
-            _active_trigger="$_trig"
-            break
-          fi
-        done
+        _active_trigger="$(_status_active_plugin_trigger)"
         if [ -n "$_active_trigger" ]; then
           printf '  %b✓%b Git Hooks:     active (git_hooks: true, .rnex/hooks — %s)\n' "$_G" "$_NC" "$_active_trigger"
         else
@@ -111,16 +119,7 @@ cmd_status() {
       ;;
     *)
       if [ "$_gh_active" -eq 1 ]; then
-        _active_trigger=""
-        for _p in $(yaml_list_plugins 2>/dev/null || true); do
-          yaml_plugin_enabled "$_p" 2>/dev/null || continue
-          _trig="$(yaml_plugin_get "$_p" "lint_trigger" 2>/dev/null || true)"
-          [ -z "$_trig" ] && _trig="$(yaml_plugin_get "$_p" "trigger" 2>/dev/null || true)"
-          if [ -n "$_trig" ] && [ "$_trig" != "manual" ]; then
-            _active_trigger="$_trig"
-            break
-          fi
-        done
+        _active_trigger="$(_status_active_plugin_trigger)"
         if [ -n "$_active_trigger" ]; then
           printf '  %b✓%b Git Hooks:     active (.rnex/hooks — post-merge auto-sync, %s)\n' "$_G" "$_NC" "$_active_trigger"
         else
@@ -145,21 +144,18 @@ cmd_status() {
   elif ! has_active_provider_instructions "$NEXUS_DIR"; then
     printf '  %b✗%b %s %b(standard instructions directive — MISSING; run "rnex sync" to create)%b\n' "$_R" "$_NC" "AGENTS.md" "$_R" "$_NC"
   fi
-  if [ -f "$NEXUS_DIR/CLAUDE.md" ]; then
-    printf '  %b✓%b %s %b(Claude instructions)%b\n' "$_G" "$_NC" "CLAUDE.md" "$_DIM" "$_NC"
-  fi
-  if [ -f "$NEXUS_DIR/GEMINI.md" ]; then
-    printf '  %b✓%b %s %b(Gemini instructions)%b\n' "$_G" "$_NC" "GEMINI.md" "$_DIM" "$_NC"
-  fi
-  if [ -f "$NEXUS_DIR/.cursorrules" ]; then
-    printf '  %b✓%b %s %b(Cursor instructions)%b\n' "$_G" "$_NC" ".cursorrules" "$_DIM" "$_NC"
-  fi
-  if [ -f "$NEXUS_DIR/.windsurfrules" ]; then
-    printf '  %b✓%b %s %b(Windsurf instructions)%b\n' "$_G" "$_NC" ".windsurfrules" "$_DIM" "$_NC"
-  fi
-  if [ -f "$NEXUS_DIR/.github/copilot-instructions.md" ]; then
-    printf '  %b✓%b %s %b(Copilot instructions)%b\n' "$_G" "$_NC" ".github/copilot-instructions.md" "$_DIM" "$_NC"
-  fi
+  for _pair in \
+    "CLAUDE.md:Claude" \
+    "GEMINI.md:Gemini" \
+    ".cursorrules:Cursor" \
+    ".windsurfrules:Windsurf" \
+    ".github/copilot-instructions.md:Copilot"; do
+    _ifile="${_pair%%:*}"
+    _ilbl="${_pair#*:}"
+    if [ -f "$NEXUS_DIR/$_ifile" ]; then
+      printf '  %b✓%b %s %b(%s instructions)%b\n' "$_G" "$_NC" "$_ifile" "$_DIM" "$_ilbl" "$_NC"
+    fi
+  done
   if [ -n "$CODE_WORKSPACE_FILE" ]; then
     if [ -f "$NEXUS_DIR/$CODE_WORKSPACE_FILE" ]; then
       printf '  %b✓%b %s %b(VS Code / Cursor workspace)%b\n' "$_G" "$_NC" "$CODE_WORKSPACE_FILE" "$_DIM" "$_NC"
@@ -178,23 +174,20 @@ cmd_status() {
   if [ -d "$NEXUS_DIR/.rnex/skills" ]; then
     printf '  %b✓%b %s %b(workspace skills)%b\n' "$_G" "$_NC" ".rnex/skills/" "$_DIM" "$_NC"
   fi
-  if [ -d "$NEXUS_DIR/.cursor/rules" ] && ls "$NEXUS_DIR/.cursor/rules"/rnex-*.md >/dev/null 2>&1; then
-    printf '  %b✓%b %s %b(Cursor user skills)%b\n' "$_G" "$_NC" ".cursor/rules/" "$_DIM" "$_NC"
-  fi
-  if [ -d "$NEXUS_DIR/.claude/skills" ] && { ls "$NEXUS_DIR/.claude/skills"/rnex-*.md >/dev/null 2>&1 || ls -d "$NEXUS_DIR/.claude/skills"/rnex-* >/dev/null 2>&1; }; then
-    printf '  %b✓%b %s %b(Claude user skills)%b\n' "$_G" "$_NC" ".claude/skills/" "$_DIM" "$_NC"
-  fi
-  if [ -d "$NEXUS_DIR/.windsurf/rules" ] && ls "$NEXUS_DIR/.windsurf/rules"/rnex-*.md >/dev/null 2>&1; then
-    printf '  %b✓%b %s %b(Windsurf user skills)%b\n' "$_G" "$_NC" ".windsurf/rules/" "$_DIM" "$_NC"
-  fi
-  if [ -d "$NEXUS_DIR/.agents/skills" ] && { ls "$NEXUS_DIR/.agents/skills"/rnex-*.md >/dev/null 2>&1 || ls -d "$NEXUS_DIR/.agents/skills"/rnex-* >/dev/null 2>&1; }; then
-    printf '  %b✓%b %s %b(Gemini user skills)%b\n' "$_G" "$_NC" ".agents/skills/" "$_DIM" "$_NC"
-  elif [ -d "$NEXUS_DIR/.gemini/skills" ] && { ls "$NEXUS_DIR/.gemini/skills"/rnex-*.md >/dev/null 2>&1 || ls -d "$NEXUS_DIR/.gemini/skills"/rnex-* >/dev/null 2>&1; }; then
-    printf '  %b✓%b %s %b(Gemini user skills)%b\n' "$_G" "$_NC" ".gemini/skills/" "$_DIM" "$_NC"
-  fi
-  if [ -d "$NEXUS_DIR/.github/skills" ] && { ls "$NEXUS_DIR/.github/skills"/rnex-*.md >/dev/null 2>&1 || ls -d "$NEXUS_DIR/.github/skills"/rnex-* >/dev/null 2>&1; }; then
-    printf '  %b✓%b %s %b(Copilot user skills)%b\n' "$_G" "$_NC" ".github/skills/" "$_DIM" "$_NC"
-  fi
+  for _spair in \
+    ".cursor/rules/:Cursor" \
+    ".claude/skills/:Claude" \
+    ".windsurf/rules/:Windsurf" \
+    ".agents/skills/:Gemini" \
+    ".gemini/skills/:Gemini" \
+    ".github/skills/:Copilot"; do
+    _sdir="${_spair%%:*}"
+    _slbl="${_spair#*:}"
+    [ "$_sdir" = ".gemini/skills/" ] && _status_has_rnex_skills "$NEXUS_DIR/.agents/skills" && continue
+    if _status_has_rnex_skills "$NEXUS_DIR/${_sdir%/}"; then
+      printf '  %b✓%b %s %b(%s user skills)%b\n' "$_G" "$_NC" "$_sdir" "$_DIM" "$_slbl" "$_NC"
+    fi
+  done
   printf '\n'
 
   printf '%bActive Plugins:%b\n' "$_BOLD" "$_NC"

package/lib/plugins.sh

@@ -205,46 +205,26 @@ sync_plugin_bundle() {
   done
 }
 
-# Sync plugins into scoped directories: .rnex/plugins/<plugin-name>/
-sync_plugins() {
-  # Clean up any bogus placeholder directories accidentally created in workspace root
-  for _bogus in \
-    "$NEXUS_DIR/\"{wiki_dir}" \
-    "$NEXUS_DIR/\"{raw_dir}" \
-    "$NEXUS_DIR/{wiki_dir}" \
-    "$NEXUS_DIR/{raw_dir}"; do
-    if [ -d "$_bogus" ]; then
-      rm -rf "$_bogus"
-      log_dim "Cleaned up leaked placeholder directory: $(basename "$_bogus")"
-    fi
-  done
-
-  # Clean up obsolete leaked root ./raw and ./wiki directories if non-default paths are configured
-  _raw_cfg="$(plugin_primary_source_dir "karpathy-llm" 2>/dev/null || true)"
-  [ -z "$_raw_cfg" ] && _raw_cfg="docs"
+# Clean up obsolete leaked root ./raw and ./wiki directories if non-default paths are configured
+_clean_leaked_plugin_dirs() {
+  _cld_root="${1:-$NEXUS_DIR}"
+  _cld_raw="$2"
+  _cld_wiki="$3"
 
-  _wiki_cfg="$(yaml_plugin_get "karpathy-llm" "wiki_dir" 2>/dev/null || true)"
-  [ -z "$_wiki_cfg" ] && _wiki_cfg=".rnex/wiki"
-  _wiki_cfg="$(printf '%s' "$_wiki_cfg" | sed -e 's/^[[:space:]]*//' -e 's/[[:space:]]*$//' | tr -d "'\"" | sed -e 's#^\./##' -e 's#^/##' -e 's#/$##')"
-
-  if [ "$_raw_cfg" != "raw" ] && [ -d "$NEXUS_DIR/raw" ] && \
+  if [ "$_cld_raw" != "raw" ] && [ -d "$_cld_root/raw" ] && \
      ! plugin_source_dirs "karpathy-llm" 2>/dev/null | grep -qx 'raw'; then
-    if ! rmdir "$NEXUS_DIR/raw" 2>/dev/null; then
+    if ! rmdir "$_cld_root/raw" 2>/dev/null; then
       _can_clean=1
-      for _f in "$NEXUS_DIR/raw"/* "$NEXUS_DIR/raw"/.[!.]* "$NEXUS_DIR/raw"/..?*; do
+      for _f in "$_cld_root/raw"/* "$_cld_root/raw"/.[!.]* "$_cld_root/raw"/..?*; do
         [ -e "$_f" ] || continue
         _b="$(basename "$_f")"
-        if [ "$_b" = ".gitkeep" ]; then
-          continue
-        fi
-        if [ -f "$NEXUS_DIR/$_raw_cfg/$_b" ] && cmp -s "$_f" "$NEXUS_DIR/$_raw_cfg/$_b"; then
-          continue
-        fi
+        [ "$_b" = ".gitkeep" ] && continue
+        [ -f "$_cld_root/$_cld_raw/$_b" ] && cmp -s "$_f" "$_cld_root/$_cld_raw/$_b" && continue
         _can_clean=0
         break
       done
       if [ "$_can_clean" -eq 1 ]; then
-        rm -rf "$NEXUS_DIR/raw"
+        rm -rf "$_cld_root/raw" 2>/dev/null || true
         log_dim "Cleaned up obsolete root raw/ directory"
       fi
     else
@@ -252,33 +232,52 @@ sync_plugins() {
     fi
   fi
 
-  if [ "$_wiki_cfg" != "wiki" ] && [ -d "$NEXUS_DIR/wiki" ]; then
-    if ! rmdir "$NEXUS_DIR/wiki" 2>/dev/null; then
+  if [ "$_cld_wiki" != "wiki" ] && [ -d "$_cld_root/wiki" ]; then
+    if ! rmdir "$_cld_root/wiki" 2>/dev/null; then
       _can_clean=1
-      for _f in "$NEXUS_DIR/wiki"/* "$NEXUS_DIR/wiki"/.[!.]* "$NEXUS_DIR/wiki"/..?*; do
+      for _f in "$_cld_root/wiki"/* "$_cld_root/wiki"/.[!.]* "$_cld_root/wiki"/..?*; do
         [ -e "$_f" ] || continue
         _b="$(basename "$_f")"
         case "$_b" in
-          index.md|_log.md|hot.md|.gitkeep)
-            continue
-            ;;
+          index.md|_log.md|hot.md|.gitkeep) continue ;;
           *)
-            if [ -f "$NEXUS_DIR/$_wiki_cfg/$_b" ] && cmp -s "$_f" "$NEXUS_DIR/$_wiki_cfg/$_b"; then
-              continue
-            fi
+            [ -f "$_cld_root/$_cld_wiki/$_b" ] && cmp -s "$_f" "$_cld_root/$_cld_wiki/$_b" && continue
             _can_clean=0
             break
             ;;
         esac
       done
       if [ "$_can_clean" -eq 1 ]; then
-        rm -rf "$NEXUS_DIR/wiki"
+        rm -rf "$_cld_root/wiki" 2>/dev/null || true
         log_dim "Cleaned up obsolete root wiki/ directory"
       fi
     else
       log_dim "Removed empty obsolete root wiki/ directory"
     fi
   fi
+}
+
+# Sync plugins into scoped directories: .rnex/plugins/<plugin-name>/
+sync_plugins() {
+  # Clean up any bogus placeholder directories accidentally created in workspace root
+  for _bogus in \
+    "$NEXUS_DIR/\"{wiki_dir}" \
+    "$NEXUS_DIR/\"{raw_dir}" \
+    "$NEXUS_DIR/{wiki_dir}" \
+    "$NEXUS_DIR/{raw_dir}"; do
+    if [ -d "$_bogus" ]; then
+      rm -rf "$_bogus"
+      log_dim "Cleaned up leaked placeholder directory: $(basename "$_bogus")"
+    fi
+  done
+
+  # Clean up obsolete leaked root ./raw and ./wiki directories if non-default paths are configured
+  _raw_cfg="$(plugin_primary_source_dir "karpathy-llm" 2>/dev/null || true)"
+  [ -n "$_raw_cfg" ] || _raw_cfg="docs"
+  _wiki_cfg="$(yaml_plugin_get "karpathy-llm" "wiki_dir" 2>/dev/null || true)"
+  [ -n "$_wiki_cfg" ] || _wiki_cfg=".rnex/wiki"
+  _wiki_cfg="$(normalize_rel_path "$_wiki_cfg")"
+  _clean_leaked_plugin_dirs "$NEXUS_DIR" "$_raw_cfg" "$_wiki_cfg"
 
   # 1. Prune plugins that are disabled or no longer enabled in config
   if [ -d "$NEXUS_DIR/.rnex/plugins" ]; then

package/lib/workspace.sh

@@ -156,7 +156,8 @@ _load_repos_dir() {
 }
 
 _load_code_workspace() {
-  _cw="$(yaml_get_top_level "code_workspace|vscode_workspace")"
+  _cw="${1:-}"
+  [ -n "$_cw" ] || _cw="$(yaml_get_top_level "code_workspace|vscode_workspace")"
   case "$_cw" in
     true|yes|1)
       _ws_basename="$(basename "$NEXUS_DIR")"

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.7.32",
+  "version": "0.7.34",
   "description": "Lightweight, zero-dependency Virtual Meta-Repo companion for multi-repo workspaces and shared AI context (no git submodules)",
   "bin": {
     "repo-nexus": "rnex",

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

@@ -1,62 +1,21 @@
 #!/bin/sh
 set -e
 _root="${RNEX_ROOT:-${NEXUS_DIR:-$PWD}}"
-
 if ! command -v merge_rnex_instructions >/dev/null 2>&1; then
-  if [ -f "$_root/.rnex/bin/rnex-env.sh" ]; then
-    . "$_root/.rnex/bin/rnex-env.sh"
-  fi
+  for _env_cand in "$_root/.rnex/bin/rnex-env.sh" "${RNEX_LIB_DIR:-}/sdk.sh" "$_root/lib/sdk.sh"; do
+    [ -n "$_env_cand" ] && [ -f "$_env_cand" ] && { . "$_env_cand"; break; }
+  done
 fi
 
-# Instructions management (always maintained when claude plugin is enabled)
 merge_rnex_instructions "$_root/CLAUDE.md"
 
-# Skills management
-_sk="$(provider_option_enabled "claude" "skills" 2>/dev/null && echo "true" || echo "false")"
-if [ "$_sk" != "true" ]; then
+if ! provider_option_enabled "claude" "skills" 2>/dev/null; then
   clean_provider_user_skills "$_root/.claude/skills"
 fi
 
-# Auto-sync hook configuration (SessionStart)
-_settings="$_root/.claude/settings.json"
 if provider_auto_sync_enabled "claude"; then
-  mkdir -p "$_root/.claude"
-  if [ ! -f "$_settings" ]; then
-    cat > "$_settings" <<'EOF'
-{
-  "hooks": {
-    "SessionStart": [
-      {
-        "command": ".rnex/bin/auto-sync.sh"
-      }
-    ]
-  }
-}
-EOF
-  elif ! grep -q "auto-sync.sh" "$_settings" 2>/dev/null; then
-    if grep -q '"SessionStart"' "$_settings" 2>/dev/null; then
-      _tmp="$(mktemp)"
-      awk '
-        /"SessionStart"[ ]*:[ ]*\[/ {
-          print
-          print "      { \"command\": \".rnex/bin/auto-sync.sh\" },"
-          next
-        }
-        { print }
-      ' "$_settings" > "$_tmp" && mv "$_tmp" "$_settings"
-    elif grep -q '"hooks"' "$_settings" 2>/dev/null; then
-      _tmp="$(mktemp)"
-      awk '
-        /"hooks"[ ]*:[ ]*\{/ {
-          print
-          print "    \"SessionStart\": [ { \"command\": \".rnex/bin/auto-sync.sh\" } ],"
-          next
-        }
-        { print }
-      ' "$_settings" > "$_tmp" && mv "$_tmp" "$_settings"
-    fi
-  fi
+  sync_claude_auto_sync_hook "$_root/.claude/settings.json"
 else
-  clean_claude_auto_sync_hook "$_settings"
+  clean_claude_auto_sync_hook "$_root/.claude/settings.json"
   rmdir "$_root/.claude" 2>/dev/null || true
 fi

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

@@ -1,11 +1,10 @@
 #!/bin/sh
 set -e
 _root="${RNEX_ROOT:-${NEXUS_DIR:-$PWD}}"
-
 if ! command -v clean_rnex_instructions >/dev/null 2>&1; then
-  if [ -f "$_root/.rnex/bin/rnex-env.sh" ]; then
-    . "$_root/.rnex/bin/rnex-env.sh"
-  fi
+  for _env_cand in "$_root/.rnex/bin/rnex-env.sh" "${RNEX_LIB_DIR:-}/sdk.sh" "$_root/lib/sdk.sh"; do
+    [ -n "$_env_cand" ] && [ -f "$_env_cand" ] && { . "$_env_cand"; break; }
+  done
 fi
 
 clean_rnex_instructions "$_root/CLAUDE.md"