repo-nexus 0.6.13 → 0.6.15

package/CHANGELOG.md

@@ -7,6 +7,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Changed
+- **Replaced `rnex fix` with `rnex sync` (with optional `--fix` flag)**:
+  - `rnex sync` without `--fix` performs a dry-run audit, checking workspace configuration, `.gitignore`, `.ignore`, AI routing instructions (`AGENTS.md`, provider files), active/disabled plugin assets, member repository scaffolding, and multi-root workspace definitions, logging any inconsistencies without mutating files.
+  - `rnex sync --fix` (or `-f`) executes full workspace reconciliation, schema upgrades, prompt/workflow synchronization, and asset repairs.
+  - `rnex fix` is maintained as a deprecated backward-compatible alias for `rnex sync --fix`, displaying a deprecation notice directing users to `rnex sync --fix`.
+  - All workspace documentation, guides, prompt templates, and AI routing instructions updated to reference `rnex sync` and `rnex sync --fix`.
+
 ### Added
 - **Modular Test Suite Architecture**:
   - Decomposed monolithic `tests/test_cli.sh` (996 lines, 36 tests) into modular, single-responsibility test suites under `tests/suites/`:

package/docs/cli/index.md

@@ -13,8 +13,8 @@ description: Fast reference cheatsheet for rnex commands, global options, enviro
 |:---|:---|:---|
 | [`rnex init`](workspace.md#rnex-init) | Workspace | Initialize a new Repo Nexus workspace. |
 | [`rnex status`](workspace.md#rnex-status) | Workspace | Inspect workspace health, clones, and AI instructions. |
-| [`rnex fix` / `sync`](workspace.md#rnex-fix-alias-sync) | Workspace | Reconcile config, routing, prompts, and plugins. |
-| [`rnex update` / `upgrade`](workspace.md#rnex-update-alias-upgrade) | Workspace | Part of fix: verify version, upgrade schema, and reconcile workspace. |
+| [`rnex sync`](workspace.md#rnex-sync) | Workspace | Check workspace consistency, or reconcile with `--fix`. |
+| [`rnex update` / `upgrade`](workspace.md#rnex-update-alias-upgrade) | Workspace | Part of sync --fix: verify version, upgrade schema, and reconcile workspace. |
 | [`rnex install`](workspace.md#rnex-install) | Workspace | Symlink `rnex` to `~/.local/bin`. |
 | [`rnex completion`](workspace.md#rnex-completion) | Workspace | Generate shell auto-completion for Zsh, Bash, or Fish. |
 | [`rnex version`](workspace.md#rnex-version) | Workspace | Display current installed CLI version. |
@@ -49,7 +49,7 @@ rnex [global-options] <command> [command-options] [arguments]
 
 ## Standardized Prompts Catalog
 
-Repo Nexus provides a standardized suite of operational prompt templates in `toolkit/prompts/` that sync to `.rnex/prompts/` during `rnex fix` or `rnex init`.
+Repo Nexus provides a standardized suite of operational prompt templates in `toolkit/prompts/` that sync to `.rnex/prompts/` during `rnex sync --fix` or `rnex init`.
 
 AI assistants navigate workflows via the catalog index at `.rnex/prompts/index.md`:
 

package/docs/cli/tooling.md

@@ -21,7 +21,7 @@ rnex hooks install [--local]
 ```
 
 #### Installed Hooks:
-* **`post-merge`**: Runs `rnex fix -y --quiet` automatically whenever `git pull` or upstream merges occur, ensuring newly added repositories and plugin updates sync instantly.
+* **`post-merge`**: Runs `rnex sync --fix -y --quiet` automatically whenever `git pull` or upstream merges occur, ensuring newly added repositories and plugin updates sync instantly.
 * **`post-commit`**: Alerts the user if documentation or wiki files were committed without running maintenance linters.
 * **`pre-commit`**: Runs pre-commit validation triggers declared by active plugins.
 * **`pre-push`**: Runs pre-push validation triggers before pushing to remote.

package/docs/cli/workspace.md

@@ -70,26 +70,29 @@ rnex status
 
 ---
 
-## `rnex fix` (alias: `sync`)
+## `rnex sync`
 
-Reconciles workspace configuration, AI routing blocks, skills, workflows, active plugins, and member clones.
+Synchronizes workspace assets, validates configuration, and audits or reconciles AI routing instructions, skills, workflows, active plugins, and member clones.
+
+- **Audit Mode (Default)**: When run without `--fix`, inspects workspace configuration, Git ignores, routing blocks, plugin assets, and member repositories, logging any issues or inconsistencies without mutating files.
+- **Reconcile Mode (`--fix`)**: Reconciles configuration schema, updates instruction files, synchronizes skills/workflows, mirrors operational prompts, and fixes inconsistencies.
 
 ### Syntax
 ```sh
-rnex fix [options]
 rnex sync [options]
 ```
 
 ### Options
 | Option | Shorthand | Type | Default | Description |
 |:---|:---|:---|:---|:---|
-| `--yes` | `-y` | boolean | `false` | Automatically confirm schema upgrades if prompted. |
+| `--fix` | `-f` | boolean | `false` | Apply reconciliation fixes across workspace, routing, plugins, and repos. |
+| `--yes` | `-y` | boolean | `false` | Automatically confirm schema upgrades if prompted (used with `--fix`). |
 | `--quiet` | `-q` | boolean | `false` | Quiet mode; suppresses non-error informational messages (ideal for hooks). |
-| `--upgrade` | | boolean | `false` | Explicitly trigger version upgrade reconciliation. |
+| `--upgrade` | | boolean | `false` | Explicitly trigger version upgrade reconciliation (implies `--fix`). |
 
-### Reconciliation Actions
+### Reconciliation Actions (with `--fix`)
 1. Upgrades configuration schema non-destructively if an older version is detected.
-2. Re-verifies `.gitignore` rules for `repos/` and local configs.
+2. Re-verifies `.gitignore` rules for `repos/` and local configs, and ensures `.ignore` contains `!repos/*`.
 3. Inserts or updates delimited routing blocks in universal `AGENTS.md` and active provider instruction files (`CLAUDE.md`, `GEMINI.md`, `.cursorrules`, `.windsurfrules`).
 4. Syncs base workflows to `.rnex/workflows/` and base skills to `.rnex/skills/`, purging any legacy `.rnex/prompts/`.
 5. Mirrors operational prompts to enabled AI providers (`.github/prompts/`, `.claude/commands/`, etc.).
@@ -102,7 +105,7 @@ rnex sync [options]
 
 ## `rnex update` (alias: `upgrade`)
 
-Runs version verification and invokes the unified `rnex fix` reconciliation engine to upgrade workspace configuration and routing instructions to match the installed CLI version.
+Runs version verification and invokes the unified `rnex sync --fix` reconciliation engine to upgrade workspace configuration and routing instructions to match the installed CLI version.
 
 ### Syntax
 ```sh
@@ -116,10 +119,10 @@ rnex upgrade [options]
 | `--yes` | `-y` | boolean | `false` | Automatically confirm schema upgrades if prompted. |
 | `--quiet` | `-q` | boolean | `false` | Suppress non-error informational messages. |
 
-### Relationship with `rnex fix`
-`rnex update` is part of the `rnex fix` command family:
+### Relationship with `rnex sync`
+`rnex update` is part of the `rnex sync` command family:
 * **Upfront Version Diagnostics**: Compares `version:` in `rnex.yaml` against the installed CLI version. If already matching, it reports that the workspace is up to date.
-* **Unified Reconciliation**: Delegates directly to `rnex fix`, ensuring configuration schema upgrades, instruction updates (`AGENTS.md`, provider files), skills/workflows sync, and plugin reconciliation occur in a single, idempotent pass.
+* **Unified Reconciliation**: Delegates directly to `rnex sync --fix`, ensuring configuration schema upgrades, instruction updates (`AGENTS.md`, provider files), skills/workflows sync, and plugin reconciliation occur in a single, idempotent pass.
 * **Non-Destructive Migration**: Upgrades schema keys while preserving comments, indentation, and custom configurations.
 
 ---

package/docs/examples/local-overrides.md

@@ -39,10 +39,10 @@ plugins:
 
 ### Apply the Overrides
 
-Run `rnex fix` to reconcile your local configuration:
+Run `rnex sync --fix` to reconcile your local configuration:
 
 ```bash
-rnex fix
+rnex sync --fix
 ```
 
 ```text

package/docs/guide/architecture.md

@@ -79,7 +79,7 @@ This workspace operates as a Repo Nexus Virtual Meta-Repo uniting independent re
 ```
 
 ::: tip Preserving Custom Instructions
-Any custom guidelines, rules, or documentation authored outside the `<!-- REPO-NEXUS:START -->` and `<!-- REPO-NEXUS:END -->` markers are strictly preserved during `rnex fix` or plugin synchronization.
+Any custom guidelines, rules, or documentation authored outside the `<!-- REPO-NEXUS:START -->` and `<!-- REPO-NEXUS:END -->` markers are strictly preserved during `rnex sync --fix` or plugin synchronization.
 :::
 
 ### 5. Multi-Root IDE Workspaces

package/docs/guide/configuration.md

@@ -90,7 +90,7 @@ plugins:
 | `version` | string | Current CLI version | Schema version compatibility check. |
 | `repos_dir` | string | `./repos` | Relative or absolute path where member repos are cloned. |
 | `code_workspace` | boolean \| string | `false` | Enables `.code-workspace` generation. Pass a string for custom filename. |
-| `git_hooks` | boolean | `true` | Configures `.rnex/hooks` as `core.hooksPath` during `rnex fix`. |
+| `git_hooks` | boolean | `true` | Configures `.rnex/hooks` as `core.hooksPath` during `rnex sync --fix`. |
 | `repos` | map | `{}` | Map of member repository specifications keyed by name. |
 | `plugins` | map | `{}` | Map of enabled plugins and their configuration options. |
 
@@ -124,9 +124,9 @@ plugins:
 After modifying configuration files directly, reconcile the workspace state:
 
 ```bash
-rnex fix
+rnex sync --fix
 ```
 
-::: tip Alias Available
-`rnex sync` is an identical alias for `rnex fix`. Both commands reconcile config, update directory structures, and regenerate instruction files.
+::: tip Audit vs. Reconcile
+Running `rnex sync` without `--fix` audits the workspace and logs any detected configuration inconsistencies without modifying files. Adding `--fix` applies the reconciliation.
 :::

package/docs/guide/workflows.md

@@ -66,7 +66,7 @@ If a command fails in any repository, `rnex exec` exits immediately with that co
 Repo Nexus includes an automated hook runner configured via `core.hooksPath = .rnex/hooks`.
 
 ### Core Automated Hooks
-1. **`post-merge`**: When you pull updates to the meta-repo (`git pull`), the hook automatically executes `rnex fix` to:
+1. **`post-merge`**: When you pull updates to the meta-repo (`git pull`), the hook automatically executes `rnex sync --fix` to:
    * Clone newly declared member repositories.
    * Update AI routing instructions (`AGENTS.md`, etc.).
    * Sync plugin changes.

package/docs/plugins/authoring.md

@@ -46,7 +46,7 @@ A plugin can contain any of the following standard directories:
 | `agents/` | Autonomous subagent declarations (`*.agent.md`). | Scoped to `.rnex/plugins/<plugin>/agents/`. Ingested by agents via `AGENTS.md` subagent routing. |
 | `instructions/` | Markdown guidelines and domain principles. | Scoped to `.rnex/plugins/<plugin>/instructions/`. |
 | `rules/` | Coding rules and architectural constraints. | Scoped to `.rnex/plugins/<plugin>/rules/`. |
-| `templates/` | Starter configuration files copied during `rnex fix`. | Copied to mapped paths specified in `templates:`. |
+| `templates/` | Starter configuration files copied during `rnex sync --fix`. | Copied to mapped paths specified in `templates:`. |
 
 > [!NOTE]
 > All AI assistants share `AGENTS.md` at workspace root. Tools, skills, workflows, and subagents stay inside `.rnex/` and are not mirrored externally. Prompts are exclusively for user invocation through IDE prompt pickers (e.g. `.github/prompts/`, `.claude/commands/`).
@@ -64,6 +64,6 @@ A plugin can contain any of the following standard directories:
    ```
 4. Reconcile workspace state:
    ```bash
-   rnex fix
+   rnex sync --fix
    ```
 5. Verify that assets were correctly scoped into `.rnex/plugins/my-plugin/`.

package/docs/plugins/index.md

@@ -116,7 +116,7 @@ plugins:
 Whenever you modify plugin configuration manually, run:
 
 ```bash
-rnex fix
+rnex sync --fix
 ```
 
 to reconcile scoped directories, prompt assets, provider mirrors, and member `.rnex/` folders.

package/lib/ai.sh

@@ -129,8 +129,8 @@ Each member repository is an autonomous Git repository. For repository-specific
 
 ## 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.
+- Run \`rnex sync --fix\` (or \`rnex sync\` to check for inconsistencies).
+- Use \`rnex sync --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>/\`).
@@ -177,8 +177,8 @@ Each member repository is an autonomous Git repository. For repository-specific
 
 ## 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.
+- Run \`rnex sync --fix\` (or \`rnex sync\` to check for inconsistencies).
+- Use \`rnex sync --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>/\`).

package/lib/commands/completion.sh

@@ -63,8 +63,8 @@ _rnex() {
     'list:List member repositories'
     'status:Inspect workspace health and status'
     'rnex-dir:Toggle .rnex directory integration for a repo'
-    'fix:Reconcile workspace, plugins, and .rnex directories'
-    'sync:Alias for fix'
+    'sync:Check workspace consistency (use --fix to reconcile)'
+    'fix:(Deprecated: use sync --fix) Reconcile workspace and plugins'
     'update:Upgrade workspace configuration and routing instructions'
     'upgrade:Alias for update'
     'hooks:Manage automated Git hooks'
@@ -127,7 +127,8 @@ 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 list -d "List repositories"
 complete -c rnex -n "__fish_use_subcommand" -a status -d "Inspect workspace status"
-complete -c rnex -n "__fish_use_subcommand" -a fix -d "Reconcile workspace"
+complete -c rnex -n "__fish_use_subcommand" -a sync -d "Check workspace consistency (use --fix to reconcile)"
+complete -c rnex -n "__fish_use_subcommand" -a fix -d "(Deprecated) Reconcile workspace"
 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"

package/lib/commands/fix.sh

@@ -1,128 +1,7 @@
 #!/bin/sh
 # shellcheck shell=sh
 # ============================================================================
-# lib/commands/fix.sh — Workspace reconciliation, upgrade, and repair
+# lib/commands/fix.sh — Backward compatibility forwarder for sync.sh
 # ============================================================================
 
-cmd_fix() {
-  require_workspace
-  ensure_repos_dir
-
-  _fix_auto_yes=0
-  _fix_quiet=0
-  _fix_upgrade_explicit=0
-
-  while [ $# -gt 0 ]; do
-    case "$1" in
-      -y|--yes) _fix_auto_yes=1 ;;
-      -q|--quiet) _fix_quiet=1 ;;
-      --upgrade) _fix_upgrade_explicit=1; _fix_auto_yes=1 ;;
-      *) ;;
-    esac
-    shift
-  done
-
-  [ "$_fix_quiet" -eq 0 ] && log_info "Reconciling Repo Nexus workspace at $NEXUS_DIR..."
-
-  # Version detection & non-destructive upgrade (integrated as single process)
-  _vc_res=0
-  version_cmp "$WORKSPACE_CONFIG_VERSION" "$RNEX_VERSION" || _vc_res=$?
-  if [ "$_vc_res" -eq 2 ]; then
-    upgrade_workspace_config "$WORKSPACE_YAML" "$RNEX_VERSION"
-    _load_workspace_version
-    _load_repos_dir
-    _load_code_workspace
-    _load_git_hooks
-    _load_copilot
-    [ "$_fix_quiet" -eq 0 ] && log_ok "Upgraded workspace configuration and routing instructions to v$RNEX_VERSION"
-  fi
-
-  # 1. Ensure .gitignore ignores repos/, .rnex/, and local configs, and strips legacy counters
-  reconcile_gitignore "$NEXUS_DIR"
-
-  # 2. Reconcile plugins (scopes, asset pruning for disabled plugins)
-  sync_plugins
-
-  # 3. Reconcile universal workspace instructions in AGENTS.md
-  merge_rnex_instructions "$NEXUS_DIR/AGENTS.md"
-
-  # 4. Sync standard skills, workflows, and provider prompts
-  sync_prompts
-
-  # 5. Reconcile Git hooks according to configuration
-  case "$GIT_HOOKS_CONFIG" in
-    false|no|0)
-      _cur_hp="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
-      if [ "$_cur_hp" = ".rnex/hooks" ] || [ "$_cur_hp" = "$NEXUS_DIR/.rnex/hooks" ]; then
-        cmd_hooks_uninstall_dir "$NEXUS_DIR"
-      fi
-      ;;
-    true|yes|1)
-      if git -C "$NEXUS_DIR" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
-        _cur_hp="$(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 "$NEXUS_DIR"
-        elif [ "${_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 "$_hooks_dir/post-commit" "post-commit"
-          _create_hook_script "$_hooks_dir/pre-commit" "pre-commit"
-          _create_hook_script "$_hooks_dir/pre-push" "pre-push"
-        fi
-      fi
-      ;;
-    *)
-      _cur_hp="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
-      if [ "$_cur_hp" = ".rnex/hooks" ] || [ "$_cur_hp" = "$NEXUS_DIR/.rnex/hooks" ]; then
-        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
-
-  # 6. Reconcile member repos
-  yaml_list_repos | while read -r _name; do
-    [ -n "$_name" ] || continue
-    if yaml_repo_enabled "$_name"; then
-      _rdir="$(resolve_repo_path "$_name")"
-      if [ -d "$_rdir" ]; then
-        sync_repo_rnex "$_name"
-      else
-        log_warn "Member repo '$_name' is missing on disk. Run: rnex clone"
-      fi
-    fi
-  done
-
-  # 7. Reconcile VS Code / Cursor multi-root workspace if configured
-  sync_code_workspace
-
-  if [ "$_fix_quiet" -eq 0 ]; then
-    log_ok "Fix complete — workspace, plugins, prompts, and member .rnex directories reconciled"
-  fi
-  return 0
-}
-
-cmd_sync() {
-  cmd_fix "$@"
-}
-
-cmd_update() {
-  require_workspace
-  _cmp=0
-  version_cmp "$WORKSPACE_CONFIG_VERSION" "$RNEX_VERSION" || _cmp=$?
-  if [ "$_cmp" -eq 0 ]; then
-    log_ok "Workspace configuration and routing instructions are already up to date (v$RNEX_VERSION)"
-  elif [ "$_cmp" -eq 1 ]; then
-    log_info "Workspace configuration version (v$WORKSPACE_CONFIG_VERSION) is newer than current CLI (v$RNEX_VERSION)"
-  fi
-  cmd_fix "$@"
-}
-
-cmd_upgrade() {
-  cmd_update "$@"
-}
+. "$RNEX_LIB_DIR/commands/sync.sh"

package/lib/commands/init.sh

@@ -98,7 +98,7 @@ cmd_init() {
   if [ -f "$_target_yaml" ]; then
     log_warn "Workspace configuration already exists at $_init_dir ($RNEX_CONFIG_FILE exists)"
     log_dim "To reconcile repos and plugins, run:"
-    log_dim "  rnex fix"
+    log_dim "  rnex sync --fix"
   else
     _init_plugins=""
     if [ "$_cli_copilot" = "true" ]; then

package/lib/commands/plugin.sh

@@ -145,7 +145,7 @@ cmd_plugin_enable() {
   fi
 
   sync_plugins
-  cmd_fix
+  cmd_sync --fix
   log_ok "Plugin '$_name' active in workspace (.rnex/plugins/$_name)"
 }
 
@@ -183,7 +183,7 @@ cmd_plugin_disable() {
   fi
 
   sync_plugins
-  cmd_fix -q
+  cmd_sync --fix -q
   log_ok "Plugin '$_name' disabled from workspace"
 }
 
@@ -222,12 +222,12 @@ cmd_plugin_update() {
     [ -n "$_pdir" ] || die "Plugin '$_pname' not found."
     log_info "Updating plugin '$_pname'..."
     sync_plugins
-    cmd_fix
+    cmd_sync --fix
     log_ok "Plugin '$_pname' updated"
   else
     log_info "Updating all enabled plugins..."
     sync_plugins
-    cmd_fix
+    cmd_sync --fix
     log_ok "All plugins updated"
   fi
 }

package/lib/commands/status.sh

@@ -44,7 +44,7 @@ cmd_status() {
   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" "$RNEX_LOCAL_CONFIG_FILE"
   else
-    printf '  %b!%b Git Ignore:    recommend running "rnex fix" to update .gitignore (repos/, local configs)\n' "$_Y" "$_NC"
+    printf '  %b!%b Git Ignore:    recommend running "rnex sync --fix" to update .gitignore (repos/, local configs)\n' "$_Y" "$_NC"
   fi
 
   _hooks_path="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
@@ -56,7 +56,7 @@ cmd_status() {
   case "$GIT_HOOKS_CONFIG" in
     false|no|0)
       if [ "$_gh_active" -eq 1 ]; then
-        printf '  %b!%b Git Hooks:     active in Git, but disabled in config (git_hooks: false; run "rnex fix" to reconcile)\n' "$_Y" "$_NC"
+        printf '  %b!%b Git Hooks:     active in Git, but disabled in config (git_hooks: false; run "rnex sync --fix" to reconcile)\n' "$_Y" "$_NC"
       else
         printf '  %b○%b Git Hooks:     disabled in configuration (git_hooks: false)\n' "$_DIM" "$_NC"
       fi
@@ -73,7 +73,7 @@ cmd_status() {
           printf '  %b✓%b Git Hooks:     active (git_hooks: true, .rnex/hooks — post-merge auto-sync)\n' "$_G" "$_NC"
         fi
       else
-        printf '  %b!%b Git Hooks:     enabled in config (git_hooks: true), but not active in Git (run "rnex fix")\n' "$_Y" "$_NC"
+        printf '  %b!%b Git Hooks:     enabled in config (git_hooks: true), but not active in Git (run "rnex sync --fix")\n' "$_Y" "$_NC"
       fi
       ;;
     *)
@@ -99,7 +99,7 @@ cmd_status() {
   if [ -f "$NEXUS_DIR/AGENTS.md" ]; then
     printf '  %b✓%b %s %b(standard instructions)%b\n' "$_G" "$_NC" "AGENTS.md" "$_DIM" "$_NC"
   else
-    printf '  %b✗%b %s %b(standard instructions — MISSING; run "rnex fix" to create)%b\n' "$_R" "$_NC" "AGENTS.md" "$_R" "$_NC"
+    printf '  %b✗%b %s %b(standard instructions — MISSING; run "rnex sync --fix" to create)%b\n' "$_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"
@@ -117,7 +117,7 @@ cmd_status() {
     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" "$_NC"
     else
-      printf '  %b✗%b %s %b(VS Code / Cursor workspace — MISSING; run "rnex fix" to create)%b\n' "$_R" "$_NC" "$CODE_WORKSPACE_FILE" "$_R" "$_NC"
+      printf '  %b✗%b %s %b(VS Code / Cursor workspace — MISSING; run "rnex sync --fix" to create)%b\n' "$_R" "$_NC" "$CODE_WORKSPACE_FILE" "$_R" "$_NC"
     fi
   fi
   for _found_cw in "$NEXUS_DIR"/*.code-workspace; do

package/lib/commands/sync.sh

@@ -0,0 +1,341 @@
+#!/bin/sh
+# shellcheck shell=sh
+# ============================================================================
+# lib/commands/sync.sh — Workspace synchronization, audit, and repair
+# ============================================================================
+
+cmd_sync() {
+  require_workspace
+  ensure_repos_dir
+
+  _sync_fix=0
+  _sync_auto_yes=0
+  _sync_quiet=0
+  _sync_upgrade_explicit=0
+
+  while [ $# -gt 0 ]; do
+    case "$1" in
+      -f|--fix) _sync_fix=1 ;;
+      -y|--yes) _sync_auto_yes=1 ;;
+      -q|--quiet) _sync_quiet=1 ;;
+      --upgrade) _sync_upgrade_explicit=1; _sync_auto_yes=1; _sync_fix=1 ;;
+      *) ;;
+    esac
+    shift
+  done
+
+  # --------------------------------------------------------------------------
+  # Reconciliation / fix mode (--fix)
+  # --------------------------------------------------------------------------
+  if [ "$_sync_fix" -eq 1 ]; then
+    [ "$_sync_quiet" -eq 0 ] && log_info "Reconciling Repo Nexus workspace at $NEXUS_DIR..."
+
+    # Version detection & non-destructive upgrade (integrated as single process)
+    _vc_res=0
+    version_cmp "$WORKSPACE_CONFIG_VERSION" "$RNEX_VERSION" || _vc_res=$?
+    if [ "$_vc_res" -eq 2 ]; then
+      upgrade_workspace_config "$WORKSPACE_YAML" "$RNEX_VERSION"
+      _load_workspace_version
+      _load_repos_dir
+      _load_code_workspace
+      _load_git_hooks
+      _load_copilot
+      [ "$_sync_quiet" -eq 0 ] && log_ok "Upgraded workspace configuration and routing instructions to v$RNEX_VERSION"
+    fi
+
+    # 1. Ensure .gitignore ignores repos/, .rnex/, and local configs, and strips legacy counters; ensure .ignore has !repos/*
+    reconcile_gitignore "$NEXUS_DIR"
+
+    # 2. Reconcile plugins (scopes, asset pruning for disabled plugins)
+    sync_plugins
+
+    # 3. Reconcile universal workspace instructions in AGENTS.md
+    merge_rnex_instructions "$NEXUS_DIR/AGENTS.md"
+
+    # 4. Sync standard skills, workflows, and provider prompts
+    sync_prompts
+
+    # 5. Reconcile Git hooks according to configuration
+    case "$GIT_HOOKS_CONFIG" in
+      false|no|0)
+        _cur_hp="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
+        if [ "$_cur_hp" = ".rnex/hooks" ] || [ "$_cur_hp" = "$NEXUS_DIR/.rnex/hooks" ]; then
+          cmd_hooks_uninstall_dir "$NEXUS_DIR"
+        fi
+        ;;
+      true|yes|1)
+        if git -C "$NEXUS_DIR" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+          _cur_hp="$(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 "$NEXUS_DIR"
+          elif [ "${_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 "$_hooks_dir/post-commit" "post-commit"
+            _create_hook_script "$_hooks_dir/pre-commit" "pre-commit"
+            _create_hook_script "$_hooks_dir/pre-push" "pre-push"
+          fi
+        fi
+        ;;
+      *)
+        _cur_hp="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
+        if [ "$_cur_hp" = ".rnex/hooks" ] || [ "$_cur_hp" = "$NEXUS_DIR/.rnex/hooks" ]; then
+          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
+
+    # 6. Reconcile member repos
+    yaml_list_repos | while read -r _name; do
+      [ -n "$_name" ] || continue
+      if yaml_repo_enabled "$_name"; then
+        _rdir="$(resolve_repo_path "$_name")"
+        if [ -d "$_rdir" ]; then
+          sync_repo_rnex "$_name"
+        else
+          log_warn "Member repo '$_name' is missing on disk. Run: rnex clone"
+        fi
+      fi
+    done
+
+    # 7. Reconcile VS Code / Cursor multi-root workspace if configured
+    sync_code_workspace
+
+    if [ "$_sync_quiet" -eq 0 ]; then
+      log_ok "Sync complete — workspace, plugins, prompts, and member .rnex directories reconciled"
+    fi
+    return 0
+  fi
+
+  # --------------------------------------------------------------------------
+  # Dry-run audit mode (without --fix) — log issues or inconsistencies only
+  # --------------------------------------------------------------------------
+  [ "$_sync_quiet" -eq 0 ] && log_info "Checking workspace synchronization at $NEXUS_DIR..."
+
+  _issues=0
+
+  # 1. Configuration version check
+  _vc_res=0
+  version_cmp "$WORKSPACE_CONFIG_VERSION" "$RNEX_VERSION" || _vc_res=$?
+  if [ "$_vc_res" -eq 2 ]; then
+    log_warn "Workspace configuration version (v$WORKSPACE_CONFIG_VERSION) is older than CLI (v$RNEX_VERSION)"
+    _issues=$((_issues + 1))
+  fi
+
+  # 2. Git ignore and search ignore checks
+  _gi="$NEXUS_DIR/.gitignore"
+  if [ ! -f "$_gi" ]; then
+    log_warn "Missing .gitignore in workspace root"
+    _issues=$((_issues + 1))
+  else
+    if ! grep -q '^\s*repos/\*' "$_gi" 2>/dev/null && ! grep -q '^repos' "$_gi" 2>/dev/null; then
+      log_warn ".gitignore missing 'repos/*'"
+      _issues=$((_issues + 1))
+    fi
+    if ! grep -qF "$RNEX_LOCAL_CONFIG_FILE" "$_gi" 2>/dev/null; then
+      log_warn ".gitignore missing '$RNEX_LOCAL_CONFIG_FILE'"
+      _issues=$((_issues + 1))
+    fi
+    if grep -q '^\.rnex/' "$_gi" 2>/dev/null || grep -q '^\.rnex$' "$_gi" 2>/dev/null; then
+      log_warn ".gitignore contains '.rnex/' (workspace assets should be tracked in Git)"
+      _issues=$((_issues + 1))
+    fi
+    if grep -q "lint_trigger_counter" "$_gi" 2>/dev/null; then
+      log_warn ".gitignore contains legacy 'lint_trigger_counter'"
+      _issues=$((_issues + 1))
+    fi
+  fi
+
+  _ign="$NEXUS_DIR/.ignore"
+  if [ ! -f "$_ign" ] || ! grep -q '!repos/\*' "$_ign" 2>/dev/null; then
+    log_warn ".ignore missing or missing '!repos/*' pattern (needed for code search & indexing)"
+    _issues=$((_issues + 1))
+  fi
+
+  # 3. Universal routing instructions check
+  if [ ! -f "$NEXUS_DIR/AGENTS.md" ]; then
+    log_warn "Missing AGENTS.md routing instructions"
+    _issues=$((_issues + 1))
+  else
+    if ! grep -q "<!-- REPO-NEXUS:START -->" "$NEXUS_DIR/AGENTS.md" 2>/dev/null || \
+       ! grep -q "<!-- REPO-NEXUS:END -->" "$NEXUS_DIR/AGENTS.md" 2>/dev/null; then
+      log_warn "AGENTS.md missing Repo Nexus delimited routing block"
+      _issues=$((_issues + 1))
+    fi
+  fi
+
+  # 4. Plugins check
+  for _p in $(yaml_list_plugins 2>/dev/null || true); do
+    [ -n "$_p" ] || continue
+    if yaml_plugin_enabled "$_p"; then
+      if [ ! -d "$NEXUS_DIR/.rnex/plugins/$_p" ]; then
+        log_warn "Active plugin '$_p' missing scoped directory at .rnex/plugins/$_p"
+        _issues=$((_issues + 1))
+      fi
+    else
+      if [ -d "$NEXUS_DIR/.rnex/plugins/$_p" ]; then
+        log_warn "Disabled plugin '$_p' still present at .rnex/plugins/$_p"
+        _issues=$((_issues + 1))
+      fi
+    fi
+  done
+
+  # Provider specific checks
+  if gemini_plugin_enabled; then
+    if [ ! -f "$NEXUS_DIR/GEMINI.md" ] || ! grep -q "<!-- REPO-NEXUS:START -->" "$NEXUS_DIR/GEMINI.md" 2>/dev/null; then
+      log_warn "GEMINI.md missing or not reconciled"
+      _issues=$((_issues + 1))
+    fi
+    if [ ! -f "$NEXUS_DIR/.geminiignore" ] || ! grep -q '!repos/\*' "$NEXUS_DIR/.geminiignore" 2>/dev/null; then
+      log_warn ".geminiignore missing or missing '!repos/*'"
+      _issues=$((_issues + 1))
+    fi
+  else
+    if [ -f "$NEXUS_DIR/.geminiignore" ] && grep -q '!repos/\*' "$NEXUS_DIR/.geminiignore" 2>/dev/null; then
+      log_warn ".geminiignore contains '!repos/*' but gemini plugin is disabled"
+      _issues=$((_issues + 1))
+    fi
+  fi
+
+  if cursor_plugin_enabled; then
+    if [ ! -f "$NEXUS_DIR/.cursorrules" ] || ! grep -q "<!-- REPO-NEXUS:START -->" "$NEXUS_DIR/.cursorrules" 2>/dev/null; then
+      log_warn ".cursorrules missing or not reconciled"
+      _issues=$((_issues + 1))
+    fi
+    if [ ! -f "$NEXUS_DIR/.cursorignore" ] || ! grep -q '!repos/\*' "$NEXUS_DIR/.cursorignore" 2>/dev/null; then
+      log_warn ".cursorignore missing or missing '!repos/*'"
+      _issues=$((_issues + 1))
+    fi
+    if [ ! -f "$NEXUS_DIR/.cursor/rules/rnex-context.mdc" ]; then
+      log_warn ".cursor/rules/rnex-context.mdc missing"
+      _issues=$((_issues + 1))
+    fi
+  else
+    if [ -f "$NEXUS_DIR/.cursorignore" ] && grep -q '!repos/\*' "$NEXUS_DIR/.cursorignore" 2>/dev/null; then
+      log_warn ".cursorignore contains '!repos/*' but cursor plugin is disabled"
+      _issues=$((_issues + 1))
+    fi
+  fi
+
+  if claude_plugin_enabled; then
+    if [ ! -f "$NEXUS_DIR/CLAUDE.md" ] || ! grep -q "<!-- REPO-NEXUS:START -->" "$NEXUS_DIR/CLAUDE.md" 2>/dev/null; then
+      log_warn "CLAUDE.md missing or not reconciled"
+      _issues=$((_issues + 1))
+    fi
+  fi
+
+  if windsurf_plugin_enabled; then
+    if [ ! -f "$NEXUS_DIR/.windsurfrules" ] || ! grep -q "<!-- REPO-NEXUS:START -->" "$NEXUS_DIR/.windsurfrules" 2>/dev/null; then
+      log_warn ".windsurfrules missing or not reconciled"
+      _issues=$((_issues + 1))
+    fi
+  fi
+
+  # Provider skills check (should NOT exist in provider dirs)
+  for _psk in "$NEXUS_DIR/.github/skills" "$NEXUS_DIR/.claude/skills" "$NEXUS_DIR/.gemini/skills" "$NEXUS_DIR/.cursor/skills" "$NEXUS_DIR/.windsurf/skills"; do
+    if [ -d "$_psk" ]; then
+      for _sub in "$_psk"/*; do
+        if [ -d "$_sub" ]; then
+          _aname="$(basename "$_sub")"
+          if [ "$_aname" = "rnex-cross-repo-feature" ] || [ "$_aname" = "rnex-workspace-audit" ] || [ "$_aname" = "rnex-wiki-lint" ] || [ "$_aname" = "rnex-wiki-ingest" ] || [ "$_aname" = "wiki-curator" ]; then
+            log_warn "Found obsolete provider skill directory: $_sub (skills should reside in .rnex/skills)"
+            _issues=$((_issues + 1))
+          fi
+        fi
+      done
+    fi
+  done
+
+  # 5. Skills and workflows in .rnex
+  if [ ! -d "$NEXUS_DIR/.rnex/skills" ]; then
+    log_warn "Standard workspace skills directory missing (.rnex/skills)"
+    _issues=$((_issues + 1))
+  fi
+  if [ ! -d "$NEXUS_DIR/.rnex/workflows" ]; then
+    log_warn "Standard workspace workflows directory missing (.rnex/workflows)"
+    _issues=$((_issues + 1))
+  fi
+
+  # 6. Git hooks
+  _cur_hp="$(git -C "$NEXUS_DIR" config --get core.hooksPath 2>/dev/null || true)"
+  case "$GIT_HOOKS_CONFIG" in
+    false|no|0)
+      if [ "$_cur_hp" = ".rnex/hooks" ] || [ "$_cur_hp" = "$NEXUS_DIR/.rnex/hooks" ]; then
+        log_warn "Git hooks active in Git, but disabled in configuration (git_hooks: false)"
+        _issues=$((_issues + 1))
+      fi
+      ;;
+    true|yes|1)
+      if git -C "$NEXUS_DIR" rev-parse --is-inside-work-tree >/dev/null 2>&1; then
+        if [ "$_cur_hp" != ".rnex/hooks" ] && [ "$_cur_hp" != "$NEXUS_DIR/.rnex/hooks" ]; then
+          log_warn "Git hooks enabled in configuration (git_hooks: true), but not active in Git"
+          _issues=$((_issues + 1))
+        fi
+      fi
+      ;;
+  esac
+
+  # 7. Member repositories
+  for _name in $(yaml_list_repos 2>/dev/null || true); do
+    [ -n "$_name" ] || continue
+    if yaml_repo_enabled "$_name"; then
+      _rdir="$(resolve_repo_path "$_name")"
+      if [ ! -d "$_rdir" ]; then
+        log_warn "Member repo '$_name' is missing on disk (run: rnex clone)"
+        _issues=$((_issues + 1))
+      elif [ ! -d "$_rdir/.rnex" ]; then
+        log_warn "Member repo '$_name' missing .rnex directory"
+        _issues=$((_issues + 1))
+      fi
+    fi
+  done
+
+  # 8. Multi-root workspace file
+  if [ -n "$CODE_WORKSPACE_FILE" ]; then
+    if [ ! -f "$NEXUS_DIR/$CODE_WORKSPACE_FILE" ]; then
+      log_warn "Multi-root workspace file missing ($CODE_WORKSPACE_FILE)"
+      _issues=$((_issues + 1))
+    fi
+  fi
+
+  if [ "$_issues" -eq 0 ]; then
+    [ "$_sync_quiet" -eq 0 ] && log_ok "Workspace is synchronized — no issues or inconsistencies found."
+    return 0
+  else
+    [ "$_sync_quiet" -eq 0 ] && log_warn "Found $_issues inconsistency(ies). Run 'rnex sync --fix' to reconcile."
+    return 1
+  fi
+}
+
+cmd_fix() {
+  _fix_is_quiet=0
+  for _arg in "$@"; do
+    case "$_arg" in
+      -q|--quiet) _fix_is_quiet=1 ;;
+    esac
+  done
+  [ "$_fix_is_quiet" -eq 0 ] && log_warn "Command 'rnex fix' is deprecated and will be removed in a future release. Use 'rnex sync --fix' instead."
+  cmd_sync --fix "$@"
+}
+
+cmd_update() {
+  require_workspace
+  _cmp=0
+  version_cmp "$WORKSPACE_CONFIG_VERSION" "$RNEX_VERSION" || _cmp=$?
+  if [ "$_cmp" -eq 0 ]; then
+    log_ok "Workspace configuration and routing instructions are already up to date (v$RNEX_VERSION)"
+  elif [ "$_cmp" -eq 1 ]; then
+    log_info "Workspace configuration version (v$WORKSPACE_CONFIG_VERSION) is newer than current CLI (v$RNEX_VERSION)"
+  fi
+  cmd_sync --fix "$@"
+}
+
+cmd_upgrade() {
+  cmd_update "$@"
+}

package/lib/commands/system.sh

@@ -50,8 +50,9 @@ cmd_help() {
     init [-y] [--code-workspace [file]] [--hooks|--no-hooks] [--copilot] [--claude] [--gemini] [--cursor] [--windsurf] [dir]
                             Initialize a new Repo Nexus workspace (default: AGENTS.md)
     install [dir]           Install rnex & repo-nexus globally into ~/.local/bin (or custom dir)
-    fix [-y] [--quiet]      Reconcile workspace, upgrade configuration & routing, sync plugins & repos (aliases: sync, update, upgrade)
-    update [-y]             Part of fix: check version, upgrade schema, and reconcile workspace (alias: upgrade)
+    sync [--fix] [-y] [--quiet] Check workspace for inconsistencies (use --fix to reconcile workspace, upgrade configuration & routing, sync plugins & repos)
+    fix [-y] [--quiet]      (Deprecated: use 'rnex sync --fix') Reconcile workspace, upgrade configuration & routing, sync plugins & repos
+    update [-y]             Part of sync --fix: check version, upgrade schema, and reconcile workspace (alias: upgrade)
     upgrade [-y]            Alias for update
     hooks <install|uninstall|status> [--local]
                             Manage automated Git hooks (--local writes to .local.rnex.yaml)
@@ -87,8 +88,9 @@ cmd_help() {
     rnex enable analytics                       # Re-enable analytics repo
     rnex list                                   # List all member repos and active branches
     rnex status                                 # Inspect workspace configuration and health
-    rnex fix                                    # Reconcile all repos, plugins, and .rnex directories
-    rnex update                                 # Upgrade workspace configuration to newest version (part of fix)
+    rnex sync                                   # Check workspace for inconsistencies
+    rnex sync --fix                             # Reconcile all repos, plugins, and .rnex directories
+    rnex update                                 # Upgrade workspace configuration to newest version (part of sync --fix)
     rnex hooks install                          # Enable automated workspace Git hooks
     rnex completion zsh                         # Generate Zsh completion script
 

package/lib/commands.sh

@@ -7,7 +7,7 @@
 . "$RNEX_LIB_DIR/commands/init.sh"
 . "$RNEX_LIB_DIR/commands/repo.sh"
 . "$RNEX_LIB_DIR/commands/status.sh"
-. "$RNEX_LIB_DIR/commands/fix.sh"
+. "$RNEX_LIB_DIR/commands/sync.sh"
 . "$RNEX_LIB_DIR/commands/plugin.sh"
 . "$RNEX_LIB_DIR/commands/completion.sh"
 . "$RNEX_LIB_DIR/commands/system.sh"

package/lib/hooks.sh

@@ -157,7 +157,7 @@ cmd_hooks() {
       require_workspace
       case "$_hook_name" in
         post-merge)
-          cmd_fix -y --quiet || true
+          cmd_sync --fix -y --quiet || true
           if yaml_plugin_enabled "karpathy-llm"; then
             _trigger="$(yaml_plugin_get "karpathy-llm" "lint_trigger")"
             if [ "$_trigger" = "git-post-merge" ] || [ "$_trigger" = "post-merge" ]; then

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "repo-nexus",
-  "version": "0.6.13",
+  "version": "0.6.15",
   "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

@@ -101,7 +101,8 @@ case "${1:-help}" in
   hooks)       shift; cmd_hooks "$@" ;;
   update|upgrade) shift; cmd_update "$@" ;;
   rnex-dir)    shift; cmd_rnex_dir "$@" ;;
-  fix|sync)    shift; cmd_fix "$@" ;;
+  sync)        shift; cmd_sync "$@" ;;
+  fix)         shift; cmd_fix "$@" ;;
   plugin)      shift; cmd_plugin "$@" ;;
   completion)  shift; cmd_completion "$@" ;;
   version|-v|--version) cmd_version ;;

package/templates/rnex.example.yaml

@@ -8,14 +8,14 @@
 #   2. Local Config (.local.rnex.yaml): Machine-specific (gitignored, highest priority),
 #      overrides enable/disable states, URLs, or local developer settings.
 #
-# Place it in your workspace root directory and run `rnex fix` to apply.
+# Place it in your workspace root directory and run `rnex sync --fix` to apply.
 #
 # For more information: https://github.com/unoxen/repo-nexus
 
 # ------------------------------------------------------------------------------
 # version — Workspace configuration schema version
 # ------------------------------------------------------------------------------
-# Used by `rnex fix` and `rnex update` to safely detect and reconcile configuration
+# Used by `rnex sync --fix` and `rnex update` to safely detect and reconcile configuration
 # and routing instructions across CLI releases.
 #
 version: 0.5.0

package/toolkit/plugins/karpathy-llm/README.md

@@ -93,7 +93,7 @@ This command:
 1. Adds `karpathy-llm` to `plugins:` in `rnex.yaml`.
 2. Copies initial templates (`wiki/index.md`, `wiki/_log.md`, `wiki/hot.md`, `raw/.gitkeep`, `.rnex/templates/wiki-page.template.md`, `.rnex/templates/LLM_WIKI.sample.md`).
 3. Scopes `rules/`, `instructions/`, and `workflows/` into `.rnex/plugins/karpathy-llm/`.
-4. Syncs scope links and AI context files across all registered member repositories via `rnex fix`.
+4. Syncs scope links and AI context files across all registered member repositories via `rnex sync --fix`.
 
 ### Option 2: Declarative in `rnex.yaml`
 
@@ -107,7 +107,7 @@ plugins:
 Then reconcile and fix:
 
 ```bash
-rnex fix
+rnex sync --fix
 ```
 
 ---

package/toolkit/prompts/rnex-workspace-audit.md

@@ -26,7 +26,7 @@ Use this prompt to audit workspace configuration integrity, member repository gi
 ## 3. Reconciliation & Remediation
 1. If any configuration issues, missing directories, or unlinked plugin assets are detected, run:
    ```sh
-   rnex fix
+   rnex sync --fix
    ```
 2. If member repositories declared in `rnex.yaml` are missing on disk, run:
    ```sh

package/toolkit/skills/rnex-workspace-audit/SKILL.md

@@ -10,4 +10,4 @@ Use this skill when auditing workspace health, validating multi-repository git s
 ## Key Rules
 1. **Health Audit**: Run `rnex status` to inspect configuration, AGENTS.md, code-workspace, gitignore, hooks, and active plugins.
 2. **Git Status Audit**: Check working tree cleanliness across member repos (`rnex exec git status -s`) and branch tracking (`rnex exec git status -uno`).
-3. **Reconciliation**: Run `rnex fix` for configuration and asset reconciliation; run `rnex clone` for missing member repository clones.
+3. **Reconciliation**: Run `rnex sync --fix` for configuration and asset reconciliation (or `rnex sync` to audit inconsistencies); run `rnex clone` for missing member repository clones.

package/toolkit/workflows/rnex-workspace-audit.md

@@ -26,7 +26,7 @@ Use this workflow to audit workspace configuration integrity, member repository
 ## 3. Reconciliation & Remediation
 1. If any configuration issues, missing directories, or unlinked plugin assets are detected, run:
    ```sh
-   rnex fix
+   rnex sync --fix
    ```
 2. If member repositories declared in `rnex.yaml` are missing on disk, run:
    ```sh