diff --git a/packages/plugin_source/README.md b/packages/plugin_source/README.md
index a22d75eb..d2c5d805 100644
--- a/packages/plugin_source/README.md
+++ b/packages/plugin_source/README.md
@@ -43,7 +43,8 @@ Future<void> main() async {
 A source that can't supply the plugin returns an `UnavailablePlugin` with the
 reasons, rather than throwing. A plugin file that can't be understood makes
 the parser throw a `PluginParseException` that names the file and the field.
-`PluginAssets.merge` combines several plugins into one set of assets.
+`PluginAssets.merge` combines several plugins into one set of assets, and
+`withPlugin` records which plugin supplied one.
 
 ## Layout
 
diff --git a/packages/plugin_source/lib/src/model/plugin_assets.dart b/packages/plugin_source/lib/src/model/plugin_assets.dart
index f672a35f..48443aa8 100644
--- a/packages/plugin_source/lib/src/model/plugin_assets.dart
+++ b/packages/plugin_source/lib/src/model/plugin_assets.dart
@@ -2,6 +2,7 @@ import 'package:plugin_source/src/model/agent_asset.dart';
 import 'package:plugin_source/src/model/hook_asset.dart';
 import 'package:plugin_source/src/model/mcp_server.dart';
 import 'package:plugin_source/src/model/skill_asset.dart';
+import 'package:plugin_source/src/plugin_ref.dart';
 
 /// {@template plugin_assets}
 /// Everything one or more plugins contribute, in a harness-neutral shape.
@@ -18,19 +19,27 @@ class const PluginAssets({
 
   /// The hooks, in the order the plugins declare them.
   final List<HookAsset> hooks = const [],
+
+  /// The plugins these come from, which the harness that installs them
+  /// itself names in its settings.
+  final List<PluginRef> plugins = const [],
 }) {
-  /// Combines what several plugins contribute into one [PluginAssets].
+  /// Combines what the [plugins] contribute into one [PluginAssets].
   ///
   /// Each skill, agent and MCP server is written to a path or key derived
   /// from its name, so the first declaration of a name wins and a later one
   /// is dropped rather than planned as a second write to the same place.
-  factory merge(Iterable<PluginAssets> assets) => PluginAssets(
+  factory merge(
+    Iterable<PluginAssets> assets, {
+    List<PluginRef> plugins = const [],
+  }) => PluginAssets(
     skills: _firstByName([for (final a in assets) ...a.skills], (s) => s.name),
     agents: _firstByName([for (final a in assets) ...a.agents], (a) => a.name),
     mcpServers: _firstByName([
       for (final a in assets) ...a.mcpServers,
     ], (s) => s.name),
     hooks: [for (final a in assets) ...a.hooks],
+    plugins: plugins,
   );
 
   /// The skills a user can invoke as a command.
diff --git a/packages/plugin_source/test/src/model/plugin_assets_test.dart b/packages/plugin_source/test/src/model/plugin_assets_test.dart
index d2d9a0e0..f84085a3 100644
--- a/packages/plugin_source/test/src/model/plugin_assets_test.dart
+++ b/packages/plugin_source/test/src/model/plugin_assets_test.dart
@@ -29,6 +29,20 @@ void main() {
       hooks: hooks,
     );
 
+    const wingspan = PluginRef(
+      name: 'wingspan',
+      repo: 'acme/wingspan',
+      version: '1.0.0',
+      gitRef: 'v1.0.0',
+    );
+
+    const flutter = PluginRef(
+      name: 'flutter',
+      repo: 'acme/flutter',
+      version: '2.0.0',
+      gitRef: 'v2.0.0',
+    );
+
     setUp(() => fs = MemoryFileSystem.test());
 
     group('invocableSkills', () {
@@ -57,6 +71,15 @@ void main() {
     });
 
     group('merge', () {
+      test('names the plugins the assets came from', () {
+        final merged = PluginAssets.merge(
+          [pluginAssets(), pluginAssets()],
+          plugins: [wingspan, flutter],
+        );
+
+        expect(merged.plugins, [wingspan, flutter]);
+      });
+
       AgentAsset agent(String name) =>
           AgentAsset(name: name, description: 'd', body: 'b', skills: const []);
 
diff --git a/packages/vgv_ai_cli/README.md b/packages/vgv_ai_cli/README.md
index bf8f1611..08756c41 100644
--- a/packages/vgv_ai_cli/README.md
+++ b/packages/vgv_ai_cli/README.md
@@ -65,6 +65,9 @@ vgv_ai install --no-claude
 
 # Also overwrite your values that conflict with the ones install writes
 vgv_ai install --force
+
+# Install just the VGV plugins you name, instead of every pinned one
+vgv_ai install --plugin vgv-wingspan
 ```
 
 `install` reads the pinned plugins from the Claude Code plugin cache when it
@@ -82,6 +85,9 @@ how `doctor` and `uninstall` tell what's yours from what's VGV's.
   are written whole. A file you edited since `install` wrote it, or one at the
   same path that `install` didn't write, is kept unless you pass `--force`.
 - **Selection:** `--only` and `--no-<harness>` can't be combined.
+- **Plugins:** without `--plugin`, every pinned plugin is installed. Pass it
+  once per plugin to name the ones you want. What a previous `install` wrote
+  for the plugins you leave out stays where it is; `uninstall` removes that.
 
 ### doctor
 
@@ -100,7 +106,8 @@ vgv_ai doctor --no-claude
 
 For each harness, `doctor` reports the files and keys that are missing, were
 changed since, or differ from what this version installs. It also compares the
-plugin versions you installed from with the ones this version pins, suggests
+plugin versions each harness was installed from with the ones this version
+pins, notes a pinned plugin a harness wasn't installed from, suggests
 configuring a harness that's installed but not configured, and warns about a
 configured harness that's no longer installed.
 
diff --git a/packages/vgv_ai_cli/lib/src/commands/doctor/doctor_command.dart b/packages/vgv_ai_cli/lib/src/commands/doctor/doctor_command.dart
index 0081940d..be60dcf3 100644
--- a/packages/vgv_ai_cli/lib/src/commands/doctor/doctor_command.dart
+++ b/packages/vgv_ai_cli/lib/src/commands/doctor/doctor_command.dart
@@ -1,6 +1,7 @@
 import 'dart:io' show Platform;
 
 import 'package:args/command_runner.dart';
+import 'package:collection/collection.dart';
 import 'package:file/file.dart';
 import 'package:mason_logger/mason_logger.dart';
 import 'package:path/path.dart' as p;
@@ -93,7 +94,11 @@ class DoctorCommand({
 
     if (reports.isEmpty) _logger.info(_nothingToCheck(manifest));
 
-    final fix = FixCommand.combine(reports.map((report) => report.fix));
+    // A section install can fix but that no one command covers would make
+    // the closing line promise more than it does, so there is none.
+    final fix = reports.any((report) => report.needsItsOwnFix)
+        ? null
+        : FixCommand.combine(reports.map((report) => report.fix));
     if (fix != null) {
       _logger
         ..info('')
@@ -160,30 +165,71 @@ class DoctorCommand({
 
   /// What a dry run of `install` for [selected] would do, or an unchecked
   /// plan, having said why, when the plugins cannot be resolved.
+  ///
+  /// Harnesses installed from different plugins are planned apart, so a
+  /// plugin one of them was installed without is not planned for it.
   Future<ContentPlan> _plan(
     InstallManifest manifest,
     Directory home,
     Set<Harness> selected,
   ) async {
     final progress = _logger.progress('Resolving plugins');
-    switch (await _resolver.resolve(home)) {
-      case ResolvedAssets(:final assets):
-        progress.complete('Resolved plugins');
-        final translation = await _translator.translate(
-          assets: assets,
-          home: home,
-          selected: selected,
-        );
-        return ContentPlan(
-          _reconciler
-              .apply(translation.changes, manifest: manifest, dryRun: true)
-              .changes,
-        );
-      case UnavailableAssets(:final plugin, :final reasons):
-        return _unchecked(progress, 'resolve $plugin', reasons);
-      case UnparseableAssets(:final plugin, :final error):
-        return _unchecked(progress, 'parse $plugin', ['$error']);
+    final changes = <AppliedChange>[];
+
+    for (final MapEntry(key: only, value: harnesses) in _byPlugins(
+      manifest,
+      selected,
+    ).entries) {
+      switch (await _resolver.resolve(home, only: only)) {
+        case ResolvedAssets(:final assets):
+          final translation = await _translator.translate(
+            assets: assets,
+            home: home,
+            selected: harnesses,
+          );
+          changes.addAll(
+            _reconciler
+                .apply(translation.changes, manifest: manifest, dryRun: true)
+                .changes,
+          );
+        case UnavailableAssets(:final plugin, :final reasons):
+          return _unchecked(progress, 'resolve $plugin', reasons);
+        case UnparseableAssets(:final plugin, :final error):
+          return _unchecked(progress, 'parse $plugin', ['$error']);
+      }
+    }
+
+    progress.complete('Resolved plugins');
+    return ContentPlan(changes);
+  }
+
+  /// [selected] grouped by the plugin names each harness was installed
+  /// from, which the map compares as sets rather than by identity.
+  Map<Set<String>, Set<Harness>> _byPlugins(
+    InstallManifest manifest,
+    Set<Harness> selected,
+  ) {
+    final groups = EqualityMap<Set<String>, Set<Harness>>(_sets);
+    for (final harness in selected) {
+      groups
+          .putIfAbsent(_installedFrom(manifest, harness), () => {})
+          .add(harness);
     }
+    return groups;
+  }
+
+  /// How a set of plugin names is compared, since two of them are the same
+  /// selection whatever order they were built in.
+  static const Equality<Set<String>> _sets = SetEquality();
+
+  /// The plugins [harness] was installed from, which for one the manifest
+  /// records none for is every pinned plugin, as `install` writes without
+  /// `--plugin`.
+  Set<String> _installedFrom(InstallManifest manifest, Harness harness) {
+    final recorded = manifest.plugins[harness]?.keys.toSet() ?? const {};
+    return recorded.isEmpty
+        ? {for (final plugin in vgvPlugins) plugin.name}
+        : recorded;
   }
 
   /// An unchecked plan, having failed [progress] and listed [reasons] for
@@ -205,10 +251,10 @@ class DoctorCommand({
     );
   }
 
-  /// The sections of the report: the plugin versions, and why content was
-  /// not checked if it was not, when a harness is [installed], the shared
-  /// skills when an [installed] harness reads them, and each harness that
-  /// is [installed] or [detected].
+  /// The sections of the report: why content was not checked if it was not,
+  /// the shared skills when an [installed] harness reads them, and each
+  /// harness that is [installed] or [detected], with the plugin versions it
+  /// was installed from.
   ///
   /// [installed] are the harnesses of the selected scope VGV configured, and
   /// [detected] those of it on this machine.
@@ -222,11 +268,17 @@ class DoctorCommand({
     final readsShared = installed.intersection(_readShared);
 
     return [
-      if (installed.isNotEmpty) _pluginsSection(manifest, installed, plan),
+      if (plan.skipped case final skipped?)
+        ReportSection(
+          title: 'Plugins',
+          installs: installed,
+          findings: [skipped],
+        ),
       if (readsShared.isNotEmpty && manifest.entriesFor(null).isNotEmpty)
         ReportSection(
           title: 'Shared',
           installs: readsShared,
+          plugins: _shared(manifest, readsShared),
           findings: _entryFindings(null, manifest, home, plan),
         ),
       for (final harness in Harness.values)
@@ -242,25 +294,6 @@ class DoctorCommand({
     ];
   }
 
-  /// The plugin versions [installed] read, and why content was not checked
-  /// if [plan] was not.
-  ReportSection _pluginsSection(
-    InstallManifest manifest,
-    Set<Harness> installed,
-    ContentPlan plan,
-  ) => ReportSection(
-    title: 'Plugins',
-    installs: installed,
-    findings: [
-      for (final plugin in vgvPlugins)
-        PluginVersion.of(
-          plugin,
-          installed: manifest.plugins[plugin.name],
-        ).finding,
-      ?plan.skipped,
-    ],
-  );
-
   /// The section for [harness], which VGV configured when [isInstalled] and
   /// is on this machine when [isDetected].
   ReportSection _harnessSection(
@@ -270,21 +303,47 @@ class DoctorCommand({
     ContentPlan plan, {
     required bool isInstalled,
     required bool isDetected,
-  }) => ReportSection(
-    title: harness.displayName,
-    installs: {harness},
-    findings: [
-      if (!isDetected)
-        const Finding.warning(
-          'not installed on this machine, but VGV AI CLI configured it',
-        ),
-      if (!isInstalled)
-        const Finding.suggestion(
-          "installed, but VGV AI CLI hasn't configured it",
-        ),
-      ..._entryFindings(harness, manifest, home, plan),
-    ],
-  );
+  }) {
+    final recorded = manifest.plugins[harness] ?? const <String, String>{};
+    return ReportSection(
+      title: harness.displayName,
+      installs: {harness},
+      plugins: _selected(recorded),
+      findings: [
+        if (!isDetected)
+          const Finding.warning(
+            'not installed on this machine, but VGV AI CLI configured it',
+          ),
+        if (!isInstalled)
+          const Finding.suggestion(
+            "installed, but VGV AI CLI hasn't configured it",
+          ),
+        if (isInstalled)
+          for (final plugin in vgvPlugins)
+            PluginVersion.of(plugin, installed: recorded[plugin.name]).finding,
+        ..._entryFindings(harness, manifest, home, plan),
+      ],
+    );
+  }
+
+  /// The plugins every harness of [readers] was installed from, or null
+  /// when they differ, since one `install` cannot then fix the skills they
+  /// share without adding a plugin one of them was left without.
+  Set<String>? _shared(InstallManifest manifest, Set<Harness> readers) {
+    final selections = EqualitySet<Set<String>>(_sets)
+      ..addAll([
+        for (final harness in readers)
+          _selected(manifest.plugins[harness] ?? const {}),
+      ]);
+    return selections.length == 1 ? selections.single : null;
+  }
+
+  /// The plugin names a fix must name, or none when [recorded] holds every
+  /// pinned plugin, which `install` writes without being asked.
+  Set<String> _selected(Map<String, String> recorded) =>
+      vgvPlugins.every((plugin) => recorded.containsKey(plugin.name))
+      ? const {}
+      : recorded.keys.toSet();
 
   /// What is wrong with the entries [owner] has in [manifest], and the
   /// files [plan] would add for it.
diff --git a/packages/vgv_ai_cli/lib/src/commands/doctor/model/fix_command.dart b/packages/vgv_ai_cli/lib/src/commands/doctor/model/fix_command.dart
index 1edb0c56..c6bd7753 100644
--- a/packages/vgv_ai_cli/lib/src/commands/doctor/model/fix_command.dart
+++ b/packages/vgv_ai_cli/lib/src/commands/doctor/model/fix_command.dart
@@ -1,3 +1,5 @@
+import 'package:collection/collection.dart';
+import 'package:plugin_source/plugin_source.dart';
 import 'package:vgv_ai_cli/src/model/model.dart';
 
 /// {@template fix_command}
@@ -9,15 +11,28 @@ class const FixCommand({
 
   /// Whether VGV's values must replace ones changed since install.
   final bool force = false,
+
+  /// The plugins to install, or empty for every pinned one.
+  ///
+  /// Named so the fix cannot install a plugin the user left out of a
+  /// harness with `install --plugin`.
+  final Set<String> plugins = const {},
 }) {
   /// One command that does what every one of [fixes] does, or null when
-  /// there are none.
+  /// there are none, or when they install different plugins and so cannot
+  /// be said in one command.
   static FixCommand? combine(Iterable<FixCommand?> fixes) {
-    final all = fixes.nonNulls;
+    final all = fixes.nonNulls.toList();
     if (all.isEmpty) return null;
+
+    final plugins = EqualitySet<Set<String>>(const SetEquality())
+      ..addAll(all.map((fix) => fix.plugins));
+    if (plugins.length > 1) return null;
+
     return FixCommand(
       harnesses: {for (final fix in all) ...fix.harnesses},
       force: all.any((fix) => fix.force),
+      plugins: plugins.single,
     );
   }
 
@@ -26,6 +41,8 @@ class const FixCommand({
     'vgv_ai install',
     for (final harness in Harness.values)
       if (harnesses.contains(harness)) '--only ${harness.name}',
+    for (final plugin in vgvPlugins)
+      if (plugins.contains(plugin.name)) '--plugin ${plugin.name}',
     if (force) '--force',
   ].join(' ');
 }
diff --git a/packages/vgv_ai_cli/lib/src/commands/doctor/model/plugin_version.dart b/packages/vgv_ai_cli/lib/src/commands/doctor/model/plugin_version.dart
index 66faf6b3..52a67e96 100644
--- a/packages/vgv_ai_cli/lib/src/commands/doctor/model/plugin_version.dart
+++ b/packages/vgv_ai_cli/lib/src/commands/doctor/model/plugin_version.dart
@@ -67,9 +67,7 @@ class const PluginVersion._({
       PluginStatus.newer => Finding.stale(
         '$name $installed installed, newer than the pinned $pinned',
       ),
-      PluginStatus.unrecorded => Finding.stale(
-        '$name not recorded, $pinned pinned',
-      ),
+      PluginStatus.unrecorded => Finding.warning('$name $pinned not installed'),
     };
   }
 }
diff --git a/packages/vgv_ai_cli/lib/src/commands/doctor/model/report_section.dart b/packages/vgv_ai_cli/lib/src/commands/doctor/model/report_section.dart
index 4c57405e..95741356 100644
--- a/packages/vgv_ai_cli/lib/src/commands/doctor/model/report_section.dart
+++ b/packages/vgv_ai_cli/lib/src/commands/doctor/model/report_section.dart
@@ -15,6 +15,11 @@ class const ReportSection({
 
   /// What was found, in the order it was found.
   required final List<Finding> findings,
+
+  /// The plugins the fix installs, empty for every pinned one, or null when
+  /// the harnesses were installed from different ones and no one `install`
+  /// fixes them all.
+  final Set<String>? plugins = const {},
 }) {
   /// Whether anything was found that is wrong.
   bool get hasProblems => findings.any((finding) => finding.isProblem);
@@ -22,12 +27,22 @@ class const ReportSection({
   /// Whether anything was found that is worth knowing, though not wrong.
   bool get hasNotices => findings.any((finding) => finding.isNotice);
 
+  /// Whether `install` fixes something here that [fix] cannot say in one
+  /// command, because the harnesses were installed from different plugins.
+  bool get needsItsOwnFix =>
+      fix == null && findings.any((finding) => finding.needsInstall);
+
   /// The one `install` command that fixes every finding `install` can fix,
-  /// or null when there are none.
-  FixCommand? get fix => findings.any((finding) => finding.needsInstall)
-      ? FixCommand(
-          harnesses: installs,
-          force: findings.any((finding) => finding.needsForce),
-        )
-      : null;
+  /// or null when there are none, or when no one command fixes them.
+  FixCommand? get fix {
+    if (plugins case final plugins?
+        when findings.any((finding) => finding.needsInstall)) {
+      return FixCommand(
+        harnesses: installs,
+        force: findings.any((finding) => finding.needsForce),
+        plugins: plugins,
+      );
+    }
+    return null;
+  }
 }
diff --git a/packages/vgv_ai_cli/lib/src/commands/install_command.dart b/packages/vgv_ai_cli/lib/src/commands/install_command.dart
index 6d3c08af..2b6dc53a 100644
--- a/packages/vgv_ai_cli/lib/src/commands/install_command.dart
+++ b/packages/vgv_ai_cli/lib/src/commands/install_command.dart
@@ -4,6 +4,7 @@ import 'package:args/command_runner.dart';
 import 'package:collection/collection.dart';
 import 'package:file/file.dart';
 import 'package:mason_logger/mason_logger.dart';
+import 'package:plugin_source/plugin_source.dart';
 import 'package:vgv_ai_cli/src/commands/harness_selection.dart';
 import 'package:vgv_ai_cli/src/commands/reporting_manifest_store.dart';
 import 'package:vgv_ai_cli/src/commands/user_home.dart';
@@ -22,6 +23,8 @@ import 'package:vgv_ai_cli/src/translate/translate.dart';
 /// * `--only` configures the named harnesses, detected or not.
 /// * `--no-<harness>` skips one detected harness. It cannot be combined with
 ///   `--only`, which already names the set.
+/// * `--plugin` installs just the named VGV plugins instead of every pinned
+///   one.
 /// {@endtemplate}
 class InstallCommand({
   required final Logger _logger,
@@ -45,6 +48,11 @@ class InstallCommand({
             'Also overwrite your values that conflict with the ones install '
             'writes.',
         negatable: false,
+      )
+      ..addMultiOption(
+        'plugin',
+        help: 'Install just these VGV plugins, instead of every pinned one.',
+        allowed: [for (final plugin in vgvPlugins) plugin.name],
       );
     addHarnessOptions('Configure the Very Good AI tooling for');
   }
@@ -134,9 +142,9 @@ class InstallCommand({
         dryRun ||
         store.save(
           from: manifest,
-          to: reconciliation.manifest.withPlugins({
-            for (final plugin in resolved.plugins) plugin.name: plugin.version,
-          }),
+          to: reconciliation.manifest.withPlugins(
+            _pluginVersions(manifest, resolved.assets.plugins, selected),
+          ),
         );
     final anyChangeFailed = applied.any(
       (change) => change.outcome == ChangeOutcome.failed,
@@ -185,14 +193,46 @@ class InstallCommand({
     return selected;
   }
 
-  /// Resolves and parses every pinned VGV plugin into one asset bundle.
+  /// The plugins `--plugin` names, or null when it names none and every
+  /// pinned plugin is installed.
+  Set<String>? get _selectedPlugins {
+    final names = argResults!['plugin'] as List<String>;
+    return names.isEmpty ? null : names.toSet();
+  }
+
+  /// The versions to record for each harness of [selected]: [installed] for
+  /// the plugins this run wrote, and what [manifest] already records for the
+  /// ones it skipped, whose files are still installed. Every other harness
+  /// keeps what it had.
+  Map<Harness, Map<String, String>> _pluginVersions(
+    InstallManifest manifest,
+    List<PluginRef> installed,
+    Set<Harness> selected,
+  ) {
+    final written = {
+      for (final plugin in installed) plugin.name: plugin.version,
+    };
+    return {
+      ...manifest.plugins,
+      for (final harness in selected)
+        harness: {
+          for (final plugin in vgvPlugins)
+            plugin.name:
+                ?(written[plugin.name] ??
+                manifest.plugins[harness]?[plugin.name]),
+        },
+    };
+  }
+
+  /// Resolves and parses the plugins `--plugin` selects into one asset
+  /// bundle, or every pinned one when it selects none.
   ///
   /// Returns `null`, having said why, when any plugin cannot be resolved or
   /// parsed.
   Future<ResolvedAssets?> _resolveAssets(Directory home) async {
     final progress = _logger.progress('Resolving plugins');
 
-    switch (await _resolver.resolve(home)) {
+    switch (await _resolver.resolve(home, only: _selectedPlugins)) {
       case final ResolvedAssets resolved:
         progress.complete(
           'Resolved ${resolved.assets.skills.length} skills and '
diff --git a/packages/vgv_ai_cli/lib/src/manifest/manifest_auditor.dart b/packages/vgv_ai_cli/lib/src/manifest/manifest_auditor.dart
index a92cb56e..49da2137 100644
--- a/packages/vgv_ai_cli/lib/src/manifest/manifest_auditor.dart
+++ b/packages/vgv_ai_cli/lib/src/manifest/manifest_auditor.dart
@@ -73,12 +73,14 @@ class const ManifestAuditor({
     final narrowed = [
       for (final ReversedEntry(:retained) in reversed) ?retained,
     ];
+    final kept = [...manifest.without(settled).entries, ...narrowed];
+    final remaining = {for (final entry in kept) entry.owner};
     return Reversal(
       entries: reversed,
-      manifest: InstallManifest([
-        ...manifest.without(settled).entries,
-        ...narrowed,
-      ], manifest.plugins),
+      manifest: InstallManifest(kept, {
+        for (final MapEntry(:key, :value) in manifest.plugins.entries)
+          if (remaining.contains(key)) key: value,
+      }),
     );
   }
 
diff --git a/packages/vgv_ai_cli/lib/src/model/install_manifest.dart b/packages/vgv_ai_cli/lib/src/model/install_manifest.dart
index c19b0874..2ad537cc 100644
--- a/packages/vgv_ai_cli/lib/src/model/install_manifest.dart
+++ b/packages/vgv_ai_cli/lib/src/model/install_manifest.dart
@@ -174,7 +174,7 @@ final class const MarkdownSections({
 
 /// {@template install_manifest}
 /// Everything VGV wrote under a home directory, by file, and the plugin
-/// versions it was written from.
+/// versions each harness was written from.
 ///
 /// `install` writes it, and `doctor` and `uninstall` read it, so this is the
 /// one place ownership is defined. It is persisted rather than recomputed
@@ -196,9 +196,9 @@ class InstallManifest extends Equatable {
   ///
   /// A malformed manifest is empty: an unrecorded file is the user's, which
   /// is the safe way to be wrong. For the same reason, an entry whose path
-  /// is absolute or leads out of [home] is dropped. A version 1 manifest is
-  /// read as one that records no plugin versions. One from a newer version
-  /// is null, because writing over it would lose everything it records.
+  /// is absolute or leads out of [home] is dropped, as are plugin versions
+  /// that are not written per harness. One from a newer version is null,
+  /// because writing over it would lose everything it records.
   static InstallManifest? decode(String source, {required String home}) {
     final Object? json;
     try {
@@ -209,25 +209,33 @@ class InstallManifest extends Equatable {
 
     return switch (json) {
       {
-        'version': 1 || InstallManifest.version,
+        'version': InstallManifest.version,
         'entries': final List<dynamic> list,
       } =>
-        InstallManifest(
-          [
-            for (final item in list)
-              ?ManifestEntry.fromJson(_resolved(item, home: home)),
-          ],
-          {
-            if (json['plugins'] case final Map<String, dynamic> plugins)
-              for (final MapEntry(:key, :value) in plugins.entries)
-                if (value is String) key: value,
-          },
-        ),
+        InstallManifest([
+          for (final item in list)
+            ?ManifestEntry.fromJson(_resolved(item, home: home)),
+        ], _plugins(json['plugins'])),
       {'version': final int other} when other > version => null,
       _ => InstallManifest(),
     };
   }
 
+  /// The versions [json] records per harness, without what this version
+  /// cannot read.
+  static Map<Harness, Map<String, String>> _plugins(Object? json) {
+    if (json is! Map<String, dynamic>) return const {};
+    return {
+      for (final MapEntry(:key, :value) in json.entries)
+        if (Harness.values.asNameMap()[key] case final harness?)
+          if (value is Map<String, dynamic>)
+            harness: {
+              for (final MapEntry(:key, :value) in value.entries)
+                if (value is String) key: value,
+            },
+    };
+  }
+
   /// [item] with its path resolved against [home], or null when the path
   /// is absolute or leads out of [home].
   static Object? _resolved(Object? item, {required String home}) {
@@ -241,12 +249,16 @@ class InstallManifest extends Equatable {
   }
 
   /// The format [encode] writes.
-  static const version = 2;
+  static const version = 1;
 
   final Map<String, ManifestEntry> _entries;
 
-  /// Each plugin's name to the version VGV's files were written from.
-  final Map<String, String> plugins;
+  /// Each harness to the plugin versions its files were written from, by
+  /// plugin name.
+  ///
+  /// Per harness rather than per home, since `install --plugin` can leave a
+  /// plugin out of one harness while another is installed from it.
+  final Map<Harness, Map<String, String>> plugins;
 
   /// Every entry, in the order they were recorded.
   Iterable<ManifestEntry> get entries => _entries.values;
@@ -279,8 +291,9 @@ class InstallManifest extends Equatable {
     );
   }
 
-  /// This manifest with [plugins] as the versions it was written from.
-  InstallManifest withPlugins(Map<String, String> plugins) {
+  /// This manifest with [plugins] as the versions each harness was written
+  /// from.
+  InstallManifest withPlugins(Map<Harness, Map<String, String>> plugins) {
     return InstallManifest(entries, plugins);
   }
 
@@ -289,7 +302,9 @@ class InstallManifest extends Equatable {
   String encode({required String home}) {
     final json = {
       'version': version,
-      'plugins': plugins,
+      'plugins': {
+        for (final MapEntry(:key, :value) in plugins.entries) key.name: value,
+      },
       'entries': [
         for (final entry in entries)
           {...entry.toJson(), 'path': p.relative(entry.path, from: home)},
diff --git a/packages/vgv_ai_cli/lib/src/resolve/model/asset_resolution.dart b/packages/vgv_ai_cli/lib/src/resolve/model/asset_resolution.dart
index 4587ca1b..285a071d 100644
--- a/packages/vgv_ai_cli/lib/src/resolve/model/asset_resolution.dart
+++ b/packages/vgv_ai_cli/lib/src/resolve/model/asset_resolution.dart
@@ -6,14 +6,11 @@ import 'package:plugin_source/plugin_source.dart';
 sealed class const AssetResolution();
 
 /// {@template resolved_assets}
-/// Every plugin in [plugins] resolved and parsed, merged into [assets].
+/// Every plugin resolved and parsed, merged into [assets], which names them.
 /// {@endtemplate}
 final class const ResolvedAssets({
   /// What the plugins contribute, merged.
   required final PluginAssets assets,
-
-  /// The plugins that were resolved, at the versions they were pinned to.
-  required final List<PluginRef> plugins,
 }) extends AssetResolution;
 
 /// {@template unavailable_assets}
diff --git a/packages/vgv_ai_cli/lib/src/resolve/plugin_resolver.dart b/packages/vgv_ai_cli/lib/src/resolve/plugin_resolver.dart
index c11cb18e..33babc25 100644
--- a/packages/vgv_ai_cli/lib/src/resolve/plugin_resolver.dart
+++ b/packages/vgv_ai_cli/lib/src/resolve/plugin_resolver.dart
@@ -18,10 +18,10 @@ class const PluginResolver({
   final PluginParser _parser = const ClaudePluginParser(),
   final List<PluginRef> _plugins = vgvPlugins,
 }) {
-  /// Resolves every plugin for [home], stopping at the first that cannot be
-  /// resolved or parsed: a half-configured harness is worse than an
-  /// unconfigured one.
-  Future<AssetResolution> resolve(Directory home) async {
+  /// Resolves the plugins [only] names for [home], or every pinned one when
+  /// it names none, stopping at the first that cannot be resolved or parsed:
+  /// a half-configured harness is worse than an unconfigured one.
+  Future<AssetResolution> resolve(Directory home, {Set<String>? only}) async {
     final sources = [
       LocalCachePluginSource(home: home),
       GitPluginSource(
@@ -30,8 +30,13 @@ class const PluginResolver({
       ),
     ];
 
+    final plugins = [
+      for (final plugin in _plugins)
+        if (only?.contains(plugin.name) ?? true) plugin,
+    ];
+
     final parsed = <PluginAssets>[];
-    for (final plugin in _plugins) {
+    for (final plugin in plugins) {
       switch (await _resolveOne(plugin, sources)) {
         case ResolvedAssets(:final assets):
           parsed.add(assets);
@@ -42,10 +47,7 @@ class const PluginResolver({
       }
     }
 
-    return ResolvedAssets(
-      assets: PluginAssets.merge(parsed),
-      plugins: _plugins,
-    );
+    return ResolvedAssets(assets: PluginAssets.merge(parsed, plugins: plugins));
   }
 
   /// [plugin] parsed from the first of [sources] holding a copy that parses.
@@ -65,10 +67,7 @@ class const PluginResolver({
       switch (await source.resolve(plugin)) {
         case ResolvedPlugin(:final directory):
           try {
-            return ResolvedAssets(
-              assets: _parser.parse(directory),
-              plugins: [plugin],
-            );
+            return ResolvedAssets(assets: _parser.parse(directory));
           } on PluginParseException catch (error) {
             unparseable = UnparseableAssets(plugin, error);
           }
diff --git a/packages/vgv_ai_cli/lib/src/translate/translators/claude_translator.dart b/packages/vgv_ai_cli/lib/src/translate/translators/claude_translator.dart
index c3aeb6e6..1dae2f81 100644
--- a/packages/vgv_ai_cli/lib/src/translate/translators/claude_translator.dart
+++ b/packages/vgv_ai_cli/lib/src/translate/translators/claude_translator.dart
@@ -29,7 +29,7 @@ class const ClaudeTranslator() extends HarnessTranslator {
       },
     },
     'enabledPlugins': {
-      for (final plugin in vgvPlugins)
+      for (final plugin in assets.plugins)
         '${plugin.name}@$vgvMarketplaceName': true,
     },
   });
diff --git a/packages/vgv_ai_cli/test/src/commands/doctor/doctor_command_test.dart b/packages/vgv_ai_cli/test/src/commands/doctor/doctor_command_test.dart
index de06c498..d7995d3f 100644
--- a/packages/vgv_ai_cli/test/src/commands/doctor/doctor_command_test.dart
+++ b/packages/vgv_ai_cli/test/src/commands/doctor/doctor_command_test.dart
@@ -28,15 +28,23 @@ class _MockProgress extends Mock implements Progress;
 /// A [PluginResolver] that answers with [resolution], and counts its calls.
 class _FakeResolver extends Fake implements PluginResolver {
   AssetResolution resolution = const ResolvedAssets(
-    assets: PluginAssets(skills: [], agents: [], mcpServers: []),
-    plugins: vgvPlugins,
+    assets: PluginAssets(
+      skills: [],
+      agents: [],
+      mcpServers: [],
+      plugins: vgvPlugins,
+    ),
   );
 
   int calls = 0;
 
+  /// The plugins each call asked for, in order.
+  final resolved = <Set<String>?>[];
+
   @override
-  Future<AssetResolution> resolve(Directory home) async {
+  Future<AssetResolution> resolve(Directory home, {Set<String>? only}) async {
     calls++;
+    resolved.add(only);
     return resolution;
   }
 }
@@ -143,14 +151,18 @@ void main() {
     };
 
     /// Installs [changes] with the real reconciler, recording the pinned
-    /// plugin versions, as `install` does, and plans them again, so they
-    /// are current unless a test changes the plan.
+    /// plugin versions for each harness it writes for, as `install` does,
+    /// and plans them again, so they are current unless a test changes the
+    /// plan.
     void install(List<PlannedChange> changes) {
+      final manifest = const Reconciler()
+          .apply(changes, manifest: store.load()!)
+          .manifest;
       store.save(
-        const Reconciler()
-            .apply(changes, manifest: store.load()!)
-            .manifest
-            .withPlugins(pinned),
+        manifest.withPlugins({
+          ...manifest.plugins,
+          for (final change in changes) ?change.harness: pinned,
+        }),
       );
       translator.changes.addAll(changes);
     }
@@ -189,12 +201,11 @@ void main() {
       final exitCode = await runDoctor();
 
       expect(exitCode, ExitCode.success.code);
-      verifyInfo('✓ Plugins');
+      verifyInfo('✓ Shared');
+      verifyInfo('✓ Codex');
       for (final plugin in vgvPlugins) {
         verifyInfo('    ${plugin.name} ${plugin.version}');
       }
-      verifyInfo('✓ Shared');
-      verifyInfo('✓ Codex');
     });
 
     test('reports nothing installed when there is no manifest', () async {
@@ -639,7 +650,7 @@ void main() {
 
       void installWith(Map<String, String> plugins) {
         install([owned('.codex/agents/a.toml', harness: Harness.codex)]);
-        store.save(store.load()!.withPlugins(plugins));
+        store.save(store.load()!.withPlugins({Harness.codex: plugins}));
       }
 
       test('an older recorded version exits 70 with the install fix', () async {
@@ -648,7 +659,7 @@ void main() {
         final exitCode = await runDoctor();
 
         expect(exitCode, ExitCode.software.code);
-        verifyInfo('✗ Plugins');
+        verifyInfo('✗ Codex');
         verifyInfo(
           '    ${wingspan.name} 0.0.1 installed, ${wingspan.version} pinned',
         );
@@ -668,41 +679,179 @@ void main() {
         verifyInfo('    Run vgv_ai install --only codex');
       });
 
-      test('a pinned plugin that was never recorded exits 70', () async {
+      test('a pinned plugin that was never installed is only noted', () async {
         installWith({});
 
         final exitCode = await runDoctor();
 
-        expect(exitCode, ExitCode.software.code);
+        expect(exitCode, ExitCode.success.code);
+        verifyInfo('    ${wingspan.name} ${wingspan.version} not installed');
+        // Nothing was recorded, so every pinned plugin is still checked.
+        expect(resolver.resolved, [
+          {for (final plugin in vgvPlugins) plugin.name},
+        ]);
+      });
+
+      test(
+        'only the plugins a harness was installed from are checked',
+        () async {
+          installWith({wingspan.name: wingspan.version});
+
+          await runDoctor();
+
+          expect(resolver.resolved, [
+            {wingspan.name},
+          ]);
+        },
+      );
+
+      test(
+        'harnesses installed from different plugins are planned apart',
+        () async {
+          install([
+            owned('.codex/agents/a.toml', harness: Harness.codex),
+            owned('.gemini/agents/a.md', harness: Harness.gemini),
+          ]);
+          store.save(
+            store.load()!.withPlugins({
+              Harness.codex: {wingspan.name: wingspan.version},
+              Harness.gemini: pinned,
+            }),
+          );
+
+          await runDoctor();
+
+          expect(
+            resolver.resolved,
+            unorderedEquals([
+              {wingspan.name},
+              {for (final plugin in vgvPlugins) plugin.name},
+            ]),
+          );
+        },
+      );
+
+      test(
+        'the fix names the plugins the harness was installed from',
+        () async {
+          install([owned('.codex/agents/a.toml', harness: Harness.codex)]);
+          store.save(
+            store.load()!.withPlugins({
+              Harness.codex: {wingspan.name: '0.0.1'},
+            }),
+          );
+
+          await runDoctor();
+
+          verifyInfo(
+            '    Run vgv_ai install --only codex --plugin ${wingspan.name}',
+          );
+        },
+      );
+
+      test('are reported under each harness they were installed for', () async {
+        install([
+          owned('.codex/agents/a.toml', harness: Harness.codex),
+          owned('.gemini/agents/a.md', harness: Harness.gemini),
+        ]);
+        store.save(
+          store.load()!.withPlugins({
+            Harness.codex: {...pinned, wingspan.name: '0.0.1'},
+            Harness.gemini: pinned,
+          }),
+        );
+
+        await runDoctor();
+
+        verifyInfo('✗ Codex');
         verifyInfo(
-          '    ${wingspan.name} not recorded, ${wingspan.version} pinned',
+          '    ${wingspan.name} 0.0.1 installed, ${wingspan.version} pinned',
+        );
+        verifyInfo('    Run vgv_ai install --only codex');
+        verifyInfo('✓ Gemini');
+      });
+
+      test('the shared fix names the plugins its readers share', () async {
+        install([
+          owned('.agents/skills/a/SKILL.md'),
+          owned('.codex/agents/a.toml', harness: Harness.codex),
+        ]);
+        store.save(
+          store.load()!.withPlugins({
+            Harness.codex: {wingspan.name: wingspan.version},
+          }),
+        );
+        homeFile('.agents/skills/a/SKILL.md').deleteSync();
+
+        await runDoctor();
+
+        verifyInfo('    missing ~/.agents/skills/a/SKILL.md');
+        verifyInfo(
+          '    Run vgv_ai install --only codex --plugin ${wingspan.name}',
+        );
+      });
+
+      test('the shared fix is left out when its readers differ', () async {
+        install([
+          owned('.agents/skills/a/SKILL.md'),
+          owned('.codex/agents/a.toml', harness: Harness.codex),
+          owned('.gemini/agents/a.md', harness: Harness.gemini),
+        ]);
+        store.save(
+          store.load()!.withPlugins({
+            Harness.codex: {wingspan.name: wingspan.version},
+            Harness.gemini: pinned,
+          }),
+        );
+        homeFile('.agents/skills/a/SKILL.md').deleteSync();
+
+        await runDoctor();
+
+        verifyInfo('    missing ~/.agents/skills/a/SKILL.md');
+        verifyNever(
+          () =>
+              logger.info('    Run vgv_ai install --only gemini --only codex'),
         );
       });
 
       test(
-        'are fixed by installing every configured harness in scope',
+        'nothing closes the report when the shared fix is left out',
         () async {
           install([
+            owned('.agents/skills/a/SKILL.md'),
             owned('.codex/agents/a.toml', harness: Harness.codex),
             owned('.gemini/agents/a.md', harness: Harness.gemini),
-            owned('.pi/agent/a.md', harness: Harness.pi),
           ]);
-          store.save(store.load()!.withPlugins({}));
+          store.save(
+            store.load()!.withPlugins({
+              Harness.codex: {wingspan.name: wingspan.version},
+              Harness.gemini: pinned,
+            }),
+          );
+          homeFile('.agents/skills/a/SKILL.md').deleteSync();
+          homeFile('.codex/agents/a.toml').deleteSync();
 
-          await runDoctor(args: ['--no-pi']);
+          await runDoctor();
 
-          verifyInfo('    Run vgv_ai install --only gemini --only codex');
+          verifyInfo(
+            '    Run vgv_ai install --only codex --plugin ${wingspan.name}',
+          );
+          verifyNever(
+            () => logger.info(
+              any(that: endsWith('to fix everything install can.')),
+            ),
+          );
         },
       );
 
-      test('are not reported when nothing in scope is configured', () async {
+      test('are not reported for a harness VGV has not configured', () async {
         installWith({});
         detect(const [Harness.codex, Harness.pi]);
 
         final exitCode = await runDoctor(args: ['--only', 'pi']);
 
         expect(exitCode, ExitCode.success.code);
-        verifyNever(() => logger.info(any(that: endsWith('Plugins'))));
+        verifyNever(() => logger.info(any(that: contains(wingspan.name))));
       });
     });
 
diff --git a/packages/vgv_ai_cli/test/src/commands/doctor/model/fix_command_test.dart b/packages/vgv_ai_cli/test/src/commands/doctor/model/fix_command_test.dart
index 92a1421b..66b4ea86 100644
--- a/packages/vgv_ai_cli/test/src/commands/doctor/model/fix_command_test.dart
+++ b/packages/vgv_ai_cli/test/src/commands/doctor/model/fix_command_test.dart
@@ -1,3 +1,4 @@
+import 'package:plugin_source/plugin_source.dart';
 import 'package:test/test.dart';
 import 'package:vgv_ai_cli/src/commands/doctor/model/model.dart';
 import 'package:vgv_ai_cli/src/model/model.dart';
@@ -18,6 +19,19 @@ void main() {
       );
     });
 
+    test('names each plugin with --plugin, in pinned order', () {
+      expect(
+        FixCommand(
+          harnesses: const {Harness.codex},
+          plugins: {for (final plugin in vgvPlugins) plugin.name},
+        ).toString(),
+        [
+          'vgv_ai install --only codex',
+          for (final plugin in vgvPlugins) '--plugin ${plugin.name}',
+        ].join(' '),
+      );
+    });
+
     group('combine', () {
       test('installs every harness any fix names', () {
         expect(
@@ -40,6 +54,36 @@ void main() {
         );
       });
 
+      test('keeps the plugins every fix installs', () {
+        expect(
+          FixCommand.combine([
+            FixCommand(
+              harnesses: const {Harness.codex},
+              plugins: {vgvPlugins.first.name},
+            ),
+            FixCommand(
+              harnesses: const {Harness.pi},
+              plugins: {vgvPlugins.first.name},
+            ),
+          ]).toString(),
+          'vgv_ai install --only codex --only pi '
+          '--plugin ${vgvPlugins.first.name}',
+        );
+      });
+
+      test('is null when the fixes install different plugins', () {
+        expect(
+          FixCommand.combine([
+            FixCommand(
+              harnesses: const {Harness.codex},
+              plugins: {vgvPlugins.first.name},
+            ),
+            const FixCommand(harnesses: {Harness.pi}),
+          ]),
+          isNull,
+        );
+      });
+
       test('is null when there is nothing to fix', () {
         expect(FixCommand.combine(const []), isNull);
         expect(FixCommand.combine(const [null, null]), isNull);
diff --git a/packages/vgv_ai_cli/test/src/commands/doctor/model/plugin_version_test.dart b/packages/vgv_ai_cli/test/src/commands/doctor/model/plugin_version_test.dart
index 8c9519e9..e23b89cc 100644
--- a/packages/vgv_ai_cli/test/src/commands/doctor/model/plugin_version_test.dart
+++ b/packages/vgv_ai_cli/test/src/commands/doctor/model/plugin_version_test.dart
@@ -63,7 +63,7 @@ void main() {
       expect(version.status, PluginStatus.unrecorded);
       expect(
         version.finding,
-        isFinding(FindingKind.stale, 'wingspan not recorded, 0.2.0 pinned'),
+        isFinding(FindingKind.warning, 'wingspan 0.2.0 not installed'),
       );
     });
   });
diff --git a/packages/vgv_ai_cli/test/src/commands/doctor/model/report_section_test.dart b/packages/vgv_ai_cli/test/src/commands/doctor/model/report_section_test.dart
index d3756eba..0aa9825a 100644
--- a/packages/vgv_ai_cli/test/src/commands/doctor/model/report_section_test.dart
+++ b/packages/vgv_ai_cli/test/src/commands/doctor/model/report_section_test.dart
@@ -75,6 +75,20 @@ void main() {
       );
     });
 
+    test('needs its own fix when no one command fixes what it found', () {
+      const unfixable = ReportSection(
+        title: 'Shared',
+        installs: {Harness.codex, Harness.gemini},
+        findings: [Finding.missing('a')],
+        plugins: null,
+      );
+
+      expect(unfixable.fix, isNull);
+      expect(unfixable.needsItsOwnFix, isTrue);
+      expect(section(const [Finding.missing('a')]).needsItsOwnFix, isFalse);
+      expect(section(const []).needsItsOwnFix, isFalse);
+    });
+
     test('has no fix when install changes nothing it found', () {
       expect(section(const []).fix, isNull);
       expect(
diff --git a/packages/vgv_ai_cli/test/src/commands/install_command_test.dart b/packages/vgv_ai_cli/test/src/commands/install_command_test.dart
index b6116c47..81c39dea 100644
--- a/packages/vgv_ai_cli/test/src/commands/install_command_test.dart
+++ b/packages/vgv_ai_cli/test/src/commands/install_command_test.dart
@@ -246,6 +246,75 @@ void main() {
       });
     });
 
+    group('--plugin', () {
+      // The manifest is only written once something is, so every run here
+      // writes one file.
+      setUp(() {
+        translator.plan = TranslationPlan(
+          harnesses: {
+            Harness.claude: TranslationResult(
+              changes: [ownChange(Harness.claude, '.claude/a.md', 'a')],
+            ),
+          },
+        );
+      });
+
+      test('installs just the plugins it names', () async {
+        final exitCode = await runInstall([
+          '--only',
+          'claude',
+          '--plugin',
+          vgvPlugins.first.name,
+        ]);
+
+        expect(exitCode, ExitCode.success.code);
+        expect(translator.assets?.plugins, [vgvPlugins.first]);
+        expect(ManifestStore(home).load()!.plugins, {
+          Harness.claude: {vgvPlugins.first.name: vgvPlugins.first.version},
+        });
+      });
+
+      test('keeps the recorded version of a plugin it skips', () async {
+        final skipped = vgvPlugins.last;
+        await runInstall(['--only', 'claude']);
+        final store = ManifestStore(home);
+        store.save(
+          store.load()!.withPlugins({
+            Harness.claude: {
+              for (final plugin in vgvPlugins) plugin.name: plugin.version,
+              skipped.name: '0.0.1',
+            },
+          }),
+        );
+
+        await runInstall([
+          '--only',
+          'claude',
+          '--plugin',
+          vgvPlugins.first.name,
+        ]);
+
+        expect(store.load()!.plugins, {
+          Harness.claude: {
+            vgvPlugins.first.name: vgvPlugins.first.version,
+            skipped.name: '0.0.1',
+          },
+        });
+      });
+
+      test('rejects a plugin it does not pin', () async {
+        final exitCode = await runInstall([
+          '--only',
+          'claude',
+          '--plugin',
+          'vgv-unknown',
+        ]);
+
+        expect(exitCode, ExitCode.usage.code);
+        expect(translator.assets, isNull);
+      });
+    });
+
     group('resolution', () {
       test('clones the plugins when there is no Claude Code cache', () async {
         final cloned = <List<String>>[];
@@ -518,7 +587,9 @@ void main() {
         final manifest = ManifestStore(home).load()!;
         expect(manifest[homeFile('.claude/a.md').path], isA<OwnedFile>());
         expect(manifest.plugins, {
-          for (final plugin in vgvPlugins) plugin.name: plugin.version,
+          Harness.claude: {
+            for (final plugin in vgvPlugins) plugin.name: plugin.version,
+          },
         });
       });
 
@@ -526,12 +597,18 @@ void main() {
         planOne();
         await runInstall(['--only', 'claude']);
         final store = ManifestStore(home);
-        store.save(store.load()!.withPlugins(const {'vgv-wingspan': '0.0.1'}));
+        store.save(
+          store.load()!.withPlugins(const {
+            Harness.claude: {'vgv-wingspan': '0.0.1'},
+          }),
+        );
 
         await runInstall(['--only', 'claude']);
 
         expect(store.load()!.plugins, {
-          for (final plugin in vgvPlugins) plugin.name: plugin.version,
+          Harness.claude: {
+            for (final plugin in vgvPlugins) plugin.name: plugin.version,
+          },
         });
       });
 
diff --git a/packages/vgv_ai_cli/test/src/manifest/manifest_auditor_test.dart b/packages/vgv_ai_cli/test/src/manifest/manifest_auditor_test.dart
index 3d786ee6..3883b16f 100644
--- a/packages/vgv_ai_cli/test/src/manifest/manifest_auditor_test.dart
+++ b/packages/vgv_ai_cli/test/src/manifest/manifest_auditor_test.dart
@@ -623,13 +623,35 @@ void main() {
           expect(manifest.file.readAsStringSync(), before);
         });
 
-        test('keeps the plugin versions it records', () {
+        test('keeps the plugin versions of a harness it leaves alone', () {
+          const recorded = {
+            Harness.codex: {'vgv-wingspan': '0.0.5'},
+          };
+          install([
+            owned(seed('.codex/a.md', 'a'), 'a', harness: Harness.codex),
+          ]);
+
+          final result = auditor.reverse(
+            manifest.load()!.withPlugins(recorded),
+            fs,
+            owners: const {Harness.claude},
+          );
+
+          expect(result.manifest.plugins, recorded);
+        });
+
+        test('forgets the plugin versions of a harness it empties', () {
+          install([owned(file('.codex/a.md'), 'a', harness: Harness.codex)]);
+
           final result = auditor.reverse(
-            InstallManifest(const [], const {'vgv-wingspan': '0.0.5'}),
+            manifest.load()!.withPlugins(const {
+              Harness.codex: {'vgv-wingspan': '0.0.5'},
+            }),
             fs,
           );
 
-          expect(result.manifest.plugins, {'vgv-wingspan': '0.0.5'});
+          expect(result.manifest.entries, isEmpty);
+          expect(result.manifest.plugins, isEmpty);
         });
 
         test('does nothing with an empty manifest', () {
diff --git a/packages/vgv_ai_cli/test/src/model/install_manifest_test.dart b/packages/vgv_ai_cli/test/src/model/install_manifest_test.dart
index e1dee865..cc87bc8b 100644
--- a/packages/vgv_ai_cli/test/src/model/install_manifest_test.dart
+++ b/packages/vgv_ai_cli/test/src/model/install_manifest_test.dart
@@ -44,7 +44,10 @@ void main() {
     test('round trips every kind of entry, and the plugin versions', () {
       final manifest = InstallManifest(
         const [owned, merged, sections],
-        const {'vgv-wingspan': '0.0.5', 'vgv-ai-flutter-plugin': '0.0.6'},
+        const {
+          Harness.claude: {'vgv-wingspan': '0.0.5'},
+          Harness.codex: {'vgv-ai-flutter-plugin': '0.0.6'},
+        },
       );
 
       final decoded = InstallManifest.decode(
@@ -79,8 +82,8 @@ void main() {
         isA<OwnedFile>().having((e) => e.sha256, 'sha256', 'abc'),
       );
       expect(decoded.plugins, {
-        'vgv-wingspan': '0.0.5',
-        'vgv-ai-flutter-plugin': '0.0.6',
+        Harness.claude: {'vgv-wingspan': '0.0.5'},
+        Harness.codex: {'vgv-ai-flutter-plugin': '0.0.6'},
       });
     });
 
@@ -88,12 +91,16 @@ void main() {
       final json = jsonDecode(
         InstallManifest(
           const [owned, merged],
-          const {'vgv-wingspan': '0.0.5'},
+          const {
+            Harness.codex: {'vgv-wingspan': '0.0.5'},
+          },
         ).encode(home: home),
       ) as Map<String, dynamic>;
 
-      expect(json['version'], 2);
-      expect(json['plugins'], {'vgv-wingspan': '0.0.5'});
+      expect(json['version'], 1);
+      expect(json['plugins'], {
+        'codex': {'vgv-wingspan': '0.0.5'},
+      });
       expect(json['entries'], [
         {
           'path': '.agents/skills/a/SKILL.md',
@@ -123,7 +130,7 @@ void main() {
       expect(
         decode(jsonEncode({owned.path: 'hash'}))!.entries,
         isEmpty,
-        reason: 'the flat format before version 1 never shipped',
+        reason: 'a document with no version is not a manifest',
       );
     });
 
@@ -139,9 +146,20 @@ void main() {
 
       expect(decode(null).plugins, isEmpty);
       expect(decode(['vgv-wingspan']).plugins, isEmpty);
+      expect(decode({'codex': 'vgv-wingspan'}).plugins, isEmpty);
+      expect(
+        decode({
+          'nope': {'vgv-wingspan': '0.0.5'},
+        }).plugins,
+        isEmpty,
+      );
       expect(
-        decode({'vgv-wingspan': 5, 'vgv-ai-flutter-plugin': '0.0.5'}).plugins,
-        {'vgv-ai-flutter-plugin': '0.0.5'},
+        decode({
+          'codex': {'vgv-wingspan': 5, 'vgv-ai-flutter-plugin': '0.0.5'},
+        }).plugins,
+        {
+          Harness.codex: {'vgv-ai-flutter-plugin': '0.0.5'},
+        },
       );
     });
 
@@ -165,11 +183,12 @@ void main() {
       );
     });
 
-    test('reads a version 1 manifest as one with no plugin versions', () {
+    test('keeps the entries when it cannot read the plugin versions', () {
       final manifest = InstallManifest.decode(
         jsonEncode({
-          'version': 1,
+          'version': InstallManifest.version,
           'entries': [onDisk(owned)],
+          'plugins': {'vgv-wingspan': '0.0.5'},
         }),
         home: home,
       )!;
@@ -248,31 +267,46 @@ void main() {
       const updated = OwnedFile(path: '/x', owner: null, sha256: 'new');
       final manifest = InstallManifest(
         const [OwnedFile(path: '/x', owner: null, sha256: 'old'), merged],
-        const {'vgv-wingspan': '0.0.5'},
+        const {
+          Harness.codex: {'vgv-wingspan': '0.0.5'},
+        },
       ).record(updated);
 
       expect(manifest.entries, [updated, merged]);
-      expect(manifest.plugins, {'vgv-wingspan': '0.0.5'});
+      expect(manifest.plugins, {
+        Harness.codex: {'vgv-wingspan': '0.0.5'},
+      });
     });
 
     test('drops the entries for the given paths', () {
       final manifest = InstallManifest(
         const [owned, merged, sections],
-        const {'vgv-wingspan': '0.0.5'},
+        const {
+          Harness.codex: {'vgv-wingspan': '0.0.5'},
+        },
       ).without([owned.path, sections.path]);
 
       expect(manifest.entries, [merged]);
-      expect(manifest.plugins, {'vgv-wingspan': '0.0.5'});
+      expect(manifest.plugins, {
+        Harness.codex: {'vgv-wingspan': '0.0.5'},
+      });
     });
 
     test('replaces the plugin versions, keeping the entries', () {
-      final manifest = InstallManifest(
-        const [owned],
-        const {'vgv-wingspan': '0.0.4'},
-      ).withPlugins(const {'vgv-wingspan': '0.0.5'});
+      final manifest =
+          InstallManifest(
+            const [owned],
+            const {
+              Harness.codex: {'vgv-wingspan': '0.0.4'},
+            },
+          ).withPlugins(const {
+            Harness.codex: {'vgv-wingspan': '0.0.5'},
+          });
 
       expect(manifest.entries, [owned]);
-      expect(manifest.plugins, {'vgv-wingspan': '0.0.5'});
+      expect(manifest.plugins, {
+        Harness.codex: {'vgv-wingspan': '0.0.5'},
+      });
     });
 
     test('equals a manifest with the same entries, in the same order', () {
@@ -293,8 +327,20 @@ void main() {
         ),
       );
       expect(
-        InstallManifest(const [owned], const {'vgv-wingspan': '0.0.5'}),
-        isNot(InstallManifest(const [owned], const {'vgv-wingspan': '0.0.4'})),
+        InstallManifest(
+          const [owned],
+          const {
+            Harness.codex: {'vgv-wingspan': '0.0.5'},
+          },
+        ),
+        isNot(
+          InstallManifest(
+            const [owned],
+            const {
+              Harness.codex: {'vgv-wingspan': '0.0.4'},
+            },
+          ),
+        ),
       );
     });
 
diff --git a/packages/vgv_ai_cli/test/src/resolve/plugin_resolver_test.dart b/packages/vgv_ai_cli/test/src/resolve/plugin_resolver_test.dart
index e444d5c3..31796fe6 100644
--- a/packages/vgv_ai_cli/test/src/resolve/plugin_resolver_test.dart
+++ b/packages/vgv_ai_cli/test/src/resolve/plugin_resolver_test.dart
@@ -131,7 +131,7 @@ void main() {
       expect(
         resolution,
         isA<ResolvedAssets>()
-            .having((r) => r.plugins, 'plugins', [wingspan, flutter])
+            .having((r) => r.assets.plugins, 'plugins', [wingspan, flutter])
             .having(
               (r) => r.assets.agents.map((agent) => agent.name),
               'agents',
@@ -271,6 +271,25 @@ void main() {
       );
     });
 
+    test('resolves only the plugins `only` names', () async {
+      cache(wingspan);
+      final resolver = PluginResolver(
+        runProcess: processes.never,
+        parser: parser,
+        plugins: const [wingspan, flutter],
+      );
+
+      final resolution = await resolver.resolve(home, only: {wingspan.name});
+
+      expect(parser.roots, [cached(wingspan)]);
+      expect(
+        resolution,
+        isA<ResolvedAssets>().having((r) => r.assets.plugins, 'plugins', [
+          wingspan,
+        ]),
+      );
+    });
+
     test('resolves the pinned VGV plugins by default', () async {
       vgvPlugins.forEach(cache);
       final resolver = PluginResolver(
@@ -282,7 +301,11 @@ void main() {
 
       expect(
         resolution,
-        isA<ResolvedAssets>().having((r) => r.plugins, 'plugins', vgvPlugins),
+        isA<ResolvedAssets>().having(
+          (r) => r.assets.plugins,
+          'plugins',
+          vgvPlugins,
+        ),
       );
     });
   });
diff --git a/packages/vgv_ai_cli/test/src/translate/_assets.dart b/packages/vgv_ai_cli/test/src/translate/_assets.dart
index d1b3335f..5c1edf54 100644
--- a/packages/vgv_ai_cli/test/src/translate/_assets.dart
+++ b/packages/vgv_ai_cli/test/src/translate/_assets.dart
@@ -73,11 +73,13 @@ PluginAssets pluginAssets({
   List<AgentAsset> agents = const [],
   List<MCPServer> mcpServers = const [],
   List<HookAsset> hooks = const [],
+  List<PluginRef> plugins = const [],
 }) => PluginAssets(
   skills: skills,
   agents: agents,
   mcpServers: mcpServers,
   hooks: hooks,
+  plugins: plugins,
 );
 
 /// Parses a rendered `---` fenced frontmatter block back into its values.
diff --git a/packages/vgv_ai_cli/test/src/translate/translators/claude_translator_test.dart b/packages/vgv_ai_cli/test/src/translate/translators/claude_translator_test.dart
index 3d9303bf..fc422bff 100644
--- a/packages/vgv_ai_cli/test/src/translate/translators/claude_translator_test.dart
+++ b/packages/vgv_ai_cli/test/src/translate/translators/claude_translator_test.dart
@@ -1,6 +1,7 @@
 import 'dart:convert';
 
 import 'package:file/memory.dart';
+import 'package:plugin_source/plugin_source.dart';
 import 'package:test/test.dart';
 import 'package:vgv_ai_cli/src/model/model.dart';
 import 'package:vgv_ai_cli/src/translate/translate.dart';
@@ -16,7 +17,9 @@ void main() {
     });
 
     test('points Claude Code at the marketplace and enables both plugins', () {
-      final settings = jsonDecode(translator.settings(pluginAssets()));
+      final settings = jsonDecode(
+        translator.settings(pluginAssets(plugins: vgvPlugins)),
+      );
 
       expect(settings, {
         'extraKnownMarketplaces': {
@@ -34,6 +37,17 @@ void main() {
       });
     });
 
+    test('enables only the plugins the assets came from', () {
+      final wingspan = vgvPlugins.first;
+      final settings = jsonDecode(
+        translator.settings(pluginAssets(plugins: [wingspan])),
+      ) as Map<String, dynamic>;
+
+      expect(settings['enabledPlugins'], {
+        '${wingspan.name}@very-good-claude-code-marketplace': true,
+      });
+    });
+
     test('spells no agents or commands, which the marketplace supplies', () {
       final fs = MemoryFileSystem.test();