diff --git a/pkg/config/config_struct.go b/pkg/config/config_struct.go
index a75677084..17738959a 100644
--- a/pkg/config/config_struct.go
+++ b/pkg/config/config_struct.go
@@ -328,9 +328,35 @@ func (v SecureModelList) MarshalYAML() (any, error) {
 }
 
 func (v *SkillsRegistriesConfig) UnmarshalJSON(data []byte) error {
-	var list []*SkillRegistryConfig
+	var list []json.RawMessage
 	if err := json.Unmarshal(data, &list); err == nil {
-		*v = list
+		decodedList := make([]*SkillRegistryConfig, 0, len(list))
+		for _, item := range list {
+			var nameOnly struct {
+				Name string `json:"name"`
+			}
+			if err := json.Unmarshal(item, &nameOnly); err != nil {
+				return err
+			}
+			registry := cloneRegistryConfig(findRegistryConfigByName(*v, nameOnly.Name))
+			if registry == nil {
+				registry = &SkillRegistryConfig{Name: nameOnly.Name}
+			}
+			if err := json.Unmarshal(item, registry); err != nil {
+				return err
+			}
+			decodedList = append(decodedList, registry)
+		}
+		if len(*v) > 0 {
+			for _, registry := range decodedList {
+				if registry == nil {
+					continue
+				}
+				v.Set(registry.Name, *registry)
+			}
+			return nil
+		}
+		*v = decodedList
 		return nil
 	}
 
@@ -345,16 +371,16 @@ func (v *SkillsRegistriesConfig) UnmarshalJSON(data []byte) error {
 			keys = append(keys, name)
 		}
 		sort.Strings(keys)
-		list = make([]*SkillRegistryConfig, 0, len(keys))
+		decodedList := make([]*SkillRegistryConfig, 0, len(keys))
 		for _, name := range keys {
 			var registry SkillRegistryConfig
 			if err := json.Unmarshal(legacy[name], &registry); err != nil {
 				return err
 			}
 			registry.Name = name
-			list = append(list, &registry)
+			decodedList = append(decodedList, &registry)
 		}
-		*v = list
+		*v = decodedList
 		return nil
 	}
 
diff --git a/pkg/config/config_struct_test.go b/pkg/config/config_struct_test.go
index f02897d28..422c9978f 100644
--- a/pkg/config/config_struct_test.go
+++ b/pkg/config/config_struct_test.go
@@ -287,6 +287,29 @@ func TestSkillsRegistriesConfigUnmarshalJSONPreservesDefaultRegistries(t *testin
 	assert.Empty(t, github.Param)
 }
 
+func TestSkillsRegistriesConfigUnmarshalJSONListPreservesDefaultRegistries(t *testing.T) {
+	registries := DefaultConfig().Tools.Skills.Registries
+
+	err := json.Unmarshal([]byte(`[
+		{
+			"name": "clawhub",
+			"base_url": "https://clawhub.example.com"
+		}
+	]`), &registries)
+	assert.NoError(t, err)
+
+	clawhub, ok := registries.Get("clawhub")
+	assert.True(t, ok)
+	assert.True(t, clawhub.Enabled)
+	assert.Equal(t, "https://clawhub.example.com", clawhub.BaseURL)
+
+	github, ok := registries.Get("github")
+	assert.True(t, ok)
+	assert.True(t, github.Enabled)
+	assert.Equal(t, "https://github.com", github.BaseURL)
+	assert.Empty(t, github.Param)
+}
+
 func TestSkillsRegistriesConfigUnmarshalYAMLAppendsNewRegistryToExistingSlice(t *testing.T) {
 	registries := DefaultConfig().Tools.Skills.Registries
 
diff --git a/pkg/skills/installer.go b/pkg/skills/installer.go
index c88cc046c..599668baf 100644
--- a/pkg/skills/installer.go
+++ b/pkg/skills/installer.go
@@ -261,6 +261,14 @@ func parseGitHubRefWithBaseURL(repo, githubBaseURL, defaultRef string) (GitHubRe
 		if len(parts) < 2 {
 			return GitHubRef{}, fmt.Errorf("invalid GitHub URL")
 		}
+		if len(parts) > 2 {
+			if parts[2] != "tree" && parts[2] != "blob" {
+				return GitHubRef{}, fmt.Errorf("invalid GitHub repository URL path %q", u.Path)
+			}
+			if len(parts) < 4 {
+				return GitHubRef{}, fmt.Errorf("invalid GitHub %s URL path %q", parts[2], u.Path)
+			}
+		}
 		ref := GitHubRef{
 			Owner:    parts[0],
 			RepoName: parts[1],
diff --git a/pkg/skills/installer_test.go b/pkg/skills/installer_test.go
index 9de991354..6c334d00f 100644
--- a/pkg/skills/installer_test.go
+++ b/pkg/skills/installer_test.go
@@ -234,6 +234,30 @@ func TestParseGitHubRefWithBaseURL(t *testing.T) {
 	if !strings.Contains(err.Error(), `invalid GitHub URL host "ghe.example.com"`) {
 		t.Fatalf("unexpected scheme mismatch error = %v", err)
 	}
+
+	_, err = parseGitHubRefWithBaseURL(
+		"https://github.com/org/repo/pull/2442",
+		"",
+		"main",
+	)
+	if err == nil {
+		t.Fatal("parseGitHubRefWithBaseURL() error = nil, want invalid repository URL path error")
+	}
+	if !strings.Contains(err.Error(), `invalid GitHub repository URL path "/org/repo/pull/2442"`) {
+		t.Fatalf("unexpected PR URL error = %v", err)
+	}
+
+	_, err = parseGitHubRefWithBaseURL(
+		"https://github.com/org/repo/tree",
+		"",
+		"main",
+	)
+	if err == nil {
+		t.Fatal("parseGitHubRefWithBaseURL() error = nil, want invalid tree URL path error")
+	}
+	if !strings.Contains(err.Error(), `invalid GitHub tree URL path "/org/repo/tree"`) {
+		t.Fatalf("unexpected short tree URL error = %v", err)
+	}
 }
 
 func TestSkillInstallerResolveGitHubRefUsesDefaultBranch(t *testing.T) {