diff --git a/CHANGELOG.md b/CHANGELOG.md
index b74c5d37ef..5a6c8015e5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,9 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Fixes
 
+- In a Shopify theme, a JSON template or section group that starts with the comment the theme editor writes at the top now links the sections it lists, at the line of each section's `type`. Before, such a file linked nothing, so most sections of an editor-saved theme looked unused. Re-index Shopify themes after upgrading. (#2494)
+- In a Shopify theme layout, `{% sections 'header-group' %}` now links to the section group `sections/header-group.json`. Before, only the singular `{% section %}` tag was linked. (#2494)
+- A `{% schema %}` written inside `{% comment %}` or `{% raw %}` in a Liquid file is no longer indexed as a definition. (#2494)
 - In VB.NET, every member of a `Structure` is now indexed, including its fields, properties, methods, constructors and nested enums. Before, only the first member was, so the rest could not be found and their callers looked empty.
 - In VB.NET and C#, what a property's `Get` and `Set` code calls, creates and reads now belongs to that property, as do C#'s `get => …` accessors and `=> …` property bodies. Before, it was dropped, so a method used only from a property looked unused.
 - In VB.NET, a field or property initializer like `= Compute()` or `As New List(Of Order)` now links what it calls and creates, and so do a `Custom Event`'s `AddHandler`, `RemoveHandler` and `RaiseEvent` blocks. Re-index VB.NET and C# projects after upgrading.
diff --git a/__tests__/liquid-shopify-editor-regressions.test.ts b/__tests__/liquid-shopify-editor-regressions.test.ts
new file mode 100644
index 0000000000..8f57ad51a0
--- /dev/null
+++ b/__tests__/liquid-shopify-editor-regressions.test.ts
@@ -0,0 +1,163 @@
+import { describe, it, expect } from 'vitest';
+import * as fs from 'fs';
+import * as os from 'os';
+import * as path from 'path';
+import { LiquidExtractor } from '../src/extraction/liquid-extractor';
+import { CodeGraph } from '../src/index';
+
+const extract = (file: string, source: string) => new LiquidExtractor(file, source).extract();
+const refs = (file: string, source: string) => extract(file, source).unresolvedReferences;
+
+describe('Shopify editor JSON and section groups', () => {
+  it.each(['\n', '\r\n'])('reads generated comments and reports type positions with %j', (newline) => {
+    const source = [
+      '/* IMPORTANT: This file is generated by the Shopify editor. */',
+      '{',
+      '  "sections": {',
+      '    "main": {',
+      '      "type": "main-product",',
+      '      "settings": { "text": "https://host/path/*literal*/" }',
+      '    },',
+      '    "duplicate": { "type": "main-product" }',
+      '  },',
+      '  "order": ["main", "duplicate"]',
+      '}',
+    ].join(newline);
+    expect(refs('templates/product.json', source).map(r => [r.referenceName, r.line, r.column]))
+      .toEqual([['sections/main-product.liquid', 5, 14]]);
+  });
+
+  it.each([
+    ['templates/customers/login.json', 'main-login'],
+    ['sections/header-group.json', 'header'],
+  ])('reads comments in %s', (file, type) => {
+    const source = `/* Generated */\n{"sections":{"main":{"type":"${type}"}},"order":["main"]}`;
+    expect(refs(file, source).map(r => r.referenceName)).toEqual([`sections/${type}.liquid`]);
+  });
+
+  it.each(['null', '[]', '{', '{"sections":[]}', '{"sections":{"main":null}}',
+    '{"sections":{"main":{"type":17}}}', '{"sections":{"main":{"type":"header"}}',
+    '{"sections":{"main":{"type":"header"}},}',
+    '/* unfinished {"sections":{"main":{"type":"header"}}}'])('does not invent dependencies from %s', source => {
+    expect(refs('templates/product.json', source)).toEqual([]);
+  });
+
+  it.each([
+    "{% sections 'header-group' %}",
+    '{%- sections "header-group" -%}',
+    "{% liquid\n  sections 'header-group'\n%}",
+  ])('links a section group to JSON: %s', source => {
+    expect(refs('layout/theme.liquid', source).map(r => r.referenceName))
+      .toEqual(['sections/header-group.json']);
+  });
+
+  it('keeps singular sections distinct from groups of the same name', () => {
+    const result = extract('layout/theme.liquid', "{% section 'header' %}{% sections 'header' %}");
+    expect(result.unresolvedReferences.map(r => r.referenceName))
+      .toEqual(['sections/header.liquid', 'sections/header.json']);
+    expect(new Set(result.nodes.map(n => n.id)).size).toBe(result.nodes.length);
+  });
+
+  it('preserves strict JSON section dependencies and gives their actual positions', () => {
+    const source = '{\n  "sections": { "main": { "type": "header" } },\n  "order": ["main"]\n}';
+    expect(refs('templates/index.json', source).map(r => [r.referenceName, r.line, r.column]))
+      .toEqual([['sections/header.liquid', 2, 34]]);
+  });
+
+  it('preserves standard Liquid assignments and suppresses commented/raw assignments', () => {
+    const source = "{% assign keep = 'hello' %}\n{% comment %}{% assign hidden = 1 %}{% endcomment %}\n" +
+      "{% raw %}{% assign hidden2 = 2 %}{% endraw %}\n{% assign after = 'world' %}";
+    const result = extract('views/page.liquid', source);
+    expect(result.nodes.filter(n => n.kind === 'variable').map(n => [n.name, n.startLine]))
+      .toEqual([['keep', 1], ['after', 4]]);
+    expect(result.unresolvedReferences).toEqual([]);
+  });
+
+  it.each([
+    "{% # sections 'ghost' %}",
+    "{% liquid\n  # sections 'ghost'\n%}",
+  ])('does not infer group dependencies from inline comments: %s', source => {
+    expect(refs('layout/theme.liquid', source)).toEqual([]);
+  });
+
+  it.each(['comment', 'raw'])('ignores schemas and group references inside %s', tag => {
+    const source = `{% ${tag} %}{% sections 'ghost' %}{% schema %}{"name":"Ghost"}{% endschema %}{% end${tag} %}\n` +
+      '{% schema %}{"name":"Live"}{% endschema %}';
+    const result = extract('sections/header.liquid', source);
+    expect(result.unresolvedReferences).toEqual([]);
+    expect(result.nodes.filter(n => n.kind === 'constant').map(n => [n.name, n.startLine]))
+      .toEqual([['Live', 2]]);
+  });
+
+  it('resolves the complete layout to group to section to snippet chain', async () => {
+    const root = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-shopify-editor-'));
+    let cg: CodeGraph | undefined;
+    try {
+      for (const dir of ['layout', 'sections', 'snippets', 'config']) fs.mkdirSync(path.join(root, dir));
+      const files = {
+        'config/settings_schema.json': '[]',
+        'layout/theme.liquid': "{% sections 'header-group' %}",
+        'sections/header-group.json': '/* Generated */\n{"type":"header","name":"Header","sections":{"main":{"type":"header"}},"order":["main"]}',
+        'sections/header.liquid': "{% render 'logo' %}",
+        'snippets/logo.liquid': '<span>Logo</span>',
+      };
+      for (const [file, source] of Object.entries(files)) fs.writeFileSync(path.join(root, file), source);
+      cg = CodeGraph.initSync(root);
+      await cg.indexAll();
+      cg.resolveReferences();
+      expect(cg.getFileDependencies('layout/theme.liquid')).toEqual(['sections/header-group.json']);
+      expect(cg.getFileDependencies('sections/header-group.json')).toEqual(['sections/header.liquid']);
+      expect(cg.getFileDependencies('sections/header.liquid')).toEqual(['snippets/logo.liquid']);
+      expect(cg.getFileDependents('sections/header.liquid')).toEqual(['sections/header-group.json']);
+    } finally {
+      cg?.close();
+      fs.rmSync(root, { recursive: true, force: true });
+    }
+  });
+
+  it('leaves commented JSON in a non-Shopify project outside the Liquid index', async () => {
+    const root = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-non-shopify-json-'));
+    let cg: CodeGraph | undefined;
+    try {
+      for (const dir of ['templates', 'sections', 'views']) fs.mkdirSync(path.join(root, dir));
+      fs.writeFileSync(path.join(root, 'templates/page.json'), '/* CMS data */\n{"sections":{"main":{"type":"hero"}}}');
+      fs.writeFileSync(path.join(root, 'sections/hero.liquid'), '<h1>{{ title }}</h1>');
+      fs.writeFileSync(path.join(root, 'views/page.liquid'), "{% assign title = 'Hello' %}");
+      cg = CodeGraph.initSync(root);
+      await cg.indexAll();
+      cg.resolveReferences();
+      expect(cg.getNodesByKind('file').map(n => n.filePath)).not.toContain('templates/page.json');
+      expect(cg.getFileDependents('sections/hero.liquid')).toEqual([]);
+      expect(cg.getNodesByKind('variable').some(n => n.name === 'title')).toBe(true);
+    } finally {
+      cg?.close();
+      fs.rmSync(root, { recursive: true, force: true });
+    }
+  });
+
+  it('keeps group references within their own theme even when a group is missing', async () => {
+    const root = fs.mkdtempSync(path.join(os.tmpdir(), 'codegraph-group-isolation-'));
+    let cg: CodeGraph | undefined;
+    try {
+      const files = {
+        'first/layout/theme.liquid': "{% sections 'header-group' %}",
+        'second/layout/theme.liquid': "{% sections 'header-group' %}",
+        'second/sections/header-group.json': '/* Generated */\n{"type":"header","name":"Header","sections":{"main":{"type":"header"}},"order":["main"]}',
+        'second/sections/header.liquid': '<header>Header</header>',
+      };
+      for (const [file, source] of Object.entries(files)) {
+        fs.mkdirSync(path.dirname(path.join(root, file)), { recursive: true });
+        fs.writeFileSync(path.join(root, file), source);
+      }
+      cg = CodeGraph.initSync(root);
+      await cg.indexAll();
+      cg.resolveReferences();
+      expect(cg.getFileDependencies('first/layout/theme.liquid')).toEqual([]);
+      expect(cg.getFileDependencies('second/layout/theme.liquid')).toEqual(['second/sections/header-group.json']);
+      expect(cg.getFileDependencies('second/sections/header-group.json')).toEqual(['second/sections/header.liquid']);
+    } finally {
+      cg?.close();
+      fs.rmSync(root, { recursive: true, force: true });
+    }
+  });
+});
diff --git a/src/extraction/liquid-extractor.ts b/src/extraction/liquid-extractor.ts
index f6d9aee60a..e90cf86b9d 100644
--- a/src/extraction/liquid-extractor.ts
+++ b/src/extraction/liquid-extractor.ts
@@ -1,12 +1,13 @@
 import { Node, Edge, ExtractionResult, ExtractionError, UnresolvedReference } from '../types';
 import { generateNodeId, NodeIdAllocator } from './tree-sitter-helpers';
+import { parseTree, findNodeAtLocation, ParseError } from 'jsonc-parser';
 
 /**
  * LiquidExtractor - Extracts relationships from Liquid template files
  *
  * Liquid is a templating language (used by Shopify, Jekyll, etc.) that doesn't
  * have traditional functions or classes. Instead, we extract:
- * - Section references ({% section 'name' %})
+ * - Section and section-group references ({% section/sections 'name' %})
  * - Snippet references ({% render 'name' %} and {% include 'name' %})
  * - Schema blocks ({% schema %}...{% endschema %})
  */
@@ -18,6 +19,7 @@ export class LiquidExtractor {
   private edges: Edge[] = [];
   private unresolvedReferences: UnresolvedReference[] = [];
   private errors: ExtractionError[] = [];
+  private suppressedRanges?: Array<[number, number]>;
 
   constructor(filePath: string, source: string) {
     this.filePath = filePath;
@@ -102,25 +104,29 @@ export class LiquidExtractor {
    * used only from a JSON template (the OS 2.0 norm) is no longer orphaned.
    */
   private extractShopifyJsonSections(fromNodeId: string): void {
-    let parsed: unknown;
-    try {
-      parsed = JSON.parse(this.source);
-    } catch {
-      return; // not valid JSON (or a partial) — nothing to link
-    }
-    const sections = (parsed as { sections?: Record<string, { type?: unknown }> })?.sections;
-    if (!sections || typeof sections !== 'object') return;
+    // Shopify's editor prepends a comment to generated templates and groups.
+    // Parse with offsets, but reject incomplete input rather than invent links.
+    const errors: ParseError[] = [];
+    const parsed = parseTree(this.source, errors, { allowTrailingComma: false });
+    if (errors.length || parsed?.type !== 'object') return;
+    const sections = findNodeAtLocation(parsed, ['sections']);
+    if (sections?.type !== 'object') return;
     const seen = new Set<string>();
-    for (const key of Object.keys(sections)) {
-      const type = sections[key]?.type;
-      if (typeof type !== 'string' || seen.has(type)) continue;
+    for (const property of sections.children ?? []) {
+      const value = property.children?.[1];
+      if (value?.type !== 'object') continue;
+      const typeNode = findNodeAtLocation(value, ['type']);
+      if (typeNode?.type !== 'string') continue;
+      const type = typeNode.value as string;
+      if (seen.has(type)) continue;
       seen.add(type);
+      const line = this.getLineNumber(typeNode.offset);
       this.unresolvedReferences.push({
         fromNodeId,
         referenceName: `sections/${type}.liquid`,
         referenceKind: 'references',
-        line: 1,
-        column: 0,
+        line,
+        column: typeNode.offset - this.getLineStart(line),
       });
     }
   }
@@ -152,18 +158,13 @@ export class LiquidExtractor {
     const blocks: Array<{ bodyStart: number; body: string }> = [];
     const tags = /\{%[-]?\s*(\w+|#)([\s\S]*?)[-]?%\}/g;
     const braced = new RegExp(`^\\{%[-]?\\s*(${tagPattern})\\s+${argPattern}`);
-    let suppressed: string | undefined;
+    const ranges = this.getSuppressedRanges();
+    let rangeIndex = 0;
     let tag;
     while ((tag = tags.exec(this.source)) !== null) {
       const name = tag[1]!;
-      if (suppressed) {
-        if (name === `end${suppressed}`) suppressed = undefined;
-        continue;
-      }
-      if (name === 'comment' || name === 'raw') {
-        suppressed = name;
-        continue;
-      }
+      while (rangeIndex < ranges.length && tag.index >= ranges[rangeIndex]![1]) rangeIndex++;
+      if (rangeIndex < ranges.length && tag.index >= ranges[rangeIndex]![0]) continue;
       if (name === 'liquid') {
         blocks.push({
           bodyStart: tag.index + tag[0].indexOf(name) + name.length,
@@ -280,12 +281,13 @@ export class LiquidExtractor {
   }
 
   /**
-   * Extract {% section 'name' %} references
+   * Extract {% section 'name' %} and {% sections 'group' %} references
    */
   private extractSectionReferences(fileNodeId: string): void {
     // Both spellings, as for render/include above.
-    for (const match of this.findTagOccurrences('section', `['"]([^'"]+)['"]`)) {
+    for (const match of this.findTagOccurrences('section|sections', `['"]([^'"]+)['"]`)) {
       const fullMatch = match.fullMatch;
+      const tagType = match.groups[0];
       const sectionName = match.groups[1];
       const line = this.getLineNumber(match.index);
 
@@ -315,13 +317,13 @@ export class LiquidExtractor {
       });
 
       // Create a component node for the section reference
-      const nodeId = this.nodeIds.generate(this.filePath, 'component', `section:${sectionName}`, line, match.index - this.getLineStart(line));
+      const nodeId = this.nodeIds.generate(this.filePath, 'component', `${tagType}:${sectionName}`, line, match.index - this.getLineStart(line));
 
       const node: Node = {
         id: nodeId,
         kind: 'component',
         name: sectionName!,
-        qualifiedName: `${this.filePath}::section:${sectionName}`,
+        qualifiedName: `${this.filePath}::${tagType}:${sectionName}`,
         filePath: this.filePath,
         language: 'liquid',
         startLine: line,
@@ -343,7 +345,7 @@ export class LiquidExtractor {
       // Add unresolved reference to the section file
       this.unresolvedReferences.push({
         fromNodeId: fileNodeId,
-        referenceName: `sections/${sectionName}.liquid`,
+        referenceName: `sections/${sectionName}.${tagType === 'sections' ? 'json' : 'liquid'}`,
         referenceKind: 'references',
         line,
         column: match.index - this.getLineStart(line),
@@ -351,15 +353,40 @@ export class LiquidExtractor {
     }
   }
 
+  /** One cached braced comment/raw scanner shared by tags and schemas. */
+  private getSuppressedRanges(): Array<[number, number]> {
+    if (this.suppressedRanges) return this.suppressedRanges;
+    const ranges: [number, number][] = [];
+    const tags = /\{%[-]?\s*(\w+|#)([\s\S]*?)[-]?%\}/g;
+    let suppressed: { name: string; start: number } | undefined;
+    let tag: RegExpExecArray | null;
+    while ((tag = tags.exec(this.source)) !== null) {
+      if (suppressed) {
+        if (tag[1] === `end${suppressed.name}`) {
+          ranges.push([suppressed.start, tags.lastIndex]);
+          suppressed = undefined;
+        }
+      } else if (tag[1] === 'comment' || tag[1] === 'raw') {
+        suppressed = { name: tag[1], start: tag.index };
+      }
+    }
+    if (suppressed) ranges.push([suppressed.start, this.source.length]);
+    this.suppressedRanges = ranges;
+    return ranges;
+  }
+
   /**
    * Extract {% schema %}...{% endschema %} blocks
    */
   private extractSchema(fileNodeId: string): void {
     // Match {% schema %}...{% endschema %}
     const schemaRegex = /\{%[-]?\s*schema\s*[-]?%\}([\s\S]*?)\{%[-]?\s*endschema\s*[-]?%\}/g;
+    const suppressedRanges = this.getSuppressedRanges();
     let match;
 
     while ((match = schemaRegex.exec(this.source)) !== null) {
+      const index = match.index;
+      if (suppressedRanges.some(([start, end]) => index >= start && index < end)) continue;
       const [fullMatch, schemaContent] = match;
       const startLine = this.getLineNumber(match.index);
       const endLine = this.getLineNumber(match.index + fullMatch.length);
diff --git a/src/resolution/shopify-themes.ts b/src/resolution/shopify-themes.ts
index 3c2f3c8b5c..16b72b6320 100644
--- a/src/resolution/shopify-themes.ts
+++ b/src/resolution/shopify-themes.ts
@@ -4,9 +4,10 @@
  * `{% render 'price' %}` renders the `snippets/price.liquid` of the theme the
  * file belongs to; `{% section 'header' %}` and a JSON template's section
  * `"type"` name a file in that theme's `sections/`. Shopify never looks in
- * another theme. The Liquid extractor records these as `snippets/<name>.liquid`
- * and `sections/<name>.liquid`, and the path matcher took any file whose path
- * ends with that, so in a repository holding several themes (a theme tool's
+ * another theme. The Liquid extractor records these as `snippets/<name>.liquid`,
+ * `sections/<name>.liquid` and, for a `{% sections %}` group,
+ * `sections/<group>.json`, and the path matcher took any file whose path ends
+ * with that, so in a repository holding several themes (a theme tool's
  * examples, a store's seasonal themes) a theme missing a section linked to
  * another theme's copy of it.
  *