fix(config): isolate broken JSONC layers and treat comment-only as empty

Address review findings on the #2923 fail-closed parse fix:

- Comment-only files produce ValueExpected with no JSON value; treat that
  as empty config instead of INVALID_JSONC. Partial object trees still throw.
- readConfigLayers no longer lets one unparseable layer abort valid sibling
  layers. Mutations still fail closed on the custom/user write target.

Co-authored-by: serkraser <serkraser@gmail.com>

packages/web/server/lib/opencode/shared.test.js

@@ -3,7 +3,7 @@ import fs from 'fs';
 import os from 'os';
 import path from 'path';
 
-import { parseMdFile, writeMdFile, readConfigFile, writeConfig } from './shared.js';
+import { parseMdFile, writeMdFile, readConfigFile, readConfigLayers, writeConfig } from './shared.js';
 import { updateAgent } from './agents.js';
 import { updateMcpConfig } from './mcp.js';
 
@@ -337,4 +337,40 @@ describe('readConfigFile / writeConfig JSONC safety (issue #2923)', () => {
       else process.env.OPENCODE_CONFIG = previousOpenCodeConfig;
     }
   });
+
+  it('returns an empty object for a comment-only config file', () => {
+    const file = writeFixture('comments.jsonc', '// placeholder\n/* still empty */\n');
+    expect(readConfigFile(file)).toEqual({});
+  });
+
+  it('keeps a valid custom layer readable when a project layer is unparseable', () => {
+    const custom = writeFixture('custom.jsonc', VALID_CONFIG);
+    const projectDir = path.join(FIXTURE_DIR, 'project');
+    const projectFile = writeFixture(path.join('project', '.opencode', 'opencode.jsonc'), PARTIAL_PARSE_CONFIG);
+    const previousOpenCodeConfig = process.env.OPENCODE_CONFIG;
+
+    try {
+      process.env.OPENCODE_CONFIG = custom;
+      const layers = readConfigLayers(projectDir);
+      expect(layers.customConfig.plugin).toEqual(['opencode-see-image']);
+      expect(layers.projectConfig).toEqual({});
+      expect(layers.mergedConfig.plugin).toEqual(['opencode-see-image']);
+      expect(layers.layerErrors).toEqual([
+        expect.objectContaining({
+          path: projectFile,
+          code: 'INVALID_JSONC',
+        }),
+      ]);
+
+      updateMcpConfig('openproject', { enabled: false }, projectDir);
+      const rewritten = JSON.parse(fs.readFileSync(custom, 'utf8'));
+      expect(rewritten.plugin).toEqual(['opencode-see-image']);
+      expect(rewritten.mcp.openproject.enabled).toBe(false);
+      expect(fs.readFileSync(projectFile, 'utf8')).toBe(PARTIAL_PARSE_CONFIG);
+      expect(fs.existsSync(`${projectFile}.openchamber.backup`)).toBe(false);
+    } finally {
+      if (previousOpenCodeConfig === undefined) delete process.env.OPENCODE_CONFIG;
+      else process.env.OPENCODE_CONFIG = previousOpenCodeConfig;
+    }
+  });
 });