diff --git a/.changeset/sturdy-badgers-bark.md b/.changeset/sturdy-badgers-bark.md
new file mode 100644
index 000000000..f794b56db
--- /dev/null
+++ b/.changeset/sturdy-badgers-bark.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 4847
+---
+**OpenCode installs no longer flag all 72 GSD skills as custom files** — the installer's file manifest now records the skills it stages for OpenCode, matching every other skills-layout runtime, so clean installs report zero custom files. The first update after upgrading may show the custom-files backup prompt once while the manifest catches up; from then on updates run without it. (#4738)
diff --git a/capabilities/opencode/capability.json b/capabilities/opencode/capability.json
index c4502e428..b38b01bc2 100644
--- a/capabilities/opencode/capability.json
+++ b/capabilities/opencode/capability.json
@@ -129,8 +129,7 @@
       },
       "skipHomePrefixSubstitution": true,
       "skipSettingsUi": true,
-      "skipUpdateBannerCommand": true,
-      "skipCodexSkillsManifest": true
+      "skipUpdateBannerCommand": true
     }
   },
   "reviewer": {
diff --git a/gsd-core/bin/lib/capability-registry.cjs b/gsd-core/bin/lib/capability-registry.cjs
index af443b529..4ea16da94 100644
--- a/gsd-core/bin/lib/capability-registry.cjs
+++ b/gsd-core/bin/lib/capability-registry.cjs
@@ -2988,8 +2988,7 @@ const capabilities = {
         },
         "skipHomePrefixSubstitution": true,
         "skipSettingsUi": true,
-        "skipUpdateBannerCommand": true,
-        "skipCodexSkillsManifest": true
+        "skipUpdateBannerCommand": true
       }
     },
     "reviewer": {
@@ -7213,8 +7212,7 @@ const runtimes = {
         },
         "skipHomePrefixSubstitution": true,
         "skipSettingsUi": true,
-        "skipUpdateBannerCommand": true,
-        "skipCodexSkillsManifest": true
+        "skipUpdateBannerCommand": true
       }
     },
     "reviewer": {
diff --git a/gsd-core/bin/lib/capability-validator.cjs b/gsd-core/bin/lib/capability-validator.cjs
index cbc8fc617..e46a68b93 100644
--- a/gsd-core/bin/lib/capability-validator.cjs
+++ b/gsd-core/bin/lib/capability-validator.cjs
@@ -1947,7 +1947,6 @@ const KNOWN_HOST_BEHAVIORS = new Set([
   'skillPriorityFrontmatter',
   'skillsGlobalOnboarding',
   'skillsManifestPrefix',
-  'skipCodexSkillsManifest',
   'skipHomePrefixSubstitution',
   'skipSettingsUi',
   'skipSharedHooksInstall',
diff --git a/tests/opencode-imperative-reference.test.cjs b/tests/opencode-imperative-reference.test.cjs
index 2894aff35..e724b73b1 100644
--- a/tests/opencode-imperative-reference.test.cjs
+++ b/tests/opencode-imperative-reference.test.cjs
@@ -14,7 +14,7 @@
  * `runtime.hostBehaviors` + the combined-family engine install path).
  */
 
-const { test } = require('node:test');
+const { test, describe, beforeEach, afterEach } = require('node:test');
 const assert = require('node:assert/strict');
 const fs = require('node:fs');
 const path = require('node:path');
@@ -123,7 +123,11 @@ test('opencode descriptor declares runtime.hostBehaviors (the folded-in behavior
   assert.equal(hb.skipHomePrefixSubstitution, true);
   assert.equal(hb.skipSettingsUi, true);
   assert.equal(hb.skipUpdateBannerCommand, true);
-  assert.equal(hb.skipCodexSkillsManifest, true);
+  // #4738: the skills-manifest exclusion is retired — opencode stages 72
+  // converted skills and its manifest must record them (the flag was carried
+  // verbatim from a pre-skills-layout era and flagged every staged skill as
+  // user-added on every update).
+  assert.equal(hb.skipCodexSkillsManifest, undefined);
   assert.equal(hb.nativePlugin.file, 'gsd-core.js');
   assert.equal(hb.nativePlugin.source, '.opencode/plugins/gsd-core.js');
 });
@@ -139,3 +143,73 @@ test('no `runtime === "opencode"` string-equality branch remains in the install
     assert.deepEqual(offenders, [], `AC2: no hardcoded runtime==='opencode' branch may remain in ${rel}; found: ${offenders.join(', ')}`);
   }
 });
+
+// ─── #4738: the opencode manifest must record the skills it stages ───────────
+
+const { cleanup, runGsdTools, createTempDir } = require('./helpers.cjs');
+const { writeManifest } = require(path.join(__dirname, '..', 'bin', 'install.js'));
+const { runMinimalInstall } = require('./helpers/install-shared.cjs');
+
+describe('#4738: writeManifest records staged skills for opencode', () => {
+  let tmpDir;
+
+  beforeEach(() => {
+    tmpDir = createTempDir('gsd-4738-manifest-');
+  });
+
+  afterEach(() => {
+    cleanup(tmpDir);
+  });
+
+  test('manifest includes skills/gsd-xxx/SKILL.md entries for opencode (mirrors the kilo sibling)', () => {
+    // Stage the structure an opencode install creates: converted skills under
+    // skills/gsd-*/SKILL.md (convertClaudeCommandToOpencodeSkill) plus the
+    // gsd-core directory writeManifest always records.
+    const skillDir = path.join(tmpDir, 'skills', 'gsd-next');
+    fs.mkdirSync(skillDir, { recursive: true });
+    fs.writeFileSync(path.join(skillDir, 'SKILL.md'), 'skill content');
+    const gsdDir = path.join(tmpDir, 'gsd-core');
+    fs.mkdirSync(gsdDir, { recursive: true });
+    fs.writeFileSync(path.join(gsdDir, 'test.md'), 'test');
+
+    writeManifest(tmpDir, 'opencode');
+
+    const manifest = JSON.parse(
+      fs.readFileSync(path.join(tmpDir, 'gsd-file-manifest.json'), 'utf8'),
+    );
+    const skillEntries = Object.keys(manifest.files).filter((k) => k.startsWith('skills/'));
+    assert.ok(skillEntries.length > 0, 'manifest has skills/ entries for opencode');
+    assert.ok(
+      skillEntries.includes('skills/gsd-next/SKILL.md'),
+      'manifest records the staged skills/gsd-next/SKILL.md',
+    );
+  });
+});
+
+describe('#4738: a clean opencode install is invisible to detect-custom-files', () => {
+  test('real --opencode --global install: manifest records staged skills and the detector reports zero custom files', (t) => {
+    const { manifest, configDir, root } = runMinimalInstall({ runtime: 'opencode', scope: 'global' });
+    t.after(() => cleanup(root));
+
+    const skillEntries = Object.keys(manifest.files).filter((k) => k.startsWith('skills/'));
+    assert.ok(
+      skillEntries.length > 0,
+      `the manifest must record the staged skills (got ${skillEntries.length} skills/ keys)`,
+    );
+    // The on-disk side is unchanged by the fix: every manifested skill exists.
+    for (const rel of skillEntries) {
+      assert.ok(fs.existsSync(path.join(configDir, rel)), `staged file exists: ${rel}`);
+    }
+
+    const result = runGsdTools(['detect-custom-files', '--config-dir', configDir], root);
+    assert.ok(result.success, `detector failed: ${result.error}`);
+    const json = JSON.parse(result.output);
+    assert.ok(Array.isArray(json.custom_files), 'the detector must emit a custom_files array');
+    assert.deepEqual(
+      json.custom_files.filter((f) => f.startsWith('skills/')),
+      [],
+      `no installer-staged skill may be flagged as user-added: ${JSON.stringify(json.custom_files)}`,
+    );
+    assert.equal(json.custom_count, 0, `a clean opencode install reports zero custom files: ${JSON.stringify(json.custom_files)}`);
+  });
+});