diff --git a/tests/codex-config.test.cjs b/tests/codex-config.test.cjs
index f27ce2b89..5be0a224f 100644
--- a/tests/codex-config.test.cjs
+++ b/tests/codex-config.test.cjs
@@ -81,6 +81,23 @@ function writeCodexConfig(codexHome, content) {
   fs.writeFileSync(path.join(codexHome, 'config.toml'), content, 'utf8');
 }
 
+function readHooksSessionStartCommands(codexHome) {
+  const hooksPath = path.join(codexHome, 'hooks.json');
+  if (!fs.existsSync(hooksPath)) return [];
+  const raw = fs.readFileSync(hooksPath, 'utf8').trim();
+  if (!raw) return [];
+  const parsed = JSON.parse(raw);
+  const table = (parsed.hooks && typeof parsed.hooks === 'object' && !Array.isArray(parsed.hooks))
+    ? parsed.hooks
+    : parsed;
+  const sessionStart = Array.isArray(table.SessionStart) ? table.SessionStart : [];
+  return sessionStart.flatMap((entry) =>
+    (Array.isArray(entry?.hooks) ? entry.hooks : [])
+      .map((hook) => hook && hook.command)
+      .filter((cmd) => typeof cmd === 'string')
+  );
+}
+
 function countMatches(content, pattern) {
   return (content.match(pattern) || []).length;
 }
@@ -1409,14 +1426,19 @@ describe('Codex install hook configuration (e2e)', () => {
     fs.rmSync(tmpDir, { recursive: true, force: true });
   });
 
-  test('Codex install copies hook file that is referenced in config.toml (#2153)', () => {
+  test('Codex install copies hook file that is referenced in hooks.json (#2153)', () => {
     // Regression test: Codex install writes gsd-check-update hook reference into
-    // config.toml but must also copy the hook file to ~/$CODEX_HOME/hooks/
+    // hooks.json and must also copy the hook file to ~/$CODEX_HOME/hooks/
     runCodexInstall(codexHome);
 
     const configContent = readCodexConfig(codexHome);
-    // config.toml must reference the hook
-    assert.ok(configContent.includes('gsd-check-update.js'), 'config.toml references gsd-check-update.js');
+    assert.ok(!configContent.includes('gsd-check-update.js'), 'config.toml does not carry managed SessionStart hooks');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    assert.equal(
+      hooksJsonCommands.some((cmd) => cmd.includes('gsd-check-update.js')),
+      true,
+      'hooks.json references gsd-check-update.js'
+    );
     // The hook file must physically exist at the referenced path
     const hookFile = path.join(codexHome, 'hooks', 'gsd-check-update.js');
     assert.ok(
@@ -1430,11 +1452,8 @@ describe('Codex install hook configuration (e2e)', () => {
 
     const content = readCodexConfig(codexHome);
     assert.ok(content.includes('[features]\ncodex_hooks = true\n'), 'writes codex_hooks feature');
-    // Codex 0.124.0+ nested schema: [[hooks.SessionStart]] + [[hooks.SessionStart.hooks]]
     const parsed = parseTomlToObject(content);
-    assert.ok(parsed.hooks && Array.isArray(parsed.hooks.SessionStart), 'writes [[hooks.SessionStart]] AoT');
-    assert.ok(Array.isArray(parsed.hooks.SessionStart[0].hooks), 'writes [[hooks.SessionStart.hooks]] sub-table');
-    assert.strictEqual(parsed.hooks.SessionStart[0].hooks[0].type, 'command', 'handler type is "command"');
+    assert.ok(!parsed.hooks || !Array.isArray(parsed.hooks.SessionStart), 'config.toml does not carry managed SessionStart hooks');
     // #3017: handler command now uses the absolute Node binary path so
     // GUI/minimal-PATH runtimes can resolve it. The shape is
     //   "<absolute-node-path>" "<hook-path>"
@@ -1444,14 +1463,11 @@ describe('Codex install hook configuration (e2e)', () => {
     const expectedRunner = JSON.parse(resolveNodeRunner());
     const expectedHookPath = path.join(codexHome, 'hooks', 'gsd-check-update.js').replace(/\\/g, '/');
     const expectedCommand = `"${expectedRunner}" "${expectedHookPath}"`;
-    assert.strictEqual(
-      parsed.hooks.SessionStart[0].hooks[0].command,
-      expectedCommand,
-      'handler command must use absolute node runner pointing at gsd-check-update.js (#3017)'
-    );
-    assert.ok(!Array.isArray(parsed.hooks), 'no flat [[hooks]] AoT emitted');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdCommands = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdCommands.length, 1, 'writes one GSD update hook in hooks.json');
+    assert.strictEqual(gsdCommands[0], expectedCommand, 'handler command must use absolute node runner pointing at gsd-check-update.js (#3017)');
     assert.strictEqual(countMatches(content, /^codex_hooks = true$/gm), 1, 'writes one codex_hooks key');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'writes one GSD update hook');
     assertNoDraftRootKeys(content);
     assertUsesOnlyEol(content, '\n');
   });
@@ -1533,7 +1549,9 @@ describe('Codex install hook configuration (e2e)', () => {
     assert.ok(content.includes('# user comment'), 'preserves user comment');
     assert.ok(content.includes('[model]\nname = "o3"'), 'preserves model section');
     assert.ok(content.includes('command = "echo custom"'), 'preserves custom hook');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'adds one GSD update hook');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'adds one GSD update hook in hooks.json');
     assertNoDraftRootKeys(content);
   });
 
@@ -1670,7 +1688,9 @@ describe('Codex install hook configuration (e2e)', () => {
     assert.ok(!content.includes('codex_hooks = false'), 'removes false codex_hooks value');
     assert.ok(content.includes('other_feature = true'), 'preserves other feature keys');
     assert.ok(content.includes('command = "echo custom"'), 'preserves custom hook');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'does not duplicate GSD update hook');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'does not duplicate GSD update hook in hooks.json');
     assertNoDraftRootKeys(content);
   });
 
@@ -1712,7 +1732,9 @@ describe('Codex install hook configuration (e2e)', () => {
     assert.strictEqual(countMatches(content, /^"codex_hooks" = true$/gm), 1, 'normalizes the quoted codex_hooks key to true');
     assert.strictEqual(countMatches(content, /^\[features\]\s*$/gm), 0, 'does not prepend a second bare features table');
     assert.ok(content.includes('other_feature = true'), 'preserves existing feature keys');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'keeps one GSD update hook');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'keeps one GSD update hook in hooks.json');
     assertNoDraftRootKeys(content);
   });
 
@@ -1733,7 +1755,9 @@ describe('Codex install hook configuration (e2e)', () => {
     assert.ok(content.includes('[features."a#b"]\nenabled = true'), 'preserves the quoted nested features table');
     assert.strictEqual(countMatches(content, /^\[features\]\s*$/gm), 1, 'adds one real top-level features table');
     assert.strictEqual(countMatches(content, /^codex_hooks = true$/gm), 1, 'adds one codex_hooks key');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'remains idempotent for the GSD hook block');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'remains idempotent for the GSD hook block in hooks.json');
     assertNoDraftRootKeys(content);
   });
 
@@ -1753,7 +1777,9 @@ describe('Codex install hook configuration (e2e)', () => {
     assert.strictEqual(countMatches(content, /^\[features\]\s*$/gm), 0, 'does not add a [features] table');
     assert.strictEqual(countMatches(content, /^features\.codex_hooks = true$/gm), 1, 'adds one dotted codex_hooks key');
     assert.ok(content.includes('features.other_feature = true'), 'preserves existing dotted features key');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'adds one GSD update hook for dotted codex_hooks and remains idempotent');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'adds one GSD update hook for dotted codex_hooks and remains idempotent');
     assertNoDraftRootKeys(content);
   });
 
@@ -1817,7 +1843,9 @@ describe('Codex install hook configuration (e2e)', () => {
     assert.strictEqual(countMatches(content, /^features\."codex_hooks" = true$/gm), 1, 'normalizes the quoted dotted key to true');
     assert.strictEqual(countMatches(content, /^features\.codex_hooks = true$/gm), 0, 'does not append a bare dotted duplicate');
     assert.ok(content.includes('features.other_feature = true'), 'preserves other dotted features keys');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'adds one GSD update hook for quoted dotted codex_hooks and remains idempotent');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'adds one GSD update hook for quoted dotted codex_hooks and remains idempotent');
     assertNoDraftRootKeys(content);
   });
 
@@ -1932,7 +1960,9 @@ describe('Codex install hook configuration (e2e)', () => {
     assert.strictEqual(countMatches(content, /^codex_hooks = true$/gm), 1, 'replaces the multiline basic-string assignment with one true value');
     assert.ok(!content.includes('multiline-basic-sentinel'), 'removes multiline basic-string continuation lines');
     assert.ok(content.includes('other_feature = true'), 'preserves following feature keys');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'remains idempotent for the GSD hook block');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'remains idempotent for the GSD hook block in hooks.json');
     assertNoDraftRootKeys(content);
   });
 
@@ -1957,7 +1987,9 @@ describe('Codex install hook configuration (e2e)', () => {
     assert.strictEqual(countMatches(content, /^codex_hooks = true$/gm), 1, 'replaces the multiline literal-string assignment with one true value');
     assert.ok(!content.includes('multiline-literal-sentinel'), 'removes multiline literal-string continuation lines');
     assert.ok(content.includes('other_feature = true'), 'preserves following feature keys');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'remains idempotent for the GSD hook block');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'remains idempotent for the GSD hook block in hooks.json');
     assertNoDraftRootKeys(content);
   });
 
@@ -1983,7 +2015,9 @@ describe('Codex install hook configuration (e2e)', () => {
     assert.ok(!content.includes('array-sentinel-1'), 'removes multiline array continuation lines');
     assert.ok(!content.includes('array-sentinel-2'), 'removes multiline array continuation lines');
     assert.ok(content.includes('other_feature = true'), 'preserves following feature keys');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'remains idempotent for the GSD hook block');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'remains idempotent for the GSD hook block in hooks.json');
     assertNoDraftRootKeys(content);
   });
 
@@ -2028,7 +2062,9 @@ describe('Codex install hook configuration (e2e)', () => {
     assert.strictEqual(countMatches(content, /^codex_hooks = true$/gm), 1, 'keeps one codex_hooks = true');
     assert.ok(content.includes('other_feature = true'), 'preserves other feature keys');
     assert.strictEqual(countMatches(content, /echo custom-after-command/g), 1, 'preserves non-GSD hook exactly once');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'keeps one GSD update hook');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'keeps one GSD update hook in hooks.json');
     assertUsesOnlyEol(content, '\r\n');
     assertNoDraftRootKeys(content);
   });
@@ -2051,7 +2087,9 @@ describe('Codex install hook configuration (e2e)', () => {
     assert.strictEqual(countMatches(content, /^\[features\]\s*$/gm), 1, 'keeps one [features] section');
     assert.strictEqual(countMatches(content, /^codex_hooks = true # keep me$/gm), 1, 'preserves the commented true value');
     assert.ok(content.includes('other_feature = true'), 'preserves other feature keys');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'adds the GSD update hook once');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'adds the GSD update hook once in hooks.json');
     assertNoDraftRootKeys(content);
   });
 
@@ -2065,13 +2103,14 @@ describe('Codex install hook configuration (e2e)', () => {
     // [features] is inserted after top-level lines, before [model] — not prepended
     assert.ok(content.includes('# first line wins\n\n[features]\ncodex_hooks = true\n'), 'inserts features after top-level lines using first newline style');
     assert.ok(content.includes(`# GSD Agent Configuration — managed by get-shit-done installer\n`), 'writes the managed agent block using the first newline style');
-    // Structural check: nested schema must be present regardless of mixed EOL
+    // Structural check: managed SessionStart hooks live in hooks.json.
     const parsedMixed = parseTomlToObject(content);
-    assert.ok(parsedMixed.hooks && Array.isArray(parsedMixed.hooks.SessionStart), 'writes [[hooks.SessionStart]] AoT with first-newline style');
-    assert.ok(Array.isArray(parsedMixed.hooks.SessionStart[0].hooks), 'writes [[hooks.SessionStart.hooks]] sub-table');
+    assert.ok(!parsedMixed.hooks || !Array.isArray(parsedMixed.hooks.SessionStart), 'does not write managed SessionStart hooks to config.toml');
+    const hooksJsonCommands = readHooksSessionStartCommands(codexHome);
+    const gsdEntries = hooksJsonCommands.filter((cmd) => cmd.includes('gsd-check-update.js'));
+    assert.strictEqual(gsdEntries.length, 1, 'writes one managed SessionStart hook to hooks.json');
     assert.ok(content.includes('[model]\r\nname = "o3"'), 'preserves the existing CRLF model lines');
     assert.strictEqual(countMatches(content, /^codex_hooks = true$/gm), 1, 'remains idempotent on repeated installs');
-    assert.strictEqual(countMatches(content, /gsd-check-update\.js/g), 1, 'does not duplicate the GSD hook block');
     assertNoDraftRootKeys(content);
   });
 });