diff --git a/.changeset/humble-pandas-purr.md b/.changeset/humble-pandas-purr.md
new file mode 100644
index 000000000..59f0baa02
--- /dev/null
+++ b/.changeset/humble-pandas-purr.md
@@ -0,0 +1,5 @@
+---
+type: Fixed
+pr: 1079
+---
+`validate agents` (and `validate health`) now cross-reference the install manifest to detect manifest-backed Codex agent pair drift: when a generated `agents/gsd-*.md` / `agents/gsd-*.toml` pair has one side missing on disk, the agent is reported as incomplete and `agents_found` is `false` (previously a false-healthy `agents_found: true, missing: []`). `validate health` names the incomplete agents and recommends re-running the installer. The check no-ops when no manifest is present. (#1058)
diff --git a/src/core.cts b/src/core.cts
index 1e9f23288..952d29889 100644
--- a/src/core.cts
+++ b/src/core.cts
@@ -211,6 +211,7 @@ interface AgentsInstalledResult {
   agents_installed: boolean;
   missing_agents: string[];
   installed_agents: string[];
+  incomplete_agents: string[];
   agents_dir: string;
   agent_runtime: string;
 }
@@ -232,6 +233,7 @@ function checkAgentsInstalled(runtime?: string): AgentsInstalledResult {
       agents_installed: false,
       missing_agents: expectedAgents,
       installed_agents: [],
+      incomplete_agents: [],
       agents_dir: agentsDir,
       agent_runtime: resolvedRuntime,
     };
@@ -259,10 +261,61 @@ function checkAgentsInstalled(runtime?: string): AgentsInstalledResult {
     }
   }
 
+  // ── Manifest-backed completeness check ──────────────────────────────────────
+  // If a gsd-file-manifest.json exists alongside the agents dir (parent dir),
+  // verify that every manifest-tracked file for each expected agent is present
+  // on disk. Missing manifest-tracked files indicate an incomplete install even
+  // when the plain presence check above passed (e.g. .md present, .toml absent).
+  // If no manifest is found the check is a no-op (graceful for claude/bundled).
+  const incomplete: string[] = [];
+  const manifestPath = path.join(path.dirname(agentsDir), 'gsd-file-manifest.json');
+  let manifestFiles: Record<string, unknown> = {};
+  try {
+    const raw = fs.readFileSync(manifestPath, 'utf8');
+    const parsed: unknown = JSON.parse(raw);
+    if (
+      parsed !== null &&
+      typeof parsed === 'object' &&
+      'files' in parsed &&
+      typeof (parsed as Record<string, unknown>)['files'] === 'object' &&
+      (parsed as Record<string, unknown>)['files'] !== null
+    ) {
+      manifestFiles = (parsed as Record<string, Record<string, unknown>>)['files'];
+    }
+  } catch {
+    // No manifest or unreadable — completeness check is skipped
+  }
+
+  if (Object.keys(manifestFiles).length > 0) {
+    for (const agent of expectedAgents) {
+      // Find all manifest keys that belong to this agent:
+      // key must be "agents/<agentName>.<ext>" with no further path segments.
+      const agentPrefix = `agents/${agent}.`;
+      const agentManifestKeys = Object.keys(manifestFiles).filter(key => {
+        if (!key.startsWith(agentPrefix)) return false;
+        const rest = key.slice(agentPrefix.length);
+        // rest must be a bare extension (no slashes, non-empty)
+        return rest.length > 0 && !rest.includes('/');
+      });
+      if (agentManifestKeys.length === 0) {
+        // Agent not tracked in manifest — skip completeness check for this agent
+        continue;
+      }
+      const allPresent = agentManifestKeys.every(key => {
+        const basename = key.slice('agents/'.length);
+        return fs.existsSync(path.join(agentsDir, basename));
+      });
+      if (!allPresent) {
+        incomplete.push(agent);
+      }
+    }
+  }
+
   return {
-    agents_installed: installed.length > 0 && missing.length === 0,
+    agents_installed: installed.length > 0 && missing.length === 0 && incomplete.length === 0,
     missing_agents: missing,
     installed_agents: installed,
+    incomplete_agents: incomplete,
     agents_dir: agentsDir,
     agent_runtime: resolvedRuntime,
   };
diff --git a/src/verify.cts b/src/verify.cts
index 94587dfed..3346ff2bb 100644
--- a/src/verify.cts
+++ b/src/verify.cts
@@ -1107,6 +1107,20 @@ function cmdValidateHealth(
           `No GSD agents found in ${agentStatus.agents_dir} — Task(subagent_type="gsd-*") will fall back to general-purpose`,
           `Run the GSD installer: npx ${PACKAGE_NAME}@latest`,
         );
+      } else if ((agentStatus.incomplete_agents).length > 0 && (agentStatus.missing_agents).length === 0) {
+        addIssue(
+          'warning',
+          'W010',
+          `Incomplete agent installs (missing generated file): ${(agentStatus.incomplete_agents).join(', ')} — affected workflows may fall back to general-purpose`,
+          `Re-run the GSD installer to complete the install: npx ${PACKAGE_NAME}@latest`,
+        );
+      } else if ((agentStatus.incomplete_agents).length > 0) {
+        addIssue(
+          'warning',
+          'W010',
+          `Missing ${(agentStatus.missing_agents).length} GSD agents: ${(agentStatus.missing_agents).join(', ')}; incomplete agent installs (missing generated file): ${(agentStatus.incomplete_agents).join(', ')} — affected workflows will fall back to general-purpose`,
+          `Run the GSD installer: npx ${PACKAGE_NAME}@latest`,
+        );
       } else {
         addIssue(
           'warning',
@@ -1624,6 +1638,7 @@ function cmdValidateAgents(cwd: string, raw: boolean): void {
       agents_found: agentStatus.agents_installed,
       installed: agentStatus.installed_agents,
       missing: agentStatus.missing_agents,
+      incomplete: agentStatus.incomplete_agents,
       expected,
     },
     raw,
diff --git a/tests/agent-install-validation.test.cjs b/tests/agent-install-validation.test.cjs
index 4dd8bce6f..27b71b9f0 100644
--- a/tests/agent-install-validation.test.cjs
+++ b/tests/agent-install-validation.test.cjs
@@ -384,3 +384,209 @@ describe('validate agents subcommand (#1371)', () => {
     assert.ok(output.expected.length > 0, 'Must have expected agents');
   });
 });
+
+// ─── Bug #1058: validate agents detects manifest-backed .md/.toml pair drift ──
+
+describe('bug #1058: validate agents detects manifest-backed .md/.toml pair drift', () => {
+  // All real agents/gsd-*.md files in the repo (used to populate fixtures)
+  const REPO_AGENTS_DIR_1058 = path.resolve(__dirname, '..', 'agents');
+
+  /**
+   * Copy all gsd-*.md files from the repo agents dir into destDir.
+   */
+  function copyAgentMdFiles(destDir) {
+    const files = fs.readdirSync(REPO_AGENTS_DIR_1058).filter(f => /^gsd-.*\.md$/.test(f));
+    for (const file of files) {
+      const src = path.join(REPO_AGENTS_DIR_1058, file);
+      const dst = path.join(destDir, file);
+      fs.copyFileSync(src, dst);
+    }
+  }
+
+  /**
+   * Build a gsd-file-manifest.json whose files map includes both .md and .toml
+   * entries for every EXPECTED_AGENTS entry.
+   */
+  function buildManifestBothPairs(agents) {
+    const files = {};
+    for (const name of agents) {
+      files[`agents/${name}.md`] = 'deadbeef';
+      files[`agents/${name}.toml`] = 'deadbeef';
+    }
+    return { version: '1.0.0', files };
+  }
+
+  let tmpDir;
+
+  afterEach(() => {
+    if (tmpDir) {
+      cleanup(tmpDir);
+      tmpDir = null;
+    }
+  });
+
+  test('agents_found=false and incomplete non-empty when .toml files are absent but manifest expects them', () => {
+    // Arrange: all .md files present, manifest says both .md and .toml are expected,
+    // but NO .toml files are created on disk.
+    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-bug-1058-missing-toml-'));
+    const agentsDir = path.join(tmpDir, 'agents');
+    fs.mkdirSync(agentsDir, { recursive: true });
+
+    // Copy real .md files
+    copyAgentMdFiles(agentsDir);
+
+    // Write manifest with both .md and .toml entries but no .toml files on disk
+    fs.writeFileSync(
+      path.join(tmpDir, 'gsd-file-manifest.json'),
+      JSON.stringify(buildManifestBothPairs(EXPECTED_AGENTS), null, 2),
+    );
+
+    // Act
+    const result = runGsdTools('validate agents --raw', tmpDir, {
+      GSD_RUNTIME: 'codex',
+      GSD_AGENTS_DIR: agentsDir,
+    });
+    assert.ok(result.success, `Command failed: ${result.error}`);
+    const output = JSON.parse(result.output);
+
+    // Assert: the completeness check must catch the missing .toml files
+    assert.strictEqual(
+      output.agents_found,
+      false,
+      `Expected agents_found=false when manifest-tracked .toml files are absent, got agents_found=${output.agents_found}`,
+    );
+    assert.ok(
+      Array.isArray(output.incomplete),
+      'Expected output.incomplete to be an array',
+    );
+    // Every agent whose .toml is absent must appear in incomplete (sorted deep-equal)
+    assert.deepStrictEqual(
+      [...output.incomplete].sort(),
+      [...EXPECTED_AGENTS].sort(),
+      `Expected incomplete to equal full EXPECTED_AGENTS set; got ${JSON.stringify(output.incomplete)}`,
+    );
+    // missing (entirely-absent .md) must be empty — these agents are not missing, only incomplete
+    assert.deepStrictEqual(
+      output.missing,
+      [],
+      `Expected missing=[] when all .md files are present; got ${JSON.stringify(output.missing)}`,
+    );
+  });
+
+  test('agents_found=false and incomplete non-empty when .md files are absent but manifest expects them', () => {
+    // Arrange: only .toml files present on disk, manifest says both .md and .toml are expected,
+    // but NO .md files exist. This is the opposite-side pair-drift case.
+    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-bug-1058-missing-md-'));
+    const agentsDir = path.join(tmpDir, 'agents');
+    fs.mkdirSync(agentsDir, { recursive: true });
+
+    // Create ONLY .toml files — deliberately skip .md files
+    for (const name of EXPECTED_AGENTS) {
+      fs.writeFileSync(path.join(agentsDir, `${name}.toml`), `name = "${name}"
+`);
+    }
+
+    // Write manifest with both .md and .toml entries
+    fs.writeFileSync(
+      path.join(tmpDir, 'gsd-file-manifest.json'),
+      JSON.stringify(buildManifestBothPairs(EXPECTED_AGENTS), null, 2),
+    );
+
+    // Act
+    const result = runGsdTools('validate agents --raw', tmpDir, {
+      GSD_RUNTIME: 'codex',
+      GSD_AGENTS_DIR: agentsDir,
+    });
+    assert.ok(result.success, `Command failed: ${result.error}`);
+    const output = JSON.parse(result.output);
+
+    // Assert: missing .md files must surface as incomplete (pair-drift detected symmetrically)
+    assert.strictEqual(
+      output.agents_found,
+      false,
+      `Expected agents_found=false when manifest-tracked .md files are absent, got agents_found=${output.agents_found}`,
+    );
+    assert.ok(
+      Array.isArray(output.incomplete),
+      'Expected output.incomplete to be an array',
+    );
+    assert.ok(
+      output.incomplete.length > 0,
+      `Expected incomplete to be non-empty when .md files are absent; got ${JSON.stringify(output.incomplete)}`,
+    );
+  });
+
+  test('agents_found=true and incomplete=[] when both .md and .toml files are present', () => {
+    // Arrange: all .md AND .toml present, manifest says both expected
+    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-bug-1058-complete-pair-'));
+    const agentsDir = path.join(tmpDir, 'agents');
+    fs.mkdirSync(agentsDir, { recursive: true });
+
+    // Copy real .md files
+    copyAgentMdFiles(agentsDir);
+
+    // Create .toml files for each expected agent
+    for (const name of EXPECTED_AGENTS) {
+      fs.writeFileSync(path.join(agentsDir, `${name}.toml`), `name = "${name}"\n`);
+    }
+
+    // Write manifest with both .md and .toml entries
+    fs.writeFileSync(
+      path.join(tmpDir, 'gsd-file-manifest.json'),
+      JSON.stringify(buildManifestBothPairs(EXPECTED_AGENTS), null, 2),
+    );
+
+    // Act
+    const result = runGsdTools('validate agents --raw', tmpDir, {
+      GSD_RUNTIME: 'codex',
+      GSD_AGENTS_DIR: agentsDir,
+    });
+    assert.ok(result.success, `Command failed: ${result.error}`);
+    const output = JSON.parse(result.output);
+
+    // Assert: complete pair => no false positive
+    assert.strictEqual(
+      output.agents_found,
+      true,
+      `Expected agents_found=true when both .md and .toml files are present; got ${output.agents_found}`,
+    );
+    assert.deepStrictEqual(
+      output.incomplete,
+      [],
+      `Expected incomplete=[] when all manifest-tracked files are present; got ${JSON.stringify(output.incomplete)}`,
+    );
+  });
+
+  test('no spurious incomplete flags when no manifest is present (protects claude/bundled installs)', () => {
+    // Arrange: all .md files present, NO manifest file at all
+    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'gsd-bug-1058-no-manifest-'));
+    const agentsDir = path.join(tmpDir, 'agents');
+    fs.mkdirSync(agentsDir, { recursive: true });
+
+    // Copy real .md files
+    copyAgentMdFiles(agentsDir);
+
+    // Explicitly do NOT write gsd-file-manifest.json
+
+    // Act
+    const result = runGsdTools('validate agents --raw', tmpDir, {
+      GSD_RUNTIME: 'codex',
+      GSD_AGENTS_DIR: agentsDir,
+    });
+    assert.ok(result.success, `Command failed: ${result.error}`);
+    const output = JSON.parse(result.output);
+
+    // Assert: without a manifest, completeness check must no-op (incomplete empty)
+    assert.deepStrictEqual(
+      output.incomplete,
+      [],
+      `Expected incomplete=[] when no manifest present; got ${JSON.stringify(output.incomplete)}`,
+    );
+    // agents_found should reflect plain file presence (all .md files copied => true)
+    assert.strictEqual(
+      output.agents_found,
+      true,
+      `Expected agents_found=true when all .md files are present and no manifest; got ${output.agents_found}`,
+    );
+  });
+});