diff --git a/src/adapters.ts b/src/adapters.ts
index 52c3a7c..17d1acf 100644
--- a/src/adapters.ts
+++ b/src/adapters.ts
@@ -4,6 +4,7 @@ import {
   validateFromDefinition,
   withRootFiles,
 } from "./targets/engine.js";
+import { normalizeManagedPath, readManagedManifest } from "./managed.js";
 import { targets as registry } from "./targets/registry.js";
 import type {
   Artifact,
@@ -47,7 +48,11 @@ export async function validateOutput(
 ): Promise<ValidationResult> {
   const root = path.resolve(dir);
   const issues: ValidationIssue[] = [];
-  await validateFromDefinition(root, issues, registry[target]);
+  const managed = await readManagedManifest(root, target);
+  const managedPaths = (managed?.files ?? []).map((file) =>
+    path.resolve(root, normalizeManagedPath(file)),
+  );
+  await validateFromDefinition(root, issues, registry[target], managedPaths);
   return {
     ok: issues.every((issue) => issue.level !== "error"),
     issues,
diff --git a/src/targets/antigravity.ts b/src/targets/antigravity.ts
index d64e379..d8399e6 100644
--- a/src/targets/antigravity.ts
+++ b/src/targets/antigravity.ts
@@ -95,7 +95,7 @@ export const antigravity: PluginTargetDefinition = {
         issues,
         "Antigravity output must contain at least one plugin directory.",
       );
-      return;
+      return pluginDirs;
     }
     for (const pluginDir of pluginDirs) {
       const manifest = await readJson(
@@ -121,6 +121,7 @@ export const antigravity: PluginTargetDefinition = {
       await validateFrontmatter(pluginDir, pluginName, "antigravity", issues);
       await validateHooksShape(pluginDir, pluginName, "hooks.json", issues);
     }
+    return pluginDirs;
   },
 
   installSnippet: {
diff --git a/src/targets/claude.ts b/src/targets/claude.ts
index 39dd207..4dde86b 100644
--- a/src/targets/claude.ts
+++ b/src/targets/claude.ts
@@ -104,13 +104,14 @@ export const claude: PluginTargetDefinition = {
       ".claude-plugin",
       "marketplace.json",
     );
+    const ownedPaths = [marketplacePath];
     const marketplace = await readJson(
       marketplacePath,
       "Marketplace manifest",
       issues,
     );
     if (!marketplace) {
-      return;
+      return ownedPaths;
     }
     validateMarketplaceBasics(marketplace, issues);
     const plugins = Array.isArray(marketplace.plugins)
@@ -118,7 +119,7 @@ export const claude: PluginTargetDefinition = {
       : [];
     if (plugins.length === 0) {
       error(issues, 'Marketplace "plugins" must be a non-empty array.');
-      return;
+      return ownedPaths;
     }
     for (const [index, entry] of plugins.entries()) {
       const pluginName = claude.validateMarketplaceEntry(
@@ -131,6 +132,7 @@ export const claude: PluginTargetDefinition = {
         continue;
       }
       const pluginDir = path.join(root, entry.source);
+      ownedPaths.push(pluginDir);
       const manifest = await readJson(
         path.join(pluginDir, ".claude-plugin", "plugin.json"),
         `${pluginName} plugin manifest`,
@@ -154,6 +156,7 @@ export const claude: PluginTargetDefinition = {
         issues,
       );
     }
+    return ownedPaths;
   },
 
   installSnippet: {
diff --git a/src/targets/codex.ts b/src/targets/codex.ts
index 2ad055a..db46b72 100644
--- a/src/targets/codex.ts
+++ b/src/targets/codex.ts
@@ -203,13 +203,14 @@ export const codex: PluginTargetDefinition = {
       "plugins",
       "marketplace.json",
     );
+    const ownedPaths = [marketplacePath];
     const marketplace = await readJson(
       marketplacePath,
       "Marketplace manifest",
       issues,
     );
     if (!marketplace) {
-      return;
+      return ownedPaths;
     }
     validateMarketplaceBasics(marketplace, issues);
     const plugins = Array.isArray(marketplace.plugins)
@@ -217,7 +218,7 @@ export const codex: PluginTargetDefinition = {
       : [];
     if (plugins.length === 0) {
       error(issues, 'Marketplace "plugins" must be a non-empty array.');
-      return;
+      return ownedPaths;
     }
     for (const [index, entry] of plugins.entries()) {
       const pluginName = codex.validateMarketplaceEntry(
@@ -233,6 +234,7 @@ export const codex: PluginTargetDefinition = {
       if (!pluginDir) {
         continue;
       }
+      ownedPaths.push(pluginDir);
       const manifest = await readJson(
         path.join(pluginDir, ".codex-plugin", "plugin.json"),
         `${pluginName} plugin manifest`,
@@ -263,6 +265,7 @@ export const codex: PluginTargetDefinition = {
       );
       await validateFrontmatter(pluginDir, pluginName, "codex", issues);
     }
+    return ownedPaths;
   },
 
   installSnippet: {
diff --git a/src/targets/copilot.ts b/src/targets/copilot.ts
index b91bf1a..4ef9804 100644
--- a/src/targets/copilot.ts
+++ b/src/targets/copilot.ts
@@ -143,18 +143,23 @@ export const copilot: PluginTargetDefinition = {
       ".claude-plugin",
       "marketplace.json",
     );
+    const mirroredMarketplacePath = path.join(
+      root,
+      ".github",
+      "plugin",
+      "marketplace.json",
+    );
+    const ownedPaths = [marketplacePath, mirroredMarketplacePath];
     const marketplace = await readJson(
       marketplacePath,
       "Marketplace manifest",
       issues,
     );
     if (!marketplace) {
-      return;
+      return ownedPaths;
     }
     validateMarketplaceBasics(marketplace, issues);
-    if (
-      !(await exists(path.join(root, ".github", "plugin", "marketplace.json")))
-    ) {
+    if (!(await exists(mirroredMarketplacePath))) {
       error(
         issues,
         "Copilot output must mirror the marketplace at .github/plugin/marketplace.json.",
@@ -165,7 +170,7 @@ export const copilot: PluginTargetDefinition = {
       : [];
     if (plugins.length === 0) {
       error(issues, 'Marketplace "plugins" must be a non-empty array.');
-      return;
+      return ownedPaths;
     }
     for (const [index, entry] of plugins.entries()) {
       const pluginName = copilot.validateMarketplaceEntry(
@@ -178,6 +183,7 @@ export const copilot: PluginTargetDefinition = {
         continue;
       }
       const pluginDir = path.join(root, entry.source);
+      ownedPaths.push(pluginDir);
       // .github/plugin/ is the authoritative copy; the root copy is only
       // checked for presence, not re-parsed.
       const manifest = await readJson(
@@ -204,6 +210,7 @@ export const copilot: PluginTargetDefinition = {
       await validateAgentFileNames(pluginDir, pluginName, issues);
       await validateFrontmatter(pluginDir, pluginName, "copilot", issues);
     }
+    return ownedPaths;
   },
 
   installSnippet: {
diff --git a/src/targets/cursor.ts b/src/targets/cursor.ts
index 2364058..bf860da 100644
--- a/src/targets/cursor.ts
+++ b/src/targets/cursor.ts
@@ -170,13 +170,14 @@ export const cursor: PluginTargetDefinition = {
       ".cursor-plugin",
       "marketplace.json",
     );
+    const ownedPaths = [marketplacePath];
     const marketplace = await readJson(
       marketplacePath,
       "Marketplace manifest",
       issues,
     );
     if (!marketplace) {
-      return;
+      return ownedPaths;
     }
     validateMarketplaceBasics(marketplace, issues);
     const plugins = Array.isArray(marketplace.plugins)
@@ -184,7 +185,7 @@ export const cursor: PluginTargetDefinition = {
       : [];
     if (plugins.length === 0) {
       error(issues, 'Marketplace "plugins" must be a non-empty array.');
-      return;
+      return ownedPaths;
     }
     for (const [index, entry] of plugins.entries()) {
       const pluginName = cursor.validateMarketplaceEntry(
@@ -197,6 +198,7 @@ export const cursor: PluginTargetDefinition = {
         continue;
       }
       const pluginDir = path.join(root, entry.source);
+      ownedPaths.push(pluginDir);
       const manifest = await readJson(
         path.join(pluginDir, ".cursor-plugin", "plugin.json"),
         `${pluginName} plugin manifest`,
@@ -227,6 +229,7 @@ export const cursor: PluginTargetDefinition = {
       );
       await validateFrontmatter(pluginDir, pluginName, "cursor", issues);
     }
+    return ownedPaths;
   },
 
   installSnippet: {
diff --git a/src/targets/engine.ts b/src/targets/engine.ts
index 729b8a1..68e0271 100644
--- a/src/targets/engine.ts
+++ b/src/targets/engine.ts
@@ -250,9 +250,14 @@ export async function validateFromDefinition(
   root: string,
   issues: ValidationIssue[],
   definition: PluginTargetDefinition,
+  managedPaths: string[] = [],
 ): Promise<void> {
-  await definition.validateOutput(root, issues);
-  await validateNoSurvivingPartialTags(root, issues);
+  const ownedPaths = await definition.validateOutput(root, issues);
+  await validateNoSurvivingPartialTags(
+    root,
+    [...ownedPaths, ...managedPaths],
+    issues,
+  );
 }
 
 function emittedPluginMetadata(
diff --git a/src/targets/types.ts b/src/targets/types.ts
index 2a08152..0593c53 100644
--- a/src/targets/types.ts
+++ b/src/targets/types.ts
@@ -130,7 +130,15 @@ export type PluginTargetDefinition = {
     root: string,
     issues: ValidationIssue[],
   ) => string | null;
-  validateOutput: (root: string, issues: ValidationIssue[]) => Promise<void>;
+  /**
+   * Validates native output and returns the files/directories owned by the
+   * target. Shared validation uses these paths instead of scanning unrelated
+   * authored and dependency files that may share the repository root.
+   */
+  validateOutput: (
+    root: string,
+    issues: ValidationIssue[],
+  ) => Promise<string[]>;
 
   installSnippet: InstallSnippetDefinition;
 
diff --git a/src/targets/validation-shared.ts b/src/targets/validation-shared.ts
index abb6518..ab0b928 100644
--- a/src/targets/validation-shared.ts
+++ b/src/targets/validation-shared.ts
@@ -83,9 +83,26 @@ export function warning(issues: ValidationIssue[], message: string): void {
  */
 export async function validateNoSurvivingPartialTags(
   root: string,
+  ownedPaths: string[],
   issues: ValidationIssue[],
 ): Promise<void> {
-  for (const file of await walkFiles(root)) {
+  const files = (
+    await Promise.all(
+      ownedPaths.map(async (ownedPath) => {
+        try {
+          return (await fs.stat(ownedPath)).isDirectory()
+            ? await walkFiles(ownedPath)
+            : [ownedPath];
+        } catch (error) {
+          if (isNotFoundError(error)) {
+            return [];
+          }
+          throw error;
+        }
+      }),
+    )
+  ).flat();
+  for (const file of [...new Set(files)]) {
     const relative = toPosix(path.relative(root, file));
     const tag = findPartialTag(await fs.readFile(file));
     if (!tag) {
diff --git a/tests/core.test.ts b/tests/core.test.ts
index 76ada4e..c137066 100644
--- a/tests/core.test.ts
+++ b/tests/core.test.ts
@@ -1841,6 +1841,10 @@ export default defineConfig({
     await access(
       path.join(root, "plugins/claude/acme/.claude-plugin/plugin.json"),
     );
+    await access(path.join(root, ".agents/plugins/marketplace.json"));
+    await access(
+      path.join(root, "plugins/codex/acme/.codex-plugin/plugin.json"),
+    );
     await access(
       path.join(root, "plugins/copilot/.claude-plugin/marketplace.json"),
     );
@@ -1851,6 +1855,26 @@ export default defineConfig({
     await expect(validateOutput("claude", root)).resolves.toMatchObject({
       ok: true,
     });
+    await expect(validateOutput("codex", root)).resolves.toMatchObject({
+      ok: true,
+    });
+  });
+
+  it("validates surviving partials in managed repository-root files", async () => {
+    const project = await recommendedShapeFixture();
+    const root = project.baseDir;
+    await build({ cwd: root });
+    await writeFile(path.join(root, "config.yaml"), "auth: {{> auth}}\n");
+
+    const result = await validateOutput("cursor", root);
+
+    expect(result.ok).toBe(false);
+    expect(result.issues).toContainEqual({
+      level: "error",
+      message: expect.stringContaining(
+        "config.yaml contains an unsubstituted partial reference {{> auth}}",
+      ),
+    });
   });
 
   it("does not register generated output dirs as source plugins on rebuild", async () => {
@@ -1862,7 +1886,7 @@ export default defineConfig({
     // Loading config again must not treat them as source plugins.
     const loaded = await loadConfig(root);
 
-    expect([...loaded.plugins.keys()]).toEqual(["core"]);
+    expect([...loaded.plugins.keys()]).toEqual([]);
   });
 
   it("merges multiple source plugins and rejects colliding files", async () => {
@@ -3851,35 +3875,64 @@ async function recommendedShapeFixture(): Promise<Project> {
 export default defineConfig({
   name: "acme-plugins",
   version: "1.0.0",
-  source: {
-    skills: "skills",
-    rootPlugin: { id: "core", description: "Acme skills." }
-  },
+  source: { partials: "partials" },
   metadata: { description: "Acme", author: { name: "Acme" }, license: "MIT" },
   targets: {
     cursor: {
       outDir: ".",
+      repositoryFiles: "repositories/cursor",
       plugins: {
-        acme: { from: ["core"], path: "plugins/cursor/acme", components: ["skills"] }
+        acme: { source: "shared/acme", path: "plugins/cursor/acme" }
       }
     },
     claude: {
       outDir: ".",
       pluginRoot: "plugins/claude",
-      plugins: { acme: { from: ["core"] } }
+      plugins: { acme: { source: "shared/acme" } }
+    },
+    codex: {
+      outDir: ".",
+      plugins: {
+        acme: {
+          source: "shared/acme",
+          path: "plugins/codex/acme",
+          entry: {
+            policy: { installation: "AVAILABLE", authentication: "NOT_REQUIRED" },
+            category: "Developer Tools"
+          }
+        }
+      }
     },
     copilot: {
       outDir: "plugins/copilot",
-      plugins: { acme: { from: ["core"] } }
+      plugins: { acme: { source: "shared/acme" } }
     }
   }
 });
 `,
-    skills: {
-      "release-notes": {
-        "SKILL.md": skill("release-notes", "Release notes skill."),
+    partials: {
+      "auth.md": "Authenticate first.",
+    },
+    shared: {
+      acme: {
+        skills: {
+          "release-notes": {
+            "SKILL.md": `${skill("release-notes", "Release notes skill.")}\n{{> auth}}\n`,
+          },
+        },
       },
     },
+    // These are authored/dependency files in the repository, not generated
+    // target output. Validation must not interpret their template syntax.
+    ".github": {
+      workflows: { "ci.yml": "# Example partial: {{> partial}}\n" },
+    },
+    node_modules: {
+      dependency: { "index.js": 'const example = "{{> dependency}}";\n' },
+    },
+    repositories: {
+      cursor: { "config.yaml": "auth: configured\n" },
+    },
   });
 }