diff --git a/packages/core/src/okf/index.ts b/packages/core/src/okf/index.ts
index 0216864..f5f9c16 100644
--- a/packages/core/src/okf/index.ts
+++ b/packages/core/src/okf/index.ts
@@ -1,7 +1,7 @@
 export * from "./types.js";
 export { parseDoc, serializeDoc, hasNonEmptyType } from "./frontmatter.js";
 export { Bundle, BundleError, replaceSection } from "./bundle.js";
-export { regenerateIndex, regenerateIndexChain } from "./indexer.js";
+export { regenerateIndex, regenerateIndexChain, pruneEmptyDirs } from "./indexer.js";
 export { appendLog, readLog } from "./logger.js";
 export { searchBundle, listTypes, type SearchOptions } from "./search.js";
 export { validateBundle } from "./validate.js";
diff --git a/packages/core/src/okf/indexer.ts b/packages/core/src/okf/indexer.ts
index 42da85e..91be9a7 100644
--- a/packages/core/src/okf/indexer.ts
+++ b/packages/core/src/okf/indexer.ts
@@ -59,6 +59,16 @@ export async function regenerateIndexChain(bundle: Bundle, dir: string): Promise
   let current = bundle.resolve(dir);
   // If given a file path, start from its directory.
   if (current.endsWith(".md")) current = path.dirname(current);
+  // The directory may have been pruned away — start from the nearest ancestor
+  // that still exists (the root always exists).
+  while (current !== bundle.root) {
+    try {
+      await fs.access(current);
+      break;
+    } catch {
+      current = path.dirname(current);
+    }
+  }
   while (true) {
     await regenerateIndex(bundle, bundle.toBundlePath(current));
     if (current === bundle.root) break;
@@ -66,6 +76,39 @@ export async function regenerateIndexChain(bundle: Bundle, dir: string): Promise
   }
 }
 
+/**
+ * Remove directories whose only content is the auto-generated index.md
+ * (issue #10: agents move/merge concepts and leave undeletable husks —
+ * delete_concept refuses reserved filenames by design, so cleanup must be
+ * deterministic). Bottom-up over the whole bundle; a directory emptied by
+ * pruning its children is pruned too. The root and dot-directories
+ * (.traces etc.) are never touched. Returns removed bundle paths.
+ */
+export async function pruneEmptyDirs(bundle: Bundle): Promise<string[]> {
+  const removed: string[] = [];
+
+  async function visit(absDir: string): Promise<void> {
+    const entries = await fs.readdir(absDir, { withFileTypes: true });
+    for (const entry of entries) {
+      if (entry.isDirectory() && !entry.name.startsWith(".")) {
+        await visit(path.join(absDir, entry.name));
+      }
+    }
+    if (absDir === bundle.root) return;
+    // Re-read: children may have been pruned during the recursion above.
+    const remaining = await fs.readdir(absDir);
+    const onlyIndex =
+      remaining.length === 0 || (remaining.length === 1 && remaining[0] === "index.md");
+    if (onlyIndex) {
+      await fs.rm(absDir, { recursive: true, force: true });
+      removed.push(bundle.toBundlePath(absDir));
+    }
+  }
+
+  await visit(bundle.root);
+  return removed;
+}
+
 function capitalize(s: string): string {
   return s.charAt(0).toUpperCase() + s.slice(1);
 }
diff --git a/packages/core/src/okf/knowledge-base.ts b/packages/core/src/okf/knowledge-base.ts
index 8d161f0..ce923c5 100644
--- a/packages/core/src/okf/knowledge-base.ts
+++ b/packages/core/src/okf/knowledge-base.ts
@@ -1,7 +1,7 @@
 import path from "node:path";
 import { simpleGit, type SimpleGit } from "simple-git";
 import { Bundle } from "./bundle.js";
-import { regenerateIndexChain } from "./indexer.js";
+import { pruneEmptyDirs, regenerateIndexChain } from "./indexer.js";
 import { appendLog, readLog } from "./logger.js";
 import { searchBundle, listTypes, type SearchOptions } from "./search.js";
 import { validateBundle } from "./validate.js";
@@ -120,6 +120,10 @@ export class KnowledgeBase {
     action: LogAction,
     logSummary: string
   ): Promise<void> {
+    // Sweep husks first (dirs holding only their auto-generated index.md) so
+    // the reindex below never resurrects a pruned directory. Whole-bundle:
+    // cheap at this scale, and it also heals husks from before this feature.
+    await pruneEmptyDirs(this.bundle);
     await regenerateIndexChain(this.bundle, path.posix.dirname(conceptPath));
     const linked = `[${conceptPath.split("/").pop()}](${conceptPath})`;
     await appendLog(this.bundle, action, logSummary || `${action} of ${linked}.`);
diff --git a/packages/core/test/okf.test.ts b/packages/core/test/okf.test.ts
index ce1ecc2..670c90d 100644
--- a/packages/core/test/okf.test.ts
+++ b/packages/core/test/okf.test.ts
@@ -270,3 +270,45 @@ describe("mutation serialization", () => {
     expect(concepts.length).toBe(8);
   });
 });
+
+describe("empty directory pruning (#10)", () => {
+  it("prunes a directory left holding only its index.md after the last concept is deleted", async () => {
+    await kb.writeConcept("/family/children/kid.md", { type: "Person", title: "Kid" }, "x", "add");
+    await kb.writeConcept("/family/parent.md", { type: "Person", title: "Parent" }, "x", "add");
+    await kb.deleteConcept("/family/children/kid.md", "moved elsewhere");
+
+    // /family/children held only index.md → gone; /family still has parent.md → kept.
+    await expect(fs.access(path.join(root, "family/children"))).rejects.toThrow();
+    await expect(fs.access(path.join(root, "family/parent.md"))).resolves.toBeUndefined();
+    // Parent index no longer lists the pruned subdirectory.
+    const familyIndex = await fs.readFile(path.join(root, "family/index.md"), "utf-8");
+    expect(familyIndex).not.toContain("children");
+  });
+
+  it("prunes emptied ancestor chains but never the root", async () => {
+    await kb.writeConcept("/a/b/c/deep.md", { type: "T", title: "Deep" }, "x", "add");
+    await kb.writeConcept("/other/keep.md", { type: "T", title: "Keep" }, "x", "add");
+    await kb.deleteConcept("/a/b/c/deep.md", "gone");
+
+    for (const dir of ["a/b/c", "a/b", "a"]) {
+      await expect(fs.access(path.join(root, dir))).rejects.toThrow();
+    }
+    await expect(fs.access(root)).resolves.toBeUndefined();
+    const rootIndex = await fs.readFile(path.join(root, "index.md"), "utf-8");
+    expect(rootIndex).not.toContain("[a](a/)");
+    expect(rootIndex).toContain("other");
+  });
+
+  it("heals pre-existing husks on the next unrelated mutation and spares dot-dirs", async () => {
+    // Simulate an old husk + a .traces dir behind the KB's back.
+    await fs.mkdir(path.join(root, "husk"), { recursive: true });
+    await fs.writeFile(path.join(root, "husk/index.md"), "# Husk\n");
+    await fs.mkdir(path.join(root, ".traces"), { recursive: true });
+    await fs.writeFile(path.join(root, ".traces/t.json"), "{}");
+
+    await kb.writeConcept("/fresh.md", { type: "T", title: "Fresh" }, "x", "add");
+
+    await expect(fs.access(path.join(root, "husk"))).rejects.toThrow();
+    await expect(fs.access(path.join(root, ".traces/t.json"))).resolves.toBeUndefined();
+  });
+});