From 53c75afbffff7efef22198eff12abbcce8d4cafc Mon Sep 17 00:00:00 2001
From: Jordan Ritter <jpr5@darkridge.com>
Date: Thu, 7 May 2026 22:08:56 -0700
Subject: [PATCH] Fix walkRoot early return to clean up stale chunks when
 source directory is missing

---
 src/__tests__/file-provider.test.ts | 23 +++++++++++++++++++++++
 src/indexing/providers/file.ts      | 17 ++++++++++++++++-
 2 files changed, 39 insertions(+), 1 deletion(-)

diff --git a/src/__tests__/file-provider.test.ts b/src/__tests__/file-provider.test.ts
index b451949..1b03136 100644
--- a/src/__tests__/file-provider.test.ts
+++ b/src/__tests__/file-provider.test.ts
@@ -297,6 +297,29 @@ describe("FileDataProvider", () => {
       // Should still return the current files
       expect(result.items.length).toBe(3);
     });
+
+    it("removes all indexed files when walkRoot does not exist", async () => {
+      mockGetIndexedItemIds.mockResolvedValueOnce(
+        new Set(["old-file.md", "another.md"]),
+      );
+      const config = {
+        ...makeGitConfig(),
+        path: "/nonexistent/path/that/does/not/exist",
+      };
+      const cloneDir = path.join(tmpDir, "clones");
+      const repoDir = path.join(cloneDir, "repo");
+      await fs.promises.mkdir(path.join(repoDir, ".git"), { recursive: true });
+
+      const warnSpy = vi.spyOn(console, "warn").mockImplementation(() => {});
+      const provider = new FileDataProvider(config, { cloneDir });
+      const result = await provider.fullAcquire();
+
+      expect(result.items).toEqual([]);
+      expect(result.removedIds).toContain("old-file.md");
+      expect(result.removedIds).toContain("another.md");
+      expect(result.removedIds).toHaveLength(2);
+      warnSpy.mockRestore();
+    });
   });
 
   // -----------------------------------------------------------------------
diff --git a/src/indexing/providers/file.ts b/src/indexing/providers/file.ts
index f24e87a..c3fe70a 100644
--- a/src/indexing/providers/file.ts
+++ b/src/indexing/providers/file.ts
@@ -90,7 +90,22 @@ export class FileDataProvider implements DataProvider {
       console.warn(
         `${this.logPrefix} Walk root not found at ${walkRoot}, skipping`,
       );
-      return { items: [], removedIds: [], stateToken };
+      let removedIds: string[] = [];
+      try {
+        const indexedPaths = await getIndexedItemIds(this.config.name);
+        removedIds = [...indexedPaths];
+        if (removedIds.length > 0) {
+          console.log(
+            `${this.logPrefix} Walk root missing: ${removedIds.length} stale files to remove from index`,
+          );
+        }
+      } catch (err) {
+        console.warn(
+          `${this.logPrefix} Failed to check for stale files:`,
+          err instanceof Error ? err.message : err,
+        );
+      }
+      return { items: [], removedIds, stateToken };
     }
 
     const allFiles = await this.walkFiles(walkRoot);