memory: base scoped commits on HEAD

src/core/memory/mod.rs

@@ -619,6 +619,15 @@ impl MemoryRepo {
         let repo = self.open_git()?;
         let mut index = repo.index().context("opening git index")?;
 
+        // A path-scoped commit starts from HEAD, not a possibly stale index.
+        // Repos created before index persistence otherwise suffer one last eviction.
+        if !repo.is_empty()? {
+            let head_tree = repo.head()?.peel_to_tree()?;
+            index
+                .read_tree(&head_tree)
+                .context("seeding git index from HEAD")?;
+        }
+
         for path in paths {
             let rel_path = self.to_relative(path);
             // Try with .md extension if not present
@@ -1475,6 +1484,45 @@ mod tests {
         assert!(!status.has_uncommitted);
     }
 
+    #[tokio::test]
+    async fn next_write_repairs_a_legacy_stale_index() {
+        let dir = TempDir::new().unwrap();
+        let repo = MemoryRepo::new("test-agent", dir.path());
+        repo.init().await.unwrap();
+        repo.write("journal/first", "first thought").await.unwrap();
+
+        let git = git2::Repository::open(repo.root()).unwrap();
+        let mut stale_index = git.index().unwrap();
+        stale_index.clear().unwrap();
+        stale_index.write().unwrap();
+        drop(stale_index);
+        drop(git);
+
+        repo.write("journal/second", "second thought")
+            .await
+            .unwrap();
+
+        let git = git2::Repository::open(repo.root()).unwrap();
+        let head = git.head().unwrap().peel_to_commit().unwrap();
+        let tree = head.tree().unwrap();
+        let index = git.index().unwrap();
+        for path in [
+            "system/persona.md",
+            "system/state.md",
+            "journal/first.md",
+            "journal/second.md",
+        ] {
+            assert!(
+                tree.get_path(Path::new(path)).is_ok(),
+                "HEAD lost {path}"
+            );
+            assert!(
+                index.get_path(Path::new(path), 0).is_some(),
+                "index lost {path}"
+            );
+        }
+    }
+
     #[tokio::test]
     async fn delete_survives_in_head_and_index() {
         let dir = TempDir::new().unwrap();