diff --git a/src/scripts/link.rs b/src/scripts/link.rs
index dad1596..90c780f 100644
--- a/src/scripts/link.rs
+++ b/src/scripts/link.rs
@@ -99,7 +99,7 @@ fn restore_one(repo: &Repo, path: &Path, report: &Report) -> Result<()> {
 
     fs::remove_file(&src).with_context(|| format!("removing {}", src.display()))?;
     move_path(&stored, &src)?;
-    prune_empty(stored.parent(), &store_root()?);
+    prune_empty(stored.parent(), &repo.base);
 
     report.line("restored", &rel);
     Ok(())
@@ -425,22 +425,24 @@ fn list_others(repo: &Repo, ignored: bool, pathspecs: &[PathBuf]) -> Result<Vec<
 struct Repo {
     root: PathBuf,
     store: PathBuf,
+    // the configured store root, above the per-repository directories
+    base: PathBuf,
 }
 
 impl Repo {
     fn discover(store: Option<&Path>) -> Result<Self> {
         let root = git_root()?;
-        let store = match store {
+        let base = match store {
             Some(store) => store.to_path_buf(),
             None => store_root()?,
         };
 
         Ok(Self {
-            root: root.clone(),
-            store: store.join(repo_components(&root)?),
+            store: base.join(repo_components(&root)?),
+            root,
+            base,
         })
     }
-
     fn relative(&self, src: &Path) -> Result<PathBuf> {
         let rel = src.strip_prefix(&self.root).map_err(|_| {
             anyhow!(