diff --git a/src/filetree.rs b/src/filetree.rs
index 1fff67ae..c74d6409 100644
--- a/src/filetree.rs
+++ b/src/filetree.rs
@@ -280,12 +280,63 @@ pub(crate) fn syncfs(d: &openat::Dir) -> Result<()> {
     rustix::fs::syncfs(d).map_err(Into::into)
 }
 
+fn copy_dir(src: &Path, dst: &Path) -> Result<()> {
+    let r = std::process::Command::new("cp")
+        .args(["-a"])
+        .arg(src)
+        .arg(dst)
+        .status()?;
+    if !r.success() {
+        anyhow::bail!("Failed to copy");
+    }
+    Ok(())
+}
+
+/// Convert path parent to temp, `fedora/foo` -> `fedora.tmp/foo`
 #[cfg(any(target_arch = "x86_64", target_arch = "aarch64"))]
-fn tmpname_for_path<P: AsRef<Path>>(path: P) -> std::path::PathBuf {
+fn tmp_for_path<P: AsRef<Path>>(path: P) -> std::path::PathBuf {
     let path = path.as_ref();
-    let mut buf = path.file_name().expect("filename").to_os_string();
-    buf.push(TMP_PREFIX);
-    path.with_file_name(buf)
+    let mut parent = String::from("");
+    if let Some(p) = path.parent() {
+        parent = format!("{}.tmp", p.display());
+    }
+    let buf = path.file_name().expect("filename").to_os_string();
+    Path::new(parent.as_str()).join(buf)
+}
+
+/// Get diff based on sub dir
+#[cfg(any(target_arch = "x86_64", target_arch = "aarch64"))]
+pub(crate) fn diff_with_prefix(diff: &FileTreeDiff, prefix: &str) -> Result<FileTreeDiff> {
+    let mut new_diff = FileTreeDiff {
+        additions: HashSet::new(),
+        removals: HashSet::new(),
+        changes: HashSet::new(),
+    };
+    for pathstr in diff.additions.iter() {
+        let path = Path::new(pathstr);
+        if let Some(parent) = path.parent() {
+            if parent.to_string_lossy().eq(prefix) {
+                new_diff.additions.insert(pathstr.to_string());
+            }
+        }
+    }
+    for pathstr in diff.changes.iter() {
+        let path = Path::new(pathstr);
+        if let Some(parent) = path.parent() {
+            if parent.to_string_lossy().eq(prefix) {
+                new_diff.changes.insert(pathstr.to_string());
+            }
+        }
+    }
+    for pathstr in diff.removals.iter() {
+        let path = Path::new(pathstr);
+        if let Some(parent) = path.parent() {
+            if parent.to_string_lossy().eq(prefix) {
+                new_diff.removals.insert(pathstr.to_string());
+            }
+        }
+    }
+    Ok(new_diff)
 }
 
 /// Given two directories, apply a diff generated from srcdir to destdir
@@ -302,40 +353,82 @@ pub(crate) fn apply_diff(
     let opts = opts.unwrap_or(&default_opts);
     cleanup_tmp(destdir).context("cleaning up temporary files")?;
 
-    // Write new and changed files
-    for pathstr in diff.additions.iter().chain(diff.changes.iter()) {
+    // Get updates based on dir
+    let mut updates = std::collections::HashSet::new();
+    for pathstr in diff
+        .additions
+        .iter()
+        .chain(diff.changes.iter())
+        .chain(diff.removals.iter())
+    {
         let path = Path::new(pathstr);
         if let Some(parent) = path.parent() {
-            destdir.ensure_dir_all(parent, DEFAULT_FILE_MODE)?;
+            updates.insert(parent.to_string_lossy().into_owned());
         }
-        let destp = tmpname_for_path(path);
-        srcdir
-            .copy_file_at(path, destdir, destp.as_path())
-            .with_context(|| format!("writing {}", &pathstr))?;
     }
-    // Ensure all of the new files are written persistently to disk
-    if !opts.skip_sync {
-        syncfs(destdir)?;
-    }
-    // Now move them all into place (TODO track interruption)
-    for path in diff.additions.iter().chain(diff.changes.iter()) {
-        let pathtmp = tmpname_for_path(path);
+    let efipath = destdir.recover_path()?;
+    for path in &updates {
+        let new_diff = diff_with_prefix(diff, path)?;
+        if !opts.skip_removals {
+            for path in new_diff.removals.iter() {
+                destdir
+                    .remove_file_optional(path)
+                    .with_context(|| format!("removing {path}"))?;
+            }
+        }
+        // Ensure all of the new files are written persistently to disk
+        if !opts.skip_sync {
+            syncfs(destdir)?;
+        }
+        // skip if there are no changes or additions
+        if new_diff.additions.len() == 0 && new_diff.changes.len() == 0 {
+            continue;
+        }
+        let src_path = efipath.join(&path);
+        let tmp_path = efipath.join(format!("{}.tmp", path));
+        if tmp_path.exists() {
+            std::fs::remove_dir_all(&tmp_path)?;
+        }
+        if let Some(parent) = tmp_path.parent() {
+            destdir.ensure_dir_all(parent, DEFAULT_FILE_MODE)?;
+        }
+        // in case there is additional with subdir
+        destdir.ensure_dir_all(&src_path, DEFAULT_FILE_MODE)?;
+        // copy original dir to tmp
+        copy_dir(&src_path, &tmp_path)
+            .with_context(|| format!("copying {:?} to {:?}", src_path, tmp_path))?;
+        assert!(destdir.exists(&tmp_path)?);
+
+        // Write new and changed files
+        for pathstr in new_diff.additions.iter().chain(new_diff.changes.iter()) {
+            let path = Path::new(pathstr);
+            let pathtmp = tmp_for_path(path);
+            if let Some(parent) = pathtmp.parent() {
+                destdir.ensure_dir_all(parent, DEFAULT_FILE_MODE)?;
+            }
+            destdir.remove_file_optional(&pathtmp)?;
+            srcdir
+                .copy_file_at(path, destdir, &pathtmp)
+                .with_context(|| format!("writing {:?} to {:?}", path, pathtmp))?;
+        }
+        // do local exchange
+        log::trace!(
+            "doing local exchange for {} and {}",
+            tmp_path.display(),
+            src_path.display()
+        );
         destdir
-            .local_rename(&pathtmp, path)
-            .with_context(|| format!("renaming {path}"))?;
-    }
-    if !opts.skip_removals {
-        for path in diff.removals.iter() {
-            destdir
-                .remove_file_optional(path)
-                .with_context(|| format!("removing {path}"))?;
+            .local_exchange(&tmp_path, &src_path)
+            .with_context(|| format!("exchange for {:?} and {:?}", tmp_path, src_path))?;
+        // finally remove the temp dir
+        log::trace!("cleanup: {}", tmp_path.display());
+        std::fs::remove_dir_all(&tmp_path).context("clean up temp")?;
+        // A second full filesystem sync to narrow any races rather than
+        // waiting for writeback to kick in.
+        if !opts.skip_sync {
+            syncfs(destdir)?;
         }
     }
-    // A second full filesystem sync to narrow any races rather than
-    // waiting for writeback to kick in.
-    if !opts.skip_sync {
-        syncfs(destdir)?;
-    }
 
     Ok(())
 }