diff --git a/cmd/entire/cli/checkpoint/parse_tree.go b/cmd/entire/cli/checkpoint/parse_tree.go
index 6bdec5bde..ae31b7e4d 100644
--- a/cmd/entire/cli/checkpoint/parse_tree.go
+++ b/cmd/entire/cli/checkpoint/parse_tree.go
@@ -282,6 +282,36 @@ func ApplyTreeChanges(
 	return storeTree(repo, result)
 }
 
+// DiffTrees computes the []TreeChange needed to transform a tree with base
+// entries into a tree with target entries. Both maps should be flat
+// (path → TreeEntry) as produced by FlattenTree.
+//
+// - Entries in target but absent/different in base: add/modify
+// - Entries in base but absent in target: delete (nil Entry)
+func DiffTrees(base, target map[string]object.TreeEntry) []TreeChange {
+	changes := make([]TreeChange, 0, len(target))
+
+	// Adds and modifications
+	for path, entry := range target {
+		baseEntry, exists := base[path]
+		if !exists || baseEntry.Hash != entry.Hash {
+			changes = append(changes, TreeChange{
+				Path:  path,
+				Entry: &object.TreeEntry{Name: entry.Name, Mode: entry.Mode, Hash: entry.Hash},
+			})
+		}
+	}
+
+	// Deletions
+	for path := range base {
+		if _, exists := target[path]; !exists {
+			changes = append(changes, TreeChange{Path: path, Entry: nil})
+		}
+	}
+
+	return changes
+}
+
 // splitFirstSegment splits "a/b/c" into ("a", "b/c"), and "file.txt" into ("file.txt", "").
 func splitFirstSegment(path string) (first, rest string) {
 	parts := strings.SplitN(path, "/", 2)
diff --git a/cmd/entire/cli/checkpoint/parse_tree_test.go b/cmd/entire/cli/checkpoint/parse_tree_test.go
index 943962b3e..20b2681dd 100644
--- a/cmd/entire/cli/checkpoint/parse_tree_test.go
+++ b/cmd/entire/cli/checkpoint/parse_tree_test.go
@@ -683,6 +683,189 @@ func TestApplyTreeChanges_MixedOperations(t *testing.T) {
 	}
 }
 
+func TestDiffTrees_BothEmpty(t *testing.T) {
+	t.Parallel()
+	changes := DiffTrees(
+		map[string]object.TreeEntry{},
+		map[string]object.TreeEntry{},
+	)
+	if len(changes) != 0 {
+		t.Errorf("expected 0 changes, got %d", len(changes))
+	}
+}
+
+func TestDiffTrees_Identical(t *testing.T) {
+	t.Parallel()
+	hash := plumbing.NewHash("aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa")
+	entries := map[string]object.TreeEntry{
+		"unchanged.txt": {Name: "unchanged.txt", Mode: filemode.Regular, Hash: hash},
+	}
+	changes := DiffTrees(entries, entries)
+	if len(changes) != 0 {
+		t.Errorf("expected 0 changes for identical trees, got %d", len(changes))
+	}
+}
+
+func TestDiffTrees_AddsOnly(t *testing.T) {
+	t.Parallel()
+	hash := plumbing.NewHash("aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa")
+	base := map[string]object.TreeEntry{}
+	target := map[string]object.TreeEntry{
+		"new.txt": {Name: "new.txt", Mode: filemode.Regular, Hash: hash},
+	}
+	changes := DiffTrees(base, target)
+	if len(changes) != 1 {
+		t.Fatalf("expected 1 change, got %d", len(changes))
+	}
+	if changes[0].Path != "new.txt" || changes[0].Entry == nil {
+		t.Error("expected add for new.txt")
+	}
+}
+
+func TestDiffTrees_DeletesOnly(t *testing.T) {
+	t.Parallel()
+	hash := plumbing.NewHash("aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa")
+	base := map[string]object.TreeEntry{
+		"old.txt": {Name: "old.txt", Mode: filemode.Regular, Hash: hash},
+	}
+	target := map[string]object.TreeEntry{}
+	changes := DiffTrees(base, target)
+	if len(changes) != 1 {
+		t.Fatalf("expected 1 change, got %d", len(changes))
+	}
+	if changes[0].Path != "old.txt" || changes[0].Entry != nil {
+		t.Error("expected delete for old.txt")
+	}
+}
+
+func TestDiffTrees_ModificationsOnly(t *testing.T) {
+	t.Parallel()
+	hashOld := plumbing.NewHash("aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa")
+	hashNew := plumbing.NewHash("bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb")
+	base := map[string]object.TreeEntry{
+		"modified.txt": {Name: "modified.txt", Mode: filemode.Regular, Hash: hashOld},
+	}
+	target := map[string]object.TreeEntry{
+		"modified.txt": {Name: "modified.txt", Mode: filemode.Regular, Hash: hashNew},
+	}
+	changes := DiffTrees(base, target)
+	if len(changes) != 1 {
+		t.Fatalf("expected 1 change, got %d", len(changes))
+	}
+	if changes[0].Path != "modified.txt" || changes[0].Entry == nil {
+		t.Error("expected modify for modified.txt")
+	}
+	if changes[0].Entry.Hash != hashNew {
+		t.Errorf("expected new hash %s, got %s", hashNew, changes[0].Entry.Hash)
+	}
+}
+
+func TestDiffTrees_Mixed(t *testing.T) {
+	t.Parallel()
+	hashA := plumbing.NewHash("aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa")
+	hashB := plumbing.NewHash("bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb")
+	hashC := plumbing.NewHash("cccccccccccccccccccccccccccccccccccccccc")
+	base := map[string]object.TreeEntry{
+		"keep.txt":   {Name: "keep.txt", Mode: filemode.Regular, Hash: hashA},
+		"modify.txt": {Name: "modify.txt", Mode: filemode.Regular, Hash: hashA},
+		"delete.txt": {Name: "delete.txt", Mode: filemode.Regular, Hash: hashA},
+	}
+	target := map[string]object.TreeEntry{
+		"keep.txt":   {Name: "keep.txt", Mode: filemode.Regular, Hash: hashA},
+		"modify.txt": {Name: "modify.txt", Mode: filemode.Regular, Hash: hashB},
+		"add.txt":    {Name: "add.txt", Mode: filemode.Regular, Hash: hashC},
+	}
+	changes := DiffTrees(base, target)
+	// Should have: modify (modify.txt), add (add.txt), delete (delete.txt) = 3 changes
+	if len(changes) != 3 {
+		t.Fatalf("expected 3 changes, got %d", len(changes))
+	}
+
+	changeMap := make(map[string]*TreeChange, len(changes))
+	for i := range changes {
+		changeMap[changes[i].Path] = &changes[i]
+	}
+
+	if c, ok := changeMap["modify.txt"]; !ok || c.Entry == nil || c.Entry.Hash != hashB {
+		t.Error("expected modify for modify.txt with new hash")
+	}
+	if c, ok := changeMap["add.txt"]; !ok || c.Entry == nil || c.Entry.Hash != hashC {
+		t.Error("expected add for add.txt")
+	}
+	if c, ok := changeMap["delete.txt"]; !ok || c.Entry != nil {
+		t.Error("expected delete for delete.txt")
+	}
+	if _, ok := changeMap["keep.txt"]; ok {
+		t.Error("keep.txt should not appear in changes")
+	}
+}
+
+// TestDiffTrees_EquivalenceWithApplyTreeChanges verifies that computing a diff
+// and applying it via ApplyTreeChanges produces the same file content as
+// FlattenTree + BuildTreeFromEntries.
+func TestDiffTrees_EquivalenceWithApplyTreeChanges(t *testing.T) {
+	t.Parallel()
+	repo := mustInitBareRepo(t)
+
+	blobA := storeBlob(t, repo, "content-a")
+	blobB := storeBlob(t, repo, "content-b")
+	blobC := storeBlob(t, repo, "content-c")
+	blobNew := storeBlob(t, repo, "new-content")
+
+	// Build base tree: a3/ckpt1/meta.json, a3/ckpt2/meta.json, b7/ckpt3/meta.json
+	ckpt1 := mustStoreTree(t, repo, []object.TreeEntry{{Name: "meta.json", Mode: filemode.Regular, Hash: blobA}})
+	ckpt2 := mustStoreTree(t, repo, []object.TreeEntry{{Name: "meta.json", Mode: filemode.Regular, Hash: blobB}})
+	ckpt3 := mustStoreTree(t, repo, []object.TreeEntry{{Name: "meta.json", Mode: filemode.Regular, Hash: blobC}})
+	shardA3 := mustStoreTree(t, repo, []object.TreeEntry{
+		{Name: "ckpt1", Mode: filemode.Dir, Hash: ckpt1},
+		{Name: "ckpt2", Mode: filemode.Dir, Hash: ckpt2},
+	})
+	shardB7 := mustStoreTree(t, repo, []object.TreeEntry{
+		{Name: "ckpt3", Mode: filemode.Dir, Hash: ckpt3},
+	})
+	baseTree := mustStoreTree(t, repo, []object.TreeEntry{
+		{Name: "a3", Mode: filemode.Dir, Hash: shardA3},
+		{Name: "b7", Mode: filemode.Dir, Hash: shardB7},
+	})
+
+	// Target: modify a3/ckpt1, add a3/ckpt4, keep a3/ckpt2, keep b7/ckpt3
+	// (no full-directory deletions — ApplyTreeChanges leaves empty dirs on delete)
+	ckpt1mod := mustStoreTree(t, repo, []object.TreeEntry{{Name: "meta.json", Mode: filemode.Regular, Hash: blobNew}})
+	ckpt4 := mustStoreTree(t, repo, []object.TreeEntry{{Name: "meta.json", Mode: filemode.Regular, Hash: blobNew}})
+	shardA3Target := mustStoreTree(t, repo, []object.TreeEntry{
+		{Name: "ckpt1", Mode: filemode.Dir, Hash: ckpt1mod},
+		{Name: "ckpt2", Mode: filemode.Dir, Hash: ckpt2},
+		{Name: "ckpt4", Mode: filemode.Dir, Hash: ckpt4},
+	})
+	targetTree := mustStoreTree(t, repo, []object.TreeEntry{
+		{Name: "a3", Mode: filemode.Dir, Hash: shardA3Target},
+		{Name: "b7", Mode: filemode.Dir, Hash: shardB7},
+	})
+
+	// Approach 1: Flatten both, DiffTrees, ApplyTreeChanges
+	baseEntries := make(map[string]object.TreeEntry)
+	if err := FlattenTree(repo, mustTreeObject(t, repo, baseTree), "", baseEntries); err != nil {
+		t.Fatalf("FlattenTree base: %v", err)
+	}
+	targetEntries := make(map[string]object.TreeEntry)
+	if err := FlattenTree(repo, mustTreeObject(t, repo, targetTree), "", targetEntries); err != nil {
+		t.Fatalf("FlattenTree target: %v", err)
+	}
+	changes := DiffTrees(baseEntries, targetEntries)
+	surgeryResult, err := ApplyTreeChanges(repo, baseTree, changes)
+	if err != nil {
+		t.Fatalf("ApplyTreeChanges() error = %v", err)
+	}
+
+	// Both should produce the same tree hash (no full-directory deletions involved)
+	if surgeryResult != targetTree {
+		surgeryFiles := flattenTreeHelper(t, repo, surgeryResult, "")
+		targetFiles := flattenTreeHelper(t, repo, targetTree, "")
+		t.Errorf("DiffTrees+ApplyTreeChanges (%s) != target tree (%s)\nsurgery: %v\ntarget:  %v",
+			surgeryResult, targetTree, surgeryFiles, targetFiles)
+	}
+}
+
 // TestUpdateSubtree_EquivalenceWithFlattenRebuild verifies that UpdateSubtree
 // produces the same result as the old FlattenTree + modify + BuildTreeFromEntries approach.
 func TestUpdateSubtree_EquivalenceWithFlattenRebuild(t *testing.T) {
diff --git a/cmd/entire/cli/strategy/cleanup.go b/cmd/entire/cli/strategy/cleanup.go
index 713981f6e..0299cc256 100644
--- a/cmd/entire/cli/strategy/cleanup.go
+++ b/cmd/entire/cli/strategy/cleanup.go
@@ -266,36 +266,37 @@ func DeleteOrphanedCheckpoints(ctx context.Context, checkpointIDs []string) (del
 		return nil, nil, fmt.Errorf("failed to get tree: %w", err)
 	}
 
-	// Flatten tree to entries
+	// Flatten tree to discover file paths, then build deletion changes
 	entries := make(map[string]object.TreeEntry)
 	if err := checkpoint.FlattenTree(repo, baseTree, "", entries); err != nil {
 		return nil, nil, fmt.Errorf("failed to flatten tree: %w", err)
 	}
 
-	// Remove entries for each checkpoint
-	checkpointSet := make(map[string]bool)
-	for _, id := range checkpointIDs {
-		checkpointSet[id] = true
+	// Build set of checkpoint paths to delete
+	checkpointPaths := make(map[string]bool)
+	for _, idStr := range checkpointIDs {
+		cpID, parseErr := id.NewCheckpointID(idStr)
+		if parseErr != nil {
+			continue // Skip invalid checkpoint IDs
+		}
+		checkpointPaths[cpID.Path()+"/"] = true
 	}
 
-	// Find and remove entries matching checkpoint paths
+	// Collect deletion changes for matching entries
+	var changes []checkpoint.TreeChange
 	for path := range entries {
-		for checkpointIDStr := range checkpointSet {
-			cpID, err := id.NewCheckpointID(checkpointIDStr)
-			if err != nil {
-				continue // Skip invalid checkpoint IDs
-			}
-			cpPath := cpID.Path()
-			if strings.HasPrefix(path, cpPath+"/") {
-				delete(entries, path)
+		for cpPrefix := range checkpointPaths {
+			if strings.HasPrefix(path, cpPrefix) {
+				changes = append(changes, checkpoint.TreeChange{Path: path, Entry: nil})
+				break
 			}
 		}
 	}
 
-	// Build new tree
-	newTreeHash, err := checkpoint.BuildTreeFromEntries(repo, entries)
+	// Apply deletions surgically
+	newTreeHash, err := checkpoint.ApplyTreeChanges(repo, parentCommit.TreeHash, changes)
 	if err != nil {
-		return nil, nil, fmt.Errorf("failed to build tree: %w", err)
+		return nil, nil, fmt.Errorf("failed to apply tree changes: %w", err)
 	}
 
 	// Create commit
diff --git a/cmd/entire/cli/strategy/push_common.go b/cmd/entire/cli/strategy/push_common.go
index 90337d2c3..aa4957428 100644
--- a/cmd/entire/cli/strategy/push_common.go
+++ b/cmd/entire/cli/strategy/push_common.go
@@ -168,20 +168,24 @@ func fetchAndMergeSessionsCommon(ctx context.Context, remote, branchName string)
 		return fmt.Errorf("failed to get remote tree: %w", err)
 	}
 
-	// Flatten both trees and combine entries
-	// Session logs have unique cond-* directories, so no conflicts expected
-	entries := make(map[string]object.TreeEntry)
-	if err := checkpoint.FlattenTree(repo, localTree, "", entries); err != nil {
+	// Compute what the remote has that differs from local, then apply surgically.
+	// Session logs have unique cond-* directories, so no conflicts expected.
+	localEntries := make(map[string]object.TreeEntry)
+	if err := checkpoint.FlattenTree(repo, localTree, "", localEntries); err != nil {
 		return fmt.Errorf("failed to flatten local tree: %w", err)
 	}
-	if err := checkpoint.FlattenTree(repo, remoteTree, "", entries); err != nil {
+	remoteEntries := make(map[string]object.TreeEntry)
+	if err := checkpoint.FlattenTree(repo, remoteTree, "", remoteEntries); err != nil {
 		return fmt.Errorf("failed to flatten remote tree: %w", err)
 	}
 
-	// Build merged tree
-	mergedTreeHash, err := checkpoint.BuildTreeFromEntries(repo, entries)
+	// DiffTrees computes changes to transform local into remote (remote wins on collision)
+	changes := checkpoint.DiffTrees(localEntries, remoteEntries)
+
+	// Apply changes surgically to the local tree
+	mergedTreeHash, err := checkpoint.ApplyTreeChanges(repo, localCommit.TreeHash, changes)
 	if err != nil {
-		return fmt.Errorf("failed to build merged tree: %w", err)
+		return fmt.Errorf("failed to apply tree changes: %w", err)
 	}
 
 	// Create merge commit with both parents