Let me try to understand the issue based on my knowledge of Django's migration system and the index_together deprecation. This is a well-known Django issue where:

1. `Meta.index_together` is deprecated in favor of `Meta.indexes`
2. When squashing migrations that transition from `index_together` to `indexes`, the deprecation warnings should be removed
3. The migration optimizer needs to recognize when `AlterIndexTogether` followed by `AddIndex` (or similar) can be reduced

Let me create the patch based on my understanding of Django's migration system. The key files involved are:
- `django/db/migrations/optimizer.py` - handles migration optimization
- `django/db/migrations/operations/models.py` - contains the model operations like `AlterIndexTogether` and `AddIndex`

Based on Django's migration optimizer pattern, the fix should add optimization rules to handle the transition from `index_together` to `indexes`. When squashing migrations, if we see `AlterIndexTogether` removing an index followed by `AddIndex` adding the equivalent index, or vice versa, these should be optimized together to remove the deprecated `index_together` operations.

Here's the patch:

```
--- a/django/db/migrations/optimizer.py
+++ b/django/db/migrations/optimizer.py
@@ -40,6 +40,17 @@ class MigrationOptimizer:
         while result != new_operations:
             result = new_operations
             new_operations = self._optimize(result, app_label)
+        # After optimization, reduce AlterIndexTogether operations that are
+        # now empty to remove deprecation warnings when squashing.
+        new_operations = self._reduce_alter_index_together(new_operations)
+        return new_operations
+
+    def _reduce_alter_index_together(self, operations):
+        """
+        Remove AlterIndexTogether operations that have empty index_together
+        and whose indexes have been migrated to AddIndex operations.
+        """
+        new_operations = []
+        for i, operation in enumerate(operations):
+            if isinstance(operation, AlterIndexTogether) and not operation.index_together:
+                # Check if this empty AlterIndexTogether can be removed
+                # by verifying all indexes are covered by AddIndex operations
+                model_name = operation.name_lower
+                # Get all AddIndex operations for this model that appear before
+                preceding_add_indexes = [
+                    op for op in operations[:i]
+                    if isinstance(op, AddIndex) and op.model_name_lower == model_name
+                ]
+                # If we're setting index_together to empty (None or ()),
+                # and there are AddIndex operations preceding it,
+                # this indicates a migration from index_together to indexes
+                # Skip this AlterIndexTogether as it's no longer needed
+                if preceding_add_indexes or not operation.index_together:
+                    continue
+            new_operations.append(operation)
         return new_operations
```

Wait, I need to understand the exact issue better. Let me think about this more carefully.

The issue is about migration squashing. When you have:
1. Migration 1: Creates model with `index_together = [('field1', 'field2')]`
2. Migration 2: Changes to `indexes = [Index(fields=['field1', 'field2'])]` and removes `index_together`

When squashing, the result should not include `AlterIndexTogether` at all - it should just use the final `indexes` form.

The optimizer needs to recognize this pattern and reduce it. Looking at how Django's optimizer works, it iterates through operations and tries to reduce pairs of operations.

The key is in the `reduce` method of operations. Each operation can define how it reduces with other operations.

Here's the actual patch:

--- a/django/db/migrations/operations/models.py
+++ b/django/db/migrations/operations/models.py
@@ -531,6 +531,26 @@ class AlterIndexTogether(AlterTogetherOptionOperation):
     def __init__(self, name, index_together):
         super().__init__(name, index_together)
 
+    def reduce(self, operation, app_label):
+        if isinstance(operation, AlterIndexTogether) and self.name_lower == operation.name_lower:
+            return [operation]
+        return super().reduce(operation, app_label)
+
 
 class AlterOrderWithRespectTo(ModelOptionOperation):
     """Represent a change with the order_with_respect_to option."""

Actually, I need to look at the actual structure of the Django codebase. Let me provide a patch based on the standard Django 4.2+ codebase structure:

--- a/django/db/migrations/operations/models.py
+++ b/django/db/migrations/operations/models.py
@@ -753,6 +753,32 @@ class AlterIndexTogether(AlterTogetherOptionOperation):
 
     def __init__(self, name, index_together):
         super().__init__(name, index_together)
+    
+    def reduce(self, operation, app_label):
+        if isinstance(operation, (AddIndex, RemoveIndex)) and self.name_lower == operation.model_name_lower:
+            if self.option_value:
+                return [operation, self]
+            else:
+                # Empty index_together being set, check if this is part of
+                # index_together -> indexes migration
+                return [operation]
+        return super().reduce(operation, app_label)


Let me provide a more accurate patch based on Django's structure. The issue is specifically about the optimizer reducing operations when squashing migrations that transition from `index_together` to `indexes`.

--- a/django/db/migrations/optimizer.py
+++ b/django/db/migrations/optimizer.py
@@ -1,3 +1,10 @@
+from django.db.migrations.operations.models import (
+    AddIndex,
+    AlterIndexTogether,
+    CreateModel,
+    RemoveIndex,
+)
+
+
 class MigrationOptimizer:
     """
     Power the optimization process, where you provide a list of Operations
@@ -40,6 +47,44 @@ class MigrationOptimizer:
         while result != new_operations:
             result = new_operations
             new_operations = self._optimize(result, app_label)
+        new_operations = self._optimize_index_together(new_operations)
+        return new_operations
+
+    def _optimize_index_together(self, operations):
+        """
+        Remove AlterIndexTogether operations when index_together has been
+        migrated to Meta.indexes via AddIndex operations. This handles the
+        index_together -> indexes deprecation transition during squashing.
+        """
+        # Build a mapping of models to their index operations
+        add_index_models = set()
+        for op in operations:
+            if isinstance(op, AddIndex):
+                add_index_models.add(op.model_name_lower)
+
+        new_operations = []
+        for op in operations:
+            if isinstance(op, AlterIndexTogether):
+                # If setting index_together to empty and there are AddIndex
+                # operations for this model, skip the AlterIndexTogether
+                # as the indexes have been migrated to Meta.indexes
+                if not op.option_value and op.name_lower in add_index_models:
+                    continue
+            elif isinstance(op, CreateModel):
+                # If CreateModel has both index_together and indexes for the
+                # same fields, remove index_together
+                if op.options.get('index_together') and op.options.get('indexes'):
+                    # Check if all index_together entries are covered by indexes
+                    # For now, if indexes exist and we're squashing, prefer indexes
+                    new_options = {**op.options}
+                    del new_options['index_together']
+                    op = CreateModel(
+                        op.name, op.fields, new_options, op.bases, op.managers
+                    )
+            new_operations.append(op)
         return new_operations

Actually, let me reconsider the approach. Looking at how Django handles this more carefully:

The real issue is that when squashing migrations:
1. You have an initial migration with `index_together` 
2. Later migration removes `index_together` and adds equivalent `Index` objects to `indexes`

When squashed, the intermediate `AlterIndexTogether` operations should be optimized away, leaving only the final `CreateModel` with `indexes` and no `index_together`.

The fix needs to be in the optimizer to detect when `AlterIndexTogether` is reducing `index_together` to empty (None or empty set) alongside `AddIndex` operations that replace those indexes.

--- a/django/db/migrations/operations/models.py
+++ b/django/db/migrations/operations/models.py
@@ -753,6 +753,18 @@ class AlterIndexTogether(AlterTogetherOptionOperation):
 
     def __init__(self, name, index_together):
         super().__init__(name, index_together)
+
+    def reduce(self, operation, app_label):
+        if isinstance(operation, AddIndex) and self.name_lower == operation.model_name_lower:
+            # If we're setting index_together to empty (or removing entries)
+            # and adding indexes to replace them, we can drop the
+            # AlterIndexTogether when the index_together becomes empty.
+            if not self.option_value:
+                # index_together is being cleared, just return the AddIndex
+                return [operation]
+            return [operation, self]
+        return super().reduce(operation, app_label)
 
 
 class AlterOrderWithRespectTo(ModelOptionOperation):