diff --git a/src/codegen/sdk/codebase/codebase_context.py b/src/codegen/sdk/codebase/codebase_context.py
index abe519558..6214c4227 100644
--- a/src/codegen/sdk/codebase/codebase_context.py
+++ b/src/codegen/sdk/codebase/codebase_context.py
@@ -2,7 +2,6 @@
 
 import os
 from collections import Counter, defaultdict
-from concurrent.futures import ThreadPoolExecutor
 from contextlib import contextmanager
 from enum import IntEnum, auto, unique
 from functools import lru_cache
@@ -16,6 +15,7 @@
 from codegen.sdk.codebase.config_parser import ConfigParser, get_config_parser_for_language
 from codegen.sdk.codebase.diff_lite import ChangeType, DiffLite
 from codegen.sdk.codebase.flagging.flags import Flags
+from codegen.sdk.codebase.io.file_io import FileIO
 from codegen.sdk.codebase.transaction_manager import TransactionManager
 from codegen.sdk.codebase.validation import get_edges, post_reset_validation
 from codegen.sdk.core.autocommit import AutoCommit, commiter
@@ -23,7 +23,6 @@
 from codegen.sdk.core.external.dependency_manager import DependencyManager, get_dependency_manager
 from codegen.sdk.core.external.language_engine import LanguageEngine, get_language_engine
 from codegen.sdk.enums import Edge, EdgeType, NodeType, ProgrammingLanguage
-from codegen.sdk.extensions.io import write_changes
 from codegen.sdk.extensions.sort import sort_editables
 from codegen.sdk.extensions.utils import uncache_all
 from codegen.sdk.typescript.external.ts_declassify.ts_declassify import TSDeclassify
@@ -37,6 +36,7 @@
     from git import Commit as GitCommit
 
     from codegen.git.repo_operator.repo_operator import RepoOperator
+    from codegen.sdk.codebase.io.io import IO
     from codegen.sdk.codebase.node_classes.node_classes import NodeClasses
     from codegen.sdk.core.dataclasses.usage import Usage
     from codegen.sdk.core.expressions import Expression
@@ -92,7 +92,6 @@ class CodebaseContext:
     pending_syncs: list[DiffLite]  # Diffs that have been applied to disk, but not the graph (to be used for sync graph)
     all_syncs: list[DiffLite]  # All diffs that have been applied to the graph (to be used for graph reset)
     _autocommit: AutoCommit
-    pending_files: set[SourceFile]
     generation: int
     parser: Parser[Expression]
     synced_commit: GitCommit | None
@@ -110,6 +109,7 @@ class CodebaseContext:
     session_options: SessionOptions = SessionOptions()
     projects: list[ProjectConfig]
     unapplied_diffs: list[DiffLite]
+    io: IO
 
     def __init__(
         self,
@@ -134,6 +134,7 @@ def __init__(
 
         # =====[ __init__ attributes ]=====
         self.projects = projects
+        self.io = FileIO()
         context = projects[0]
         self.node_classes = get_node_classes(context.programming_language)
         self.config = config
@@ -165,7 +166,6 @@ def __init__(
         self.pending_syncs = []
         self.all_syncs = []
         self.unapplied_diffs = []
-        self.pending_files = set()
         self.flags = Flags()
 
     def __repr__(self):
@@ -259,7 +259,13 @@ def _reset_files(self, syncs: list[DiffLite]) -> None:
                 files_to_remove.append(sync.path)
                 modified_files.add(sync.path)
         logger.info(f"Writing {len(files_to_write)} files to disk and removing {len(files_to_remove)} files")
-        write_changes(files_to_remove, files_to_write)
+        for file in files_to_remove:
+            self.io.delete_file(file)
+        to_save = set()
+        for file, content in files_to_write:
+            self.io.write_file(file, content)
+            to_save.add(file)
+        self.io.save_files(to_save)
 
     @stopwatch
     def reset_codebase(self) -> None:
@@ -270,7 +276,7 @@ def reset_codebase(self) -> None:
     def undo_applied_diffs(self) -> None:
         self.transaction_manager.clear_transactions()
         self.reset_codebase()
-        self.check_changes()
+        self.io.check_changes()
         self.pending_syncs.clear()  # Discard pending changes
         if len(self.all_syncs) > 0:
             logger.info(f"Unapplying {len(self.all_syncs)} diffs to graph. Current graph commit: {self.synced_commit}")
@@ -432,7 +438,7 @@ def _process_diff_files(self, files_to_sync: Mapping[SyncType, list[Path]], incr
 
         # Step 5: Add new files as nodes to graph (does not yet add edges)
         for filepath in files_to_sync[SyncType.ADD]:
-            content = filepath.read_text(errors="ignore")
+            content = self.io.read_text(filepath)
             # TODO: this is wrong with context changes
             if filepath.suffix in self.extensions:
                 file_cls = self.node_classes.file_cls
@@ -634,17 +640,6 @@ def remove_edge(self, u: NodeId, v: NodeId, *, edge_type: EdgeType | None = None
                     continue
             self._graph.remove_edge_from_index(edge)
 
-    def check_changes(self) -> None:
-        for file in self.pending_files:
-            file.check_changes()
-        self.pending_files.clear()
-
-    def write_files(self, files: set[Path] | None = None) -> None:
-        to_write = set(filter(lambda f: f.filepath in files, self.pending_files)) if files is not None else self.pending_files
-        with ThreadPoolExecutor() as exec:
-            exec.map(lambda f: f.write_pending_content(), to_write)
-        self.pending_files.difference_update(to_write)
-
     @lru_cache(maxsize=10000)
     def to_absolute(self, filepath: PathLike | str) -> Path:
         path = Path(filepath)
@@ -684,7 +679,7 @@ def commit_transactions(self, sync_graph: bool = True, sync_file: bool = True, f
 
         # Write files if requested
         if sync_file:
-            self.write_files(files)
+            self.io.save_files(files)
 
         # Sync the graph if requested
         if sync_graph and len(self.pending_syncs) > 0:
diff --git a/src/codegen/sdk/codebase/io/file_io.py b/src/codegen/sdk/codebase/io/file_io.py
new file mode 100644
index 000000000..081be4f22
--- /dev/null
+++ b/src/codegen/sdk/codebase/io/file_io.py
@@ -0,0 +1,51 @@
+import logging
+from concurrent.futures import ThreadPoolExecutor
+from pathlib import Path
+
+from codegen.sdk.codebase.io.io import IO, BadWriteError
+
+logger = logging.getLogger(__name__)
+
+
+class FileIO(IO):
+    """IO implementation that writes files to disk, and tracks pending changes."""
+
+    files: dict[Path, bytes]
+
+    def __init__(self):
+        self.files = {}
+
+    def write_bytes(self, path: Path, content: bytes) -> None:
+        self.files[path] = content
+
+    def read_bytes(self, path: Path) -> bytes:
+        if path in self.files:
+            return self.files[path]
+        else:
+            return path.read_bytes()
+
+    def save_files(self, files: set[Path] | None = None) -> None:
+        to_save = set(filter(lambda f: f in files, self.files)) if files is not None else self.files.keys()
+        with ThreadPoolExecutor() as exec:
+            exec.map(lambda path: path.write_bytes(self.files[path]), to_save)
+        if files is None:
+            self.files.clear()
+        else:
+            for path in to_save:
+                del self.files[path]
+
+    def check_changes(self) -> None:
+        if self.files:
+            logger.error(BadWriteError("Directly called file write without calling commit_transactions"))
+        self.files.clear()
+
+    def delete_file(self, path: Path) -> None:
+        self.untrack_file(path)
+        if path.exists():
+            path.unlink()
+
+    def untrack_file(self, path: Path) -> None:
+        self.files.pop(path, None)
+
+    def file_exists(self, path: Path) -> bool:
+        return path.exists()
diff --git a/src/codegen/sdk/codebase/io/io.py b/src/codegen/sdk/codebase/io/io.py
new file mode 100644
index 000000000..3321f072b
--- /dev/null
+++ b/src/codegen/sdk/codebase/io/io.py
@@ -0,0 +1,50 @@
+from abc import ABC, abstractmethod
+from pathlib import Path
+
+
+class BadWriteError(Exception):
+    pass
+
+
+class IO(ABC):
+    def write_file(self, path: Path, content: str | bytes | None) -> None:
+        if content is None:
+            self.untrack_file(path)
+        elif isinstance(content, str):
+            self.write_text(path, content)
+        else:
+            self.write_bytes(path, content)
+
+    def write_text(self, path: Path, content: str) -> None:
+        self.write_bytes(path, content.encode("utf-8"))
+
+    @abstractmethod
+    def untrack_file(self, path: Path) -> None:
+        pass
+
+    @abstractmethod
+    def write_bytes(self, path: Path, content: bytes) -> None:
+        pass
+
+    @abstractmethod
+    def read_bytes(self, path: Path) -> bytes:
+        pass
+
+    def read_text(self, path: Path) -> str:
+        return self.read_bytes(path).decode("utf-8")
+
+    @abstractmethod
+    def save_files(self, files: set[Path] | None = None) -> None:
+        pass
+
+    @abstractmethod
+    def check_changes(self) -> None:
+        pass
+
+    @abstractmethod
+    def delete_file(self, path: Path) -> None:
+        pass
+
+    @abstractmethod
+    def file_exists(self, path: Path) -> bool:
+        pass
diff --git a/src/codegen/sdk/codebase/transactions.py b/src/codegen/sdk/codebase/transactions.py
index d2e71f8fa..31d48b2e1 100644
--- a/src/codegen/sdk/codebase/transactions.py
+++ b/src/codegen/sdk/codebase/transactions.py
@@ -1,4 +1,3 @@
-import os
 from collections.abc import Callable
 from difflib import unified_diff
 from enum import IntEnum
@@ -267,7 +266,7 @@ def __init__(
 
     def execute(self) -> None:
         """Renames the file"""
-        self.file.write_pending_content()
+        self.file.ctx.io.save_files({self.file.path})
         self.file_path.rename(self.new_file_path)
 
     def get_diff(self) -> DiffLite:
@@ -292,8 +291,7 @@ def __init__(
 
     def execute(self) -> None:
         """Removes the file"""
-        os.remove(self.file_path)
-        self.file._pending_content_bytes = None
+        self.file.ctx.io.delete_file(self.file.path)
 
     def get_diff(self) -> DiffLite:
         """Gets the diff produced by this transaction"""
diff --git a/src/codegen/sdk/core/codebase.py b/src/codegen/sdk/core/codebase.py
index 0324c05ed..ca2a6087b 100644
--- a/src/codegen/sdk/core/codebase.py
+++ b/src/codegen/sdk/core/codebase.py
@@ -481,17 +481,17 @@ def get_file(self, filepath: str, *, optional: bool = False, ignore_case: bool =
 
         def get_file_from_path(path: Path) -> File | None:
             try:
-                return File.from_content(path, path.read_text(), self.ctx, sync=False)
+                return File.from_content(path, self.ctx.io.read_text(path), self.ctx, sync=False)
             except UnicodeDecodeError:
                 # Handle when file is a binary file
-                return File.from_content(path, path.read_bytes(), self.ctx, sync=False, binary=True)
+                return File.from_content(path, self.ctx.io.read_bytes(path), self.ctx, sync=False, binary=True)
 
         # Try to get the file from the graph first
         file = self.ctx.get_file(filepath, ignore_case=ignore_case)
         if file is not None:
             return file
         absolute_path = self.ctx.to_absolute(filepath)
-        if absolute_path.exists():
+        if self.ctx.io.file_exists(absolute_path):
             return get_file_from_path(absolute_path)
         elif ignore_case:
             parent = absolute_path.parent
diff --git a/src/codegen/sdk/core/file.py b/src/codegen/sdk/core/file.py
index 67c2faf20..540800190 100644
--- a/src/codegen/sdk/core/file.py
+++ b/src/codegen/sdk/core/file.py
@@ -11,6 +11,7 @@
 from typing import TYPE_CHECKING, Generic, Literal, Self, TypeVar, override
 
 from tree_sitter import Node as TSNode
+from typing_extensions import deprecated
 
 from codegen.sdk._proxy import proxy_property
 from codegen.sdk.codebase.codebase_context import CodebaseContext
@@ -45,10 +46,6 @@
 logger = logging.getLogger(__name__)
 
 
-class BadWriteError(Exception):
-    pass
-
-
 @apidoc
 class File(Editable[None]):
     """Represents a generic file.
@@ -66,7 +63,6 @@ class File(Editable[None]):
     file_path: str
     path: Path
     node_type: Literal[NodeType.FILE] = NodeType.FILE
-    _pending_content_bytes: bytes | None = None
     _directory: Directory | None
     _pending_imports: set[str]
     _binary: bool = False
@@ -117,10 +113,8 @@ def from_content(cls, filepath: str | Path, content: str | bytes, ctx: CodebaseC
         if not path.exists():
             update_graph = True
             path.parent.mkdir(parents=True, exist_ok=True)
-            if not binary:
-                path.write_text(content)
-            else:
-                path.write_bytes(content)
+            ctx.io.write_file(path, content)
+            ctx.io.save_files({path})
 
         new_file = cls(filepath, ctx, ts_node=None, binary=binary)
         return new_file
@@ -133,10 +127,7 @@ def content_bytes(self) -> bytes:
 
         TODO: move rest of graph sitter to operate in bytes to prevent multi byte character issues?
         """
-        # Check against None due to possibility of empty byte
-        if self._pending_content_bytes is None:
-            return self.path.read_bytes()
-        return self._pending_content_bytes
+        return self.ctx.io.read_bytes(self.path)
 
     @property
     @reader
@@ -162,31 +153,18 @@ def content(self) -> str:
 
     @noapidoc
     def write(self, content: str | bytes, to_disk: bool = False) -> None:
-        """Writes string contents to the file."""
-        self.write_bytes(content.encode("utf-8") if isinstance(content, str) else content, to_disk=to_disk)
-
-    @noapidoc
-    def write_bytes(self, content_bytes: bytes, to_disk: bool = False) -> None:
-        self._pending_content_bytes = content_bytes
-        self.ctx.pending_files.add(self)
+        """Writes contents to the file."""
+        self.ctx.io.write_file(self.path, content)
         if to_disk:
-            self.write_pending_content()
+            self.ctx.io.save_files({self.path})
             if self.ts_node.start_byte == self.ts_node.end_byte:
                 # TS didn't parse anything, register a write to make sure the transaction manager can restore the file later.
                 self.edit("")
 
     @noapidoc
-    def write_pending_content(self) -> None:
-        if self._pending_content_bytes is not None:
-            self.path.write_bytes(self._pending_content_bytes)
-            self._pending_content_bytes = None
-            logger.debug("Finished write_pending_content")
-
-    @noapidoc
-    @writer
-    def check_changes(self) -> None:
-        if self._pending_content_bytes is not None:
-            logger.error(BadWriteError("Directly called file write without calling commit_transactions"))
+    @deprecated("Use write instead")
+    def write_bytes(self, content_bytes: bytes, to_disk: bool = False) -> None:
+        self.write(content_bytes, to_disk=to_disk)
 
     @property
     @reader
@@ -272,7 +250,7 @@ def remove(self) -> None:
             None
         """
         self.transaction_manager.add_file_remove_transaction(self)
-        self._pending_content_bytes = None
+        self.ctx.io.write_file(self.path, None)
 
     @property
     def filepath(self) -> str:
@@ -596,10 +574,11 @@ def from_content(cls, filepath: str | PathLike | Path, content: str, ctx: Codeba
             return None
 
         update_graph = False
-        if not path.exists():
+        if not ctx.io.file_exists(path):
             update_graph = True
             path.parent.mkdir(parents=True, exist_ok=True)
-            path.write_text(content)
+            ctx.io.write_file(path, content)
+            ctx.io.save_files({path})
 
         if update_graph and sync:
             ctx.add_single_file(path)
diff --git a/src/codegen/sdk/extensions/io.pyx b/src/codegen/sdk/extensions/io.pyx
deleted file mode 100644
index 6b2c8fcd8..000000000
--- a/src/codegen/sdk/extensions/io.pyx
+++ /dev/null
@@ -1,12 +0,0 @@
-from pathlib import Path
-from concurrent.futures import ThreadPoolExecutor
-import os
-
-
-def write_changes(files_to_remove: list[Path], files_to_write: list[tuple[Path, bytes]]):
-    # Start at the oldest sync and then apply non-conflicting newer changes
-    with ThreadPoolExecutor() as executor:
-        for file_to_remove in files_to_remove:
-            executor.submit(os.remove, file_to_remove)
-        for file_to_write, content in files_to_write:
-            executor.submit(file_to_write.write_bytes, content)
diff --git a/tests/unit/codegen/sdk/io/test_file_io.py b/tests/unit/codegen/sdk/io/test_file_io.py
new file mode 100644
index 000000000..6f8148e4f
--- /dev/null
+++ b/tests/unit/codegen/sdk/io/test_file_io.py
@@ -0,0 +1,63 @@
+import pytest
+
+from codegen.sdk.codebase.io.file_io import FileIO
+
+
+@pytest.fixture
+def file_io():
+    return FileIO()
+
+
+def test_write_and_read_bytes(file_io, tmp_path):
+    test_file = tmp_path / "test.txt"
+    content = b"test content"
+
+    file_io.write_bytes(test_file, content)
+    assert file_io.read_bytes(test_file) == content
+    assert not test_file.exists()
+
+
+def test_read_bytes_nonexistent_file(file_io, tmp_path):
+    test_file = tmp_path / "test.txt"
+    test_content = b"test content"
+
+    # Create a real file
+    test_file.write_bytes(test_content)
+
+    # Reading should load from disk
+    assert file_io.read_bytes(test_file) == test_content
+
+
+def test_save_file(file_io, tmp_path):
+    test_file = tmp_path / "test.txt"
+    content = b"test content"
+
+    file_io.write_bytes(test_file, content)
+    file_io.save_files({test_file})
+
+    assert test_file.exists()
+    assert test_file.read_bytes() == content
+
+
+def test_check_changes_with_pending_changes(file_io, tmp_path, caplog):
+    test_file = tmp_path / "test.txt"
+    file_io.write_bytes(test_file, b"test content")
+
+    file_io.check_changes()
+
+    assert "Directly called file write without calling commit_transactions" in caplog.text
+
+
+def test_check_changes_no_pending_changes(file_io):
+    file_io.check_changes()  # Should not raise any exception
+
+
+def test_delete_file(file_io, tmp_path):
+    test_file = tmp_path / "test.txt"
+    test_file.write_bytes(b"test content")
+
+    file_io.read_bytes(test_file)  # Load into memory
+    file_io.delete_file(test_file)
+
+    assert not test_file.exists()
+    assert test_file not in file_io.files