diff --git a/checkpoint/store.py b/checkpoint/store.py
index ec770fc..93f3e24 100644
--- a/checkpoint/store.py
+++ b/checkpoint/store.py
@@ -12,6 +12,7 @@
 import json
 import os
 import shutil
+import sys
 import time
 from datetime import datetime, timedelta
 from pathlib import Path
@@ -97,7 +98,7 @@ def track_file_edit(session_id: str, file_path: str) -> str | None:
     except OSError:
         return None
     if size > _MAX_FILE_SIZE:
-        print(f"[checkpoint] skipping large file ({size} bytes): {file_path}")
+        print(f"[checkpoint] skipping large file ({size} bytes): {file_path}", file=sys.stderr)
         return None
 
     # Copy file to backups/
@@ -107,7 +108,7 @@ def track_file_edit(session_id: str, file_path: str) -> str | None:
     try:
         shutil.copy2(str(p), str(backup_path))
     except Exception as e:
-        print(f"[checkpoint] backup failed for {file_path}: {e}")
+        print(f"[checkpoint] backup failed for {file_path}: {e}", file=sys.stderr)
         return None
 
     return backup_name
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000..f935fc6
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,14 @@
+"""Shared pytest fixtures for all tests."""
+
+from __future__ import annotations
+
+import pytest
+
+
+# --------------- quota stub (avoids ImportError on CI for calc_cost) --------
+
+@pytest.fixture(autouse=True)
+def _no_quota(monkeypatch):
+    """Disable quota.record_usage so tests never hit the real billing path."""
+    import quota
+    monkeypatch.setattr(quota, "record_usage", lambda *a, **kw: None)
diff --git a/tests/helpers.py b/tests/helpers.py
new file mode 100644
index 0000000..7d37a79
--- /dev/null
+++ b/tests/helpers.py
@@ -0,0 +1,27 @@
+"""Reusable test helpers (importable from any test module)."""
+
+from __future__ import annotations
+
+from agent import AssistantTurn
+
+
+def scripted_stream(captured_schemas: list, turns: list[dict]):
+    """Return a fake ``stream()`` callable that yields pre-defined turns.
+
+    *captured_schemas* receives the ``tool_schemas`` kwarg from each call,
+    letting tests assert on schema injection.  *turns* is a list of dicts,
+    each with optional ``text`` and ``tool_calls`` keys.
+    """
+    cursor = iter(turns)
+
+    def fake_stream(**kwargs):
+        captured_schemas.append(kwargs.get("tool_schemas") or [])
+        spec = next(cursor)
+        yield AssistantTurn(
+            text=spec.get("text", ""),
+            tool_calls=spec.get("tool_calls") or [],
+            in_tokens=1,
+            out_tokens=1,
+        )
+
+    return fake_stream
diff --git a/tests/test_checkpoint_e2e.py b/tests/test_checkpoint_e2e.py
new file mode 100644
index 0000000..09ff441
--- /dev/null
+++ b/tests/test_checkpoint_e2e.py
@@ -0,0 +1,112 @@
+"""End-to-end: drive a real agent.run() conversation where the LLM calls Write,
+and verify the checkpoint hook intercepts the call and files a backup to disk.
+
+Only the LLM provider is mocked (via monkeypatching agent.stream). The Write
+tool, checkpoint hooks and checkpoint store all run for real against tmp_path.
+"""
+from __future__ import annotations
+
+import pytest
+
+import tools as _tools_init  # noqa: F401 - force built-in tool registration
+from agent import AgentState, run
+from providers import AssistantTurn
+from checkpoint import hooks as checkpoint_hooks
+from checkpoint import store as checkpoint_store
+
+
+def _scripted_stream(turns):
+    cursor = iter(turns)
+
+    def fake_stream(**_kwargs):
+        spec = next(cursor)
+        yield AssistantTurn(
+            text=spec.get("text", ""),
+            tool_calls=spec.get("tool_calls") or [],
+            in_tokens=1, out_tokens=1,
+        )
+
+    return fake_stream
+
+
+@pytest.fixture
+def sandboxed_checkpoints(tmp_path, monkeypatch):
+    """Run checkpoint store against tmp_path and install hooks on built-in tools."""
+    monkeypatch.setattr(
+        checkpoint_store, "_checkpoints_root", lambda: tmp_path / ".checkpoints"
+    )
+    checkpoint_store.reset_file_versions()
+    checkpoint_hooks.set_session("e2e-session")
+    checkpoint_hooks.reset_tracked()
+    checkpoint_hooks.install_hooks()
+    yield tmp_path
+    checkpoint_hooks.reset_tracked()
+
+
+def test_llm_write_triggers_checkpoint_backup(monkeypatch, sandboxed_checkpoints):
+    """When the LLM calls Write, the checkpoint hook must back the pre-edit file up.
+
+    Pre-populate a small file, then let the LLM overwrite it via the Write
+    tool. The hook should copy the old content into checkpoints/.../backups/
+    before the Write executes, so the backup holds the original bytes.
+    """
+    target = sandboxed_checkpoints / "hello.py"
+    target.write_text("print('before')\n", encoding="utf-8")
+
+    turns = [
+        {"tool_calls": [{
+            "id": "w1",
+            "name": "Write",
+            "input": {"file_path": str(target), "content": "print('after')\n"},
+        }]},
+        {"text": "done"},
+    ]
+    monkeypatch.setattr("agent.stream", _scripted_stream(turns))
+
+    state = AgentState()
+    config = {"model": "test", "permission_mode": "accept-all",
+              "_session_id": "e2e-session"}
+    list(run("overwrite the file", state, config, "system prompt"))
+
+    # After the turn: Write applied the new content
+    assert target.read_text(encoding="utf-8") == "print('after')\n"
+
+    # And the checkpoint hook filed a backup with the pre-edit content
+    backups_dir = sandboxed_checkpoints / ".checkpoints" / "e2e-session" / "backups"
+    backups = list(backups_dir.iterdir())
+    assert backups, "checkpoint hook did not create a backup file"
+    assert any(b.read_text(encoding="utf-8") == "print('before')\n" for b in backups)
+
+
+def test_oversized_write_logs_to_stderr_not_stdout(
+    monkeypatch, sandboxed_checkpoints, capfd
+):
+    """Over the _MAX_FILE_SIZE threshold the hook skips + logs — to stderr only.
+
+    This is the actual user-visible contract of PR #47: checkpoint skips must
+    not pollute stdout (which carries the conversation transcript), they must
+    land on stderr where operators look.
+    """
+    monkeypatch.setattr(checkpoint_store, "_MAX_FILE_SIZE", 20)
+    big = sandboxed_checkpoints / "big.py"
+    big.write_text("x" * 100, encoding="utf-8")
+
+    turns = [
+        {"tool_calls": [{
+            "id": "w1",
+            "name": "Write",
+            "input": {"file_path": str(big), "content": "y" * 100},
+        }]},
+        {"text": "ok"},
+    ]
+    monkeypatch.setattr("agent.stream", _scripted_stream(turns))
+
+    state = AgentState()
+    list(run("rewrite", state, {"model": "test", "permission_mode": "accept-all",
+                                 "_session_id": "e2e-session",
+                                 "disabled_tools": ["Agent"]},
+              "sys"))
+
+    out, errtxt = capfd.readouterr()
+    assert "[checkpoint] skipping large file" in errtxt
+    assert "[checkpoint] skipping large file" not in out
diff --git a/tests/test_checkpoint_store.py b/tests/test_checkpoint_store.py
new file mode 100644
index 0000000..13160a2
--- /dev/null
+++ b/tests/test_checkpoint_store.py
@@ -0,0 +1,61 @@
+"""Integration tests for checkpoint store: stderr capture + large file skip."""
+from __future__ import annotations
+
+import pytest
+
+import checkpoint.store as store
+
+
+@pytest.fixture(autouse=True)
+def isolate_store(tmp_path, monkeypatch):
+    """Redirect checkpoint root to tmp_path and reset global state."""
+    monkeypatch.setattr(store, "_checkpoints_root", lambda: tmp_path / "checkpoints")
+    store.reset_file_versions()
+
+
+def test_large_file_skipped_and_logged_to_stderr(tmp_path, monkeypatch, capsys):
+    monkeypatch.setattr(store, "_MAX_FILE_SIZE", 50)
+    big_file = tmp_path / "big.txt"
+    big_file.write_bytes(b"x" * 100)
+
+    result = store.track_file_edit("test-session", str(big_file))
+
+    assert result is None
+    captured = capsys.readouterr()
+    assert "[checkpoint] skipping large file" in captured.err
+    assert "100 bytes" in captured.err
+    assert captured.out == ""
+
+
+def test_normal_file_backed_up(tmp_path, capsys):
+    small_file = tmp_path / "small.txt"
+    content = b"hello world"
+    small_file.write_bytes(content)
+
+    result = store.track_file_edit("test-session", str(small_file))
+
+    assert result is not None
+    backup_dir = tmp_path / "checkpoints" / "test-session" / "backups"
+    backup_path = backup_dir / result
+    assert backup_path.exists()
+    assert backup_path.read_bytes() == content
+    captured = capsys.readouterr()
+    assert captured.err == ""
+
+
+def test_backup_failure_logged_to_stderr(tmp_path, monkeypatch, capsys):
+    normal_file = tmp_path / "normal.txt"
+    normal_file.write_bytes(b"some data")
+
+    def failing_copy(*args, **kwargs):
+        raise PermissionError("access denied")
+
+    monkeypatch.setattr(store.shutil, "copy2", failing_copy)
+
+    result = store.track_file_edit("test-session", str(normal_file))
+
+    assert result is None
+    captured = capsys.readouterr()
+    assert "[checkpoint] backup failed" in captured.err
+    assert "access denied" in captured.err
+    assert captured.out == ""