diff --git a/signac/__main__.py b/signac/__main__.py
index 57e5639bc..d144291ef 100644
--- a/signac/__main__.py
+++ b/signac/__main__.py
@@ -93,6 +93,8 @@
 )
 
 
+SHELL_HISTORY_FN = os.sep.join((".signac", "shell_history"))
+
 warnings.simplefilter("default")
 
 
@@ -861,7 +863,7 @@ def jobs():
         else:  # interactive
             if READLINE:
                 if "PyPy" not in platform.python_implementation():
-                    fn_hist = project.fn(".signac_shell_history")
+                    fn_hist = project.fn(SHELL_HISTORY_FN)
                     try:
                         readline.read_history_file(fn_hist)
                         readline.set_history_length(1000)
diff --git a/signac/contrib/migration/v1_to_v2.py b/signac/contrib/migration/v1_to_v2.py
index 733682741..31eb02831 100644
--- a/signac/contrib/migration/v1_to_v2.py
+++ b/signac/contrib/migration/v1_to_v2.py
@@ -49,4 +49,16 @@ def _migrate_v1_to_v2(root_directory):
     v1_fn = os.path.join(root_directory, "signac.rc")
     v2_fn = _get_project_config_fn(root_directory)
     os.mkdir(os.path.dirname(v2_fn))
-    os.rename(v1_fn, v2_fn)
+    os.replace(v1_fn, v2_fn)
+
+    # Now move all other files.
+    files_to_move = {
+        ".signac_shell_history": os.sep.join((".signac", "shell_history")),
+        ".signac_sp_cache.json.gz": os.sep.join(
+            (".signac", "statepoint_cache.json.gz")
+        ),
+    }
+    for src, dst in files_to_move.items():
+        os.replace(
+            os.sep.join((root_directory, src)), os.sep.join((root_directory, dst))
+        )
diff --git a/signac/contrib/project.py b/signac/contrib/project.py
index 73d70d694..e1d741895 100644
--- a/signac/contrib/project.py
+++ b/signac/contrib/project.py
@@ -112,7 +112,7 @@ class Project:
     KEY_DATA = "signac_data"
     "The project's datastore key."
 
-    FN_CACHE = ".signac_sp_cache.json.gz"
+    FN_CACHE = os.sep.join((".signac", "statepoint_cache.json.gz"))
     "The default filename for the state point cache file."
 
     _use_pandas_for_html_repr = True  # toggle use of pandas for html repr
diff --git a/tests/test_project.py b/tests/test_project.py
index 4156a8f04..f6373e989 100644
--- a/tests/test_project.py
+++ b/tests/test_project.py
@@ -1,6 +1,7 @@
 # Copyright (c) 2017 The Regents of the University of Michigan
 # All rights reserved.
 # This software is licensed under the BSD 3-Clause License.
+import gzip
 import io
 import itertools
 import json
@@ -35,6 +36,7 @@
     StatepointParsingError,
     WorkspaceError,
 )
+from signac.contrib.hashing import calc_id
 from signac.contrib.linked_view import _find_all_links
 from signac.contrib.project import JobsCursor, Project  # noqa: F401
 from signac.contrib.schema import ProjectSchema
@@ -2473,6 +2475,7 @@ def test_project_schema_version_migration(self, implicit_version):
         from signac.contrib.migration import apply_migrations
 
         with TemporaryDirectory() as dirname:
+            # Create v1 config file.
             cfg_fn = os.path.join(dirname, "signac.rc")
             with open(cfg_fn, "w") as f:
                 f.write(
@@ -2484,6 +2487,21 @@ def test_project_schema_version_migration(self, implicit_version):
                     )
                 )
 
+            # Create a shell history file.
+            history_fn = os.path.join(dirname, ".signac_shell_history")
+            with open(history_fn, "w") as f:
+                f.write("print(project)")
+
+            # Create a statepoint cache. Note that this cache does not
+            # correspond to actual statepoints since we don't currently have
+            # any in this project, but that's fine for migration testing.
+            history_fn = os.path.join(dirname, ".signac_sp_cache.json.gz")
+            sp = {"a": 1}
+            with gzip.open(history_fn, "wb") as f:
+                f.write(json.dumps({calc_id(sp): sp}).encode())
+
+            # If no schema version is present in the config it is equivalent to
+            # version 0, so we test both explicit and implicit versions.
             config = read_config_file(cfg_fn)
             if implicit_version:
                 del config["schema_version"]
@@ -2491,6 +2509,7 @@ def test_project_schema_version_migration(self, implicit_version):
             else:
                 assert config["schema_version"] == "0"
             config.write()
+
             err = io.StringIO()
             with redirect_stderr(err):
                 apply_migrations(dirname)
@@ -2502,6 +2521,8 @@ def test_project_schema_version_migration(self, implicit_version):
             assert "0 to 1" in err.getvalue()
             assert "1 to 2" in err.getvalue()
             assert os.path.isfile(project.fn(PROJECT_CONFIG_FN))
+            assert os.path.isfile(project.fn(os.sep.join((".signac", "shell_history"))))
+            assert os.path.isfile(project.fn(Project.FN_CACHE))
 
 
 class TestProjectPickling(TestProjectBase):