diff --git a/git_trace2_event_log_base.py b/git_trace2_event_log_base.py
index 063d101c6..637dffb56 100644
--- a/git_trace2_event_log_base.py
+++ b/git_trace2_event_log_base.py
@@ -98,6 +98,8 @@ class BaseEventLog:
         try:
             env[KEY] = self._full_sid
         except UnicodeEncodeError:
+            # This is a specific fallback for Windows for string-vs-bytes.
+            # pyrefly: ignore
             env[KEY] = self._full_sid.encode()
 
         if repo_source_version is not None:
diff --git a/main.py b/main.py
index 2aa8ebe57..58541232a 100755
--- a/main.py
+++ b/main.py
@@ -37,6 +37,8 @@ import repo_logging
 
 
 try:
+    # Optional third-party module.
+    # pyrefly: ignore
     import kerberos
 except ImportError:
     kerberos = None
diff --git a/platform_utils_win32.py b/platform_utils_win32.py
index 6f3292612..f5624d5bb 100644
--- a/platform_utils_win32.py
+++ b/platform_utils_win32.py
@@ -17,6 +17,8 @@ from ctypes import wintypes
 import errno
 
 
+# Windows-only ctypes APIs are not in typeshed when checking on non-Windows.
+# pyrefly: ignore
 kernel32 = ctypes.WinDLL("kernel32", use_last_error=True)
 
 UCHAR = ctypes.c_ubyte
@@ -164,7 +166,9 @@ def _create_symlink(source, link_name, dwFlags):
         # "the unprivileged create flag is unsupported below Windows 10 (1703,
         # v10.0.14972). retry without it."
         if not CreateSymbolicLinkW(link_name, source, dwFlags):
+            # pyrefly: ignore
             code = ctypes.get_last_error()
+            # pyrefly: ignore
             error_desc = ctypes.FormatError(code).strip()
             if code == ERROR_PRIVILEGE_NOT_HELD:
                 raise OSError(errno.EPERM, error_desc, link_name)
@@ -190,7 +194,9 @@ def readlink(path):
     )
     if reparse_point_handle == INVALID_HANDLE_VALUE:
         _raise_winerror(
-            ctypes.get_last_error(), f'Error opening symbolic link "{path}"'
+            # pyrefly: ignore
+            ctypes.get_last_error(),
+            f'Error opening symbolic link "{path}"',
         )
     target_buffer = ctypes.c_buffer(MAXIMUM_REPARSE_DATA_BUFFER_SIZE)
     n_bytes_returned = wintypes.DWORD()
@@ -207,7 +213,9 @@ def readlink(path):
     CloseHandle(reparse_point_handle)
     if not io_result:
         _raise_winerror(
-            ctypes.get_last_error(), f'Error reading symbolic link "{path}"'
+            # pyrefly: ignore
+            ctypes.get_last_error(),
+            f'Error reading symbolic link "{path}"',
         )
     rdb = REPARSE_DATA_BUFFER.from_buffer(target_buffer)
     if rdb.ReparseTag == IO_REPARSE_TAG_SYMLINK:
@@ -221,6 +229,8 @@ def readlink(path):
 
 
 def _raise_winerror(code, error_desc):
+    # pyrefly: ignore
     win_error_desc = ctypes.FormatError(code).strip()
     error_desc = f"{error_desc}: {win_error_desc}"
+    # pyrefly: ignore
     raise ctypes.WinError(code, error_desc)
diff --git a/progress.py b/progress.py
index 2cbac97b1..ba5c5f9ca 100644
--- a/progress.py
+++ b/progress.py
@@ -20,6 +20,8 @@ import time
 try:
     import threading as _threading
 except ImportError:
+    # This module was removed in Python 3.9, but we still support Python 3.6.
+    # pyrefly: ignore
     import dummy_threading as _threading
 
 import repo_trace
diff --git a/pyproject.toml b/pyproject.toml
index ceba41ffd..72da86a01 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -58,3 +58,63 @@ markers = """
 # dirs of all tests for the last 3 runs, and each e2e test has its own checkout.
 # Use `-o tmp_path_retention_policy=all` to inspect the dirs of passing tests.
 tmp_path_retention_policy = "failed"
+
+# https://pyrefly.org/en/docs/configuration/
+[tool.pyrefly]
+project-includes = [
+    # go/keep-sorted start
+    "**/*.py*",
+    "release/update-hooks",
+    "release/update-manpages",
+    "repo",
+    "run_tests",
+    # go/keep-sorted end
+]
+# We use relative module imports for our own modules.
+enable-fallback-search-path = true
+# NB: Do not add more modules here.  We need to shrink this list.
+project-excludes = [
+    "command.py",
+    "git_command.py",
+    "git_config.py",
+    "git_refs.py",
+    "git_status.py",
+    "git_superproject.py",
+    "main.py",
+    "manifest_xml.py",
+    "project.py",
+    "subcmds/branches.py",
+    "subcmds/cherry_pick.py",
+    "subcmds/config.py",
+    "subcmds/diffmanifests.py",
+    "subcmds/forall.py",
+    "subcmds/gc.py",
+    "subcmds/grep.py",
+    "subcmds/help.py",
+    "subcmds/info.py",
+    "subcmds/init.py",
+    "subcmds/manifest.py",
+    "subcmds/rebase.py",
+    "subcmds/selfupdate.py",
+    "subcmds/smartsync.py",
+    "subcmds/stage.py",
+    "subcmds/start.py",
+    "subcmds/status.py",
+    "subcmds/sync.py",
+    "subcmds/upload.py",
+    "subcmds/version.py",
+    "subcmds/wipe.py",
+    "tests/e2e/harness.py",
+    "tests/e2e/test_groups.py",
+    "tests/test_command.py",
+    "tests/test_git_command.py",
+    "tests/test_git_config.py",
+    "tests/test_git_superproject.py",
+    "tests/test_git_trace2_event_log.py",
+    "tests/test_manifest_xml.py",
+    "tests/test_project.py",
+    "tests/test_subcmds_info.py",
+    "tests/test_subcmds_sync.py",
+    "tests/test_subcmds_wipe.py",
+    "tests/test_wrapper.py",
+]
diff --git a/pyrefly b/pyrefly
new file mode 120000
index 000000000..934c8cd80
--- /dev/null
+++ b/pyrefly
@@ -0,0 +1 @@
+run_tests
\ No newline at end of file
diff --git a/run_tests b/run_tests
index 21af64f10..a2cb2dd38 100755
--- a/run_tests
+++ b/run_tests
@@ -25,7 +25,8 @@
 #   'flake8-bugbear==26.9.30',
 #   'flake8-comprehensions==3.17.0',
 #   'flake8-import-restrictions==2.1',
-#   'isort==5.10.1'
+#   'isort==5.10.1',
+#   'pyrefly==1.4.0',
 # ]
 # ///
 
@@ -40,6 +41,7 @@ import sys
 import black
 import flake8.main.cli
 import isort.main
+import pyrefly.__main__
 import pytest
 
 
@@ -169,6 +171,30 @@ def run_isort():
     ).returncode
 
 
+def run_pyrefly() -> int:
+    """Returns the exit code from pyrefly."""
+    argv = ["--version"]
+    log_cmd("pyrefly", argv)
+    subprocess.run(
+        [pyrefly.__main__.get_pyrefly_bin()] + argv,
+        check=True,
+        cwd=ROOT_DIR,
+    )
+
+    argv = [
+        "check",
+        "--verbose",
+        "--output-format=full-text",
+        "--progress-bar=simple",
+    ]
+    log_cmd("pyrefly", argv)
+    return subprocess.run(
+        [pyrefly.__main__.get_pyrefly_bin()] + argv,
+        check=False,
+        cwd=ROOT_DIR,
+    ).returncode
+
+
 def run_check_metadata():
     """Returns the exit code from check-metadata."""
     argv = []
@@ -215,6 +241,7 @@ def main_run_tests(argv: list[str]) -> int:
         run_black,
         run_flake8,
         run_isort,
+        run_pyrefly,
         run_check_metadata,
         run_update_manpages,
     )
@@ -223,6 +250,14 @@ def main_run_tests(argv: list[str]) -> int:
     return 1 if sum(c() for c in checks) else 0
 
 
+def main_pyrefly(argv: list[str]) -> int:
+    """The pyrefly program."""
+    result = subprocess.run(
+        [pyrefly.__main__.get_pyrefly_bin()] + argv, check=False
+    )
+    return result.returncode
+
+
 main_black = black.main
 main_flake8 = flake8.main.cli.main
 main_isort = isort.main.main
diff --git a/run_tests.uv.lock b/run_tests.uv.lock
index 1c791596f..b9ab171c0 100644
--- a/run_tests.uv.lock
+++ b/run_tests.uv.lock
@@ -1,46 +1,46 @@
-attrs==25.4.0 ; python_full_version < '3.12' \
+attrs==25.4.0 \
     --hash=sha256:3e2be3ccc931d6c0cda7d37122b992d6d4b905968a437da7843cff016e2c41e8 \
     --hash=sha256:adcf7e2a1fb3b36ac48d97835bb6d8ade15b8dcce26aba8bf1d14847b57a3373
     # via flake8-bugbear
-black==25.1.0 ; python_full_version < '3.12' \
+black==25.1.0 \
     --hash=sha256:95e8176dae143ba9097f351d174fdaf0ccd29efb414b362ae3fd72bf0f710717 \
     --hash=sha256:c9ed033e41998dd45d6f19bf9923e2444cb401185ccb26d1a2101a9049637c1f
-click==8.4.1 ; python_full_version < '3.12' \
+click==8.4.1 \
     --hash=sha256:482be17c6991b8c19c5429a1e995d9b0efdbb63172824c41f99965dc0ade8ec2
     # via black
-colorama==0.4.6 ; python_full_version < '3.12' and sys_platform == 'win32' \
+colorama==0.4.6 ; sys_platform == 'win32' \
     --hash=sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6 \
     --hash=sha256:8a5a9494346d7ae2d8f599e4661738007d2df56dbbf4ccbbf7a6a23679a3a302
     # via
     #   click
     #   pytest
-execnet==2.1.1 ; python_full_version < '3.12' \
+execnet==2.1.1 \
     --hash=sha256:26dee51f1b80cebd6d0ca8e74dd8745419761d3bef34163928cbebbdc4749fdc \
     --hash=sha256:58d6d58362e52bfab78f40ebfed9575a3334c41593bee4eb5fcda518290018dc
     # via pytest-xdist
-flake8==7.4.1 ; python_full_version < '3.12' \
+flake8==7.4.1 \
     --hash=sha256:7ff3b14668bfec70da5ce3eeaf1756098330598a9a69f1ee312ed315d27c6508
     # via
     #   flake8-bugbear
     #   flake8-comprehensions
-flake8-bugbear==26.9.30 ; python_full_version < '3.12' \
+flake8-bugbear==26.9.30 \
     --hash=sha256:d0fec65b92eb79adde488515c925c33afabbf85d194bd881e845c71444960fc5
-flake8-comprehensions==3.17.0 ; python_full_version < '3.12' \
+flake8-comprehensions==3.17.0 \
     --hash=sha256:3943a9c6f2593c3bc5cc64106c2f89d63c6ecd49c8343597f8257b8fcfc8b0a2
-flake8-import-restrictions==2.1 ; python_full_version < '3.12' \
+flake8-import-restrictions==2.1 \
     --hash=sha256:77522e76b82a6ccb25820b1e195825a695094ceded23a18c1b5ce026c23e1071
-iniconfig==2.3.0 ; python_full_version < '3.12' \
+iniconfig==2.3.0 \
     --hash=sha256:e6ae3625a739878eeb4baf25f17a0b4e9d985421e45b897d1332ed7478f822d9 \
     --hash=sha256:f631c04d2c48c52b84d0d0549c99ff3859c98df65b3101406327ecc7d53fbf12
     # via pytest
-isort==5.10.1 ; python_full_version < '3.12' \
+isort==5.10.1 \
     --hash=sha256:6f62d78e2f89b4500b080fe3a81690850cd254227f27f75c3a0c491a1f351ba7 \
     --hash=sha256:ec0da0d88470e89ade75bf1e2ea7b4349ec906f95c84aff08e4d41dea6864d25
-mccabe==0.7.0 ; python_full_version < '3.12' \
+mccabe==0.7.0 \
     --hash=sha256:6c2d30ab6be0e4a46919781807b4f0d834ebdd6c6e3dca0bda5a15f863427b6e \
     --hash=sha256:b85abd0a321cdd357d0be34adbf49cf01453a857a23e94d44612ec6f159cb261
     # via flake8
-mypy-extensions==1.1.0 ; python_full_version < '3.12' \
+mypy-extensions==1.1.0 \
     --hash=sha256:1be4cccdb0f2482337c4743e60421de3a356cd97508abadd57d47403e94f5505 \
     --hash=sha256:1be4cccdb0f2482337c4743e60421de3a356cd97508abadd57d47403e94f5505 \
     --hash=sha256:1be4cccdb0f2482337c4743e60421de3a356cd97508abadd57d47403e94f5505 \
@@ -51,33 +51,38 @@ mypy-extensions==1.1.0 ; python_full_version < '3.12' \
     --hash=sha256:1be4cccdb0f2482337c4743e60421de3a356cd97508abadd57d47403e94f5505 \
     --hash=sha256:4ec363d206d93f233330fa7f08eefe9a382dd1e326112a94244f95ec2f22f10e
     # via black
-packaging==26.2 ; python_full_version < '3.12' \
+packaging==26.2 \
     --hash=sha256:5fc45236b9446107ff2415ce77c807cee2862cb6fac22b8a73826d0693b0980e
     # via
     #   black
     #   pytest
-pathspec==1.0.4 ; python_full_version < '3.12' \
+pathspec==1.0.4 \
     --hash=sha256:eeaf9fc7cbc0a4492b666be276f38956baa67cd3faca745462db83d98f1cef87 \
     --hash=sha256:fb6ae2fd4e7c921a165808a552060e722767cfa526f99ca5156ed2ce45a5c723
     # via black
-platformdirs==4.9.2 ; python_full_version < '3.12' \
+platformdirs==4.9.2 \
     --hash=sha256:9170634f126f8efdae22fb58ae8a0eaa86f38365bc57897a6c4f781d1f5875bd \
     --hash=sha256:ef245e78eb7a2ba57599bdb39c4ff323cfae3de356a47207b58bb29e7f479f46
     # via black
-pluggy==1.6.0 ; python_full_version < '3.12' \
+pluggy==1.6.0 \
     --hash=sha256:88349c39e440567519b15b27a781bcd3430de6bae17c44c37e758795be96dc5a \
     --hash=sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746
     # via pytest
-pycodestyle==2.15.0 ; python_full_version < '3.12' \
+pycodestyle==2.15.0 \
     --hash=sha256:12fd2f73c7b8ee8845a0431111df8faf4c1a07d6e64e2ee7f0c74014dab14181
     # via flake8
-pyflakes==4.0.3 ; python_full_version < '3.12' \
+pyflakes==4.0.3 \
     --hash=sha256:330ba92b8c1db2eb0b8f4068f6c58674e2649a99e334769aa50e3e9c5b11c23a
     # via flake8
-pytest==8.3.4 ; python_full_version < '3.12' \
+pyrefly==1.4.0 \
+    --hash=sha256:460cec39bc8743915e9c2c8c10ba926ad0b29b099d89c1859fb97e0059f42fa7 \
+    --hash=sha256:5a6370d686b6cbbac8869832f09a52012888371956fbc68d446a349bc85ccd43 \
+    --hash=sha256:7aff37c2b711c8240ed650da0c6148237b327bf7e5dfacee65884f1adea22305 \
+    --hash=sha256:b6951f51687304caebfedf13dd1a943aeafdbc95abcc4e24a683b97467a77007
+pytest==8.3.4 \
     --hash=sha256:00cba7845d2dccfe5403025a688d60ceae228b1ddaa866d2eb86b2edb6923e73 \
     --hash=sha256:50e16d954148559c9a74109af1eaf0c945ba2d8f30f0a3d3335edde19788b6f6
     # via pytest-xdist
-pytest-xdist==3.8.0 ; python_full_version < '3.12' \
+pytest-xdist==3.8.0 \
     --hash=sha256:202ca578cfeb7370784a8c33d6d05bc6e13b4f25b5053c30a152269fd10f0b88 \
     --hash=sha256:9e659fa2eacbed776070a08a075eff2d9c8e010bab4eea169640c22a1b079f2c
diff --git a/setup.py b/setup.py
index 77de5cadb..31bbdcbe7 100755
--- a/setup.py
+++ b/setup.py
@@ -17,6 +17,8 @@
 
 import os
 
+# Not installed in the test virtualenv.
+# pyrefly: ignore
 import setuptools
 
 
diff --git a/subcmds/sync.py b/subcmds/sync.py
index 0d4012d5b..bfa3fa645 100644
--- a/subcmds/sync.py
+++ b/subcmds/sync.py
@@ -39,6 +39,8 @@ import xmlrpc.client
 try:
     import threading as _threading
 except ImportError:
+    # This module was removed in Python 3.9, but we still support Python 3.6.
+    # pyrefly: ignore
     import dummy_threading as _threading
 
 try: