diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index be34b2a7f..4bea67e88 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -124,7 +124,7 @@ jobs:
           sudo modprobe fuse
           sudo chmod 666 /dev/fuse
           sudo chown root:$USER /etc/fuse.conf
-          sudo apt-get install fuse3 libfuse-dev rpm pkg-config
+          sudo apt-get install fuse3 libfuse-dev rpm pkg-config git-annex
         if: matrix.os == 'ubuntu-latest'
 
       - name: Install Libraries on macOS
@@ -137,6 +137,7 @@ jobs:
           brew untap --force homebrew/cask
           brew update
           brew install --cask macfuse
+          brew install git-annex
         if: matrix.os == 'macos-11'
 
       - name: Install Libraries on Windows
diff --git a/cmd/gitannex/e2e_test.go b/cmd/gitannex/e2e_test.go
new file mode 100644
index 000000000..87704df87
--- /dev/null
+++ b/cmd/gitannex/e2e_test.go
@@ -0,0 +1,159 @@
+package gitannex
+
+import (
+	"encoding/json"
+	"errors"
+	"fmt"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"runtime"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+
+	"github.com/rclone/rclone/fs"
+	"github.com/rclone/rclone/lib/buildinfo"
+)
+
+// checkRcloneBinaryVersion runs whichever rclone is on the PATH and checks
+// whether it reports a version that matches the test's expectations. Returns
+// nil when the version is the expected version, otherwise returns an error.
+func checkRcloneBinaryVersion() error {
+	// versionInfo is a subset of information produced by "core/version".
+	type versionInfo struct {
+		Version string
+		IsGit   bool
+		GoTags  string
+	}
+
+	cmd := exec.Command("rclone", "rc", "--loopback", "core/version")
+	stdout, err := cmd.Output()
+	if err != nil {
+		return fmt.Errorf("failed to get rclone version: %w", err)
+	}
+
+	var parsed versionInfo
+	if err := json.Unmarshal(stdout, &parsed); err != nil {
+		return fmt.Errorf("failed to parse rclone version: %w", err)
+	}
+	if parsed.Version != fs.Version {
+		return fmt.Errorf("expected version %q, but got %q", fs.Version, parsed.Version)
+	}
+	if !parsed.IsGit {
+		return errors.New("expected rclone to be a dev build")
+	}
+	_, tagString := buildinfo.GetLinkingAndTags()
+	if parsed.GoTags != tagString {
+		return fmt.Errorf("expected tag string %q, but got %q", tagString, parsed.GoTags)
+	}
+	return nil
+}
+
+// This end-to-end test runs `git annex testremote` in a temporary git repo.
+// This test will be skipped unless the `rclone` binary on PATH reports the
+// expected version.
+//
+// When run on CI, an rclone binary built from HEAD will be on the PATH. When
+// running locally, you will likely need to ensure the current binary is on the
+// PATH like so:
+//
+//	go build && PATH="$(realpath .):$PATH" go test -v ./cmd/gitannex/...
+//
+// In the future, this test will probably be extended to test a number of
+// parameters like repo layouts, and runtime may suffer from a combinatorial
+// explosion.
+func TestEndToEnd(t *testing.T) {
+	if testing.Short() {
+		t.Skip("Skipping due to short mode.")
+	}
+
+	// TODO: Support this test on Windows. Need to evaluate the semantics of the
+	// HOME and PATH environment variables.
+	switch runtime.GOOS {
+	case "darwin",
+		"freebsd",
+		"linux",
+		"netbsd",
+		"openbsd",
+		"plan9",
+		"solaris":
+	default:
+		t.Skipf("GOOS %q is not supported.", runtime.GOOS)
+	}
+
+	if err := checkRcloneBinaryVersion(); err != nil {
+		t.Skipf("Skipping due to rclone version: %s", err)
+	}
+
+	if _, err := exec.LookPath("git-annex"); err != nil {
+		t.Skipf("Skipping because git-annex was not found: %s", err)
+	}
+
+	// Create a temp directory and chdir there, just in case.
+	originalWd, err := os.Getwd()
+	require.NoError(t, err)
+	tempDir := t.TempDir()
+	require.NoError(t, os.Chdir(tempDir))
+	defer func() { require.NoError(t, os.Chdir(originalWd)) }()
+
+	// Flesh out subdirectories of the temp directory:
+	//
+	//  .
+	//  |-- bin
+	//  |   `-- git-annex-remote-rclone-builtin -> ${PATH_TO_RCLONE_BINARY}
+	//  |-- ephemeralRepo
+	//  `-- user
+	//  	`-- .config
+	//  		`-- rclone
+	//  			`-- rclone.conf
+
+	binDir := filepath.Join(tempDir, "bin")
+	homeDir := filepath.Join(tempDir, "user")
+	configDir := filepath.Join(homeDir, ".config")
+	rcloneConfigDir := filepath.Join(configDir, "rclone")
+	ephemeralRepoDir := filepath.Join(tempDir, "ephemeralRepo")
+	for _, dir := range []string{binDir, homeDir, configDir, rcloneConfigDir, ephemeralRepoDir} {
+		require.NoError(t, os.Mkdir(dir, 0700))
+	}
+
+	// Install the symlink that enables git-annex to invoke "rclone gitannex"
+	// without explicitly specifying the subcommand.
+	rcloneBinaryPath, err := exec.LookPath("rclone")
+	require.NoError(t, err)
+	require.NoError(t, os.Symlink(
+		rcloneBinaryPath,
+		filepath.Join(binDir, "git-annex-remote-rclone-builtin")))
+
+	// Install the rclone.conf file that defines the remote.
+	rcloneConfigPath := filepath.Join(rcloneConfigDir, "rclone.conf")
+	rcloneConfigContents := "[MyRcloneRemote]\ntype = local"
+	require.NoError(t, os.WriteFile(rcloneConfigPath, []byte(rcloneConfigContents), 0600))
+
+	// NOTE: These commands must be run with HOME pointing at an ephemeral
+	// directory, rather than the real home directory.
+	cmds := [][]string{
+		{"git", "annex", "version"},
+		{"git", "config", "--global", "user.name", "User Name"},
+		{"git", "config", "--global", "user.email", "user@example.com"},
+		{"git", "init"},
+		{"git", "annex", "init"},
+		{"git", "annex", "initremote", "MyTestRemote",
+			"type=external", "externaltype=rclone-builtin", "encryption=none",
+			"rcloneremotename=MyRcloneRemote", "rcloneprefix=" + ephemeralRepoDir},
+		{"git", "annex", "testremote", "MyTestRemote"},
+	}
+
+	for _, args := range cmds {
+		fmt.Printf("+ %v\n", args)
+		cmd := exec.Command(args[0], args[1:]...)
+		cmd.Dir = ephemeralRepoDir
+		cmd.Env = []string{
+			"HOME=" + homeDir,
+			"PATH=" + os.Getenv("PATH") + ":" + binDir,
+		}
+		cmd.Stdout = os.Stdout
+		cmd.Stderr = os.Stderr
+		require.NoError(t, cmd.Run())
+	}
+}
diff --git a/cmd/gitannex/run-git-annex-testremote.sh b/cmd/gitannex/run-git-annex-testremote.sh
deleted file mode 100755
index 98a848df7..000000000
--- a/cmd/gitannex/run-git-annex-testremote.sh
+++ /dev/null
@@ -1,52 +0,0 @@
-#!/usr/bin/env bash
-#
-# End-to-end tests for "rclone gitannex". This script runs the `git-annex
-# testremote` suite against "rclone gitannex" in an ephemeral git-annex repo.
-#
-# Assumptions:
-#
-#   * This system has an rclone remote configured named "git-annex-builtin-test-remote".
-#
-#   * If it uses rclone's "local" backend, /tmp/git-annex-builtin-test-remote exists.
-
-set -e
-
-TEST_DIR="$(realpath "$(mktemp -d)")"
-mkdir "$TEST_DIR/bin"
-
-function cleanup()
-{
-    rm -rf "$TEST_DIR"
-}
-
-trap cleanup EXIT
-
-RCLONE_DIR="$(git rev-parse --show-toplevel)"
-
-rm -rf /tmp/git-annex-builtin-test-remote/*
-
-set -x
-
-pushd "$RCLONE_DIR"
-go build -o "$TEST_DIR/bin" ./
-
-ln -s "$(realpath "$TEST_DIR/bin/rclone")" "$TEST_DIR/bin/git-annex-remote-rclone-builtin"
-popd
-
-pushd "$TEST_DIR"
-
-git init
-git annex init
-
-REMOTE_NAME=git-annex-builtin-test-remote
-PREFIX=/tmp/git-annex-builtin-test-remote
-
-PATH="$PATH:$TEST_DIR/bin" git annex initremote $REMOTE_NAME \
-    type=external externaltype=rclone-builtin encryption=none \
-    rcloneremotename=$REMOTE_NAME \
-    rcloneprefix="$PREFIX"
-
-PATH="$PATH:$(realpath bin)" git annex testremote $REMOTE_NAME
-
-popd
-rm -rf "$TEST_DIR"