diff --git a/src/claudesync/cli/main.py b/src/claudesync/cli/main.py
index b3df3c1..594eec3 100644
--- a/src/claudesync/cli/main.py
+++ b/src/claudesync/cli/main.py
@@ -1,6 +1,11 @@
 import click
 import click_completion
 import click_completion.core
+import json
+import os
+import subprocess
+import urllib.request
+from pkg_resources import get_distribution
 
 from claudesync.cli.chat import chat
 from claudesync.config_manager import ConfigManager
@@ -54,6 +59,83 @@ def status(config):
         click.echo(f"{key.replace('_', ' ').capitalize()}: {value or 'Not set'}")
 
 
+@cli.command()
+@click.pass_context
+def upgrade(config):
+    """Upgrade ClaudeSync to the latest version and reset configuration, preserving sessionKey."""
+    current_version = get_distribution("claudesync").version
+
+    # Check for the latest version
+    try:
+        with urllib.request.urlopen(
+            "https://pypi.org/pypi/claudesync/json"
+        ) as response:
+            data = json.loads(response.read())
+            latest_version = data["info"]["version"]
+
+        if current_version == latest_version:
+            click.echo(
+                f"You are already on the latest version of ClaudeSync (v{current_version})."
+            )
+            return
+    except Exception as e:
+        click.echo(f"Unable to check for the latest version: {str(e)}")
+        click.echo("Proceeding with the upgrade process.")
+
+    config_path = os.path.expanduser("~/.claudesync/config.json")
+    session_key = None
+    session_key_expiry = None
+
+    # Read existing configuration
+    if os.path.exists(config_path):
+        with open(config_path, "r") as f:
+            old_config = json.load(f)
+            session_key = old_config.get("session_key")
+            session_key_expiry = old_config.get("session_key_expiry")
+
+        # Backup existing configuration
+        backup_path = f"{config_path}.v{current_version}.bak"
+        os.rename(config_path, backup_path)
+        click.echo(f"Existing configuration backed up to: {backup_path}")
+
+    # Upgrade ClaudeSync
+    click.echo(f"Upgrading ClaudeSync from v{current_version} to v{latest_version}...")
+    try:
+        subprocess.run(["pip", "install", "--upgrade", "claudesync"], check=True)
+        click.echo("ClaudeSync has been successfully upgraded.")
+    except subprocess.CalledProcessError:
+        click.echo(
+            "Failed to upgrade ClaudeSync. Please try manually: pip install --upgrade claudesync"
+        )
+
+    # Create new configuration with preserved sessionKey
+    if session_key and session_key_expiry:
+        new_config = {
+            "session_key": session_key,
+            "session_key_expiry": session_key_expiry,
+        }
+        with open(config_path, "w") as f:
+            json.dump(new_config, f, indent=2)
+        click.echo("New configuration created with preserved sessionKey.")
+    else:
+        click.echo("No sessionKey found in the old configuration.")
+
+    # Inform user about the upgrade process
+    click.echo("\nUpgrade process completed:")
+    click.echo(
+        f"1. Your previous configuration (v{current_version}) has been backed up."
+    )
+    click.echo(
+        f"2. ClaudeSync has been upgraded from v{current_version} to v{latest_version}."
+    )
+    click.echo(
+        "3. A new configuration has been created, preserving your sessionKey if it existed."
+    )
+    click.echo(
+        "\nPlease run 'claudesync api login' to complete your configuration setup."
+    )
+
+
 cli.add_command(api)
 cli.add_command(organization)
 cli.add_command(project)
diff --git a/src/claudesync/config_manager.py b/src/claudesync/config_manager.py
index 58e8d09..b90a2db 100644
--- a/src/claudesync/config_manager.py
+++ b/src/claudesync/config_manager.py
@@ -42,6 +42,7 @@ def _get_default_config(self):
             "max_file_size": 32 * 1024,
             "two_way_sync": False,
             "curl_use_file_input": False,
+            "prune_remote_files": False,
             "submodule_detect_filenames": [
                 "pom.xml",
                 "build.gradle",
@@ -99,7 +100,6 @@ def _get_default_config(self):
                         "go.mod",
                     ],
                 },
-                "prune_remote_files": True,
             },
         }