Update readme with fully working process.

sync_instance_with_server.bat

@@ -20,39 +20,48 @@ if %ERRORLEVEL% NEQ 0 (
     exit /b 1
 )
 
-:: Process each folder
+:: Create a temporary directory for the git operations
+set "TEMP_GIT_DIR=%TEMP%\mc_git_sync"
+if exist "%TEMP_GIT_DIR%" rd /s /q "%TEMP_GIT_DIR%"
+mkdir "%TEMP_GIT_DIR%"
+cd "%TEMP_GIT_DIR%"
+
+:: Initialize git repo
+git init
+git remote add origin "%REPO_URL%"
+git config core.sparseCheckout true
+
+:: Set up sparse checkout for selected folders
+del /q .git\info\sparse-checkout 2>nul
 for %%F in (%SYNC_FOLDERS%) do (
-    echo Processing %%F...
-    
-    :: Create directory if it doesn't exist
-    if not exist "%~dp0%%F" mkdir "%~dp0%%F"
-    
-    :: Initialize git in the directory if not already done
-    if not exist "%~dp0%%F\.git" (
-        cd "%~dp0%%F"
-        git init
-        git remote add origin "%REPO_URL%"
-        :: Configure sparse checkout
-        git config core.sparseCheckout true
-        :: Set up sparse checkout to only get this directory
-        echo %%F> .git/info/sparse-checkout
-        :: Initial fetch of just this directory
-        git fetch --depth 1 origin main
-        git checkout main
-    ) else (
-        :: Just pull updates if git is already initialized
-        cd "%~dp0%%F"
-        git fetch origin main
-        git reset --hard origin/main
+    echo %%F/>> .git\info\sparse-checkout
+)
+
+:: Fetch latest content
+git fetch --depth 1 origin main
+git checkout main
+
+:: Copy contents to instance folders
+for %%F in (%SYNC_FOLDERS%) do (
+    if exist "%TEMP_GIT_DIR%\%%F" (
+        echo Syncing %%F...
+        :: Create target directory if it doesn't exist
+        if not exist "%~dp0%%F" mkdir "%~dp0%%F"
+        :: Copy contents, updating only newer files
+        robocopy "%TEMP_GIT_DIR%\%%F" "%~dp0%%F" /E /XO /NP /NFL /NDL
     )
 )
 
+:: Clean up
+cd "%~dp0"
+rd /s /q "%TEMP_GIT_DIR%"
+
 echo.
 echo Sync completed successfully!
 echo.
 echo This sync has:
 echo - Updated all tracked files from the repository
-echo - Kept your local untracked files intact
+echo - Preserved your local untracked files
 echo.
 
 pause