Here is the sharepoint installer batch file that you can copy Master page,Application page, create new folder , generate new site using command line and store the site using command line.
echo Copying the feature...
:: Copy Master File
copy /Y simple1.master "%CommonProgramFiles%\Microsoft Shared\web server extensions\12\Template\Layouts\"
:: Copy aspx file
copy /Y LoginUser.aspx "%CommonProgramFiles%\Microsoft Shared\web server extensions\12\Template\Layouts\"
:: Make Folder for the UserControl
mkdir "%CommonProgramFiles%\Microsoft Shared\web server extensions\12\Template\Layouts\UserControl"
:: Copy the UserControl into the UserCOntrol Folder
copy /Y RecoverPassword.ascx "%CommonProgramFiles%\Microsoft Shared\web server extensions\12\Template\Layouts\UserControl\"
:: Copy Images and Css
copy /Y *.gif "%CommonProgramFiles%\Microsoft Shared\web server extensions\12\Template\Layouts\1033\Images\"
copy /Y *.css "%CommonProgramFiles%\Microsoft Shared\web server extensions\12\Template\Layouts\1033\styles\"
echo Activating the feature...
pushd %programfiles%\common files\microsoft shared\web server extensions\12\bin
:: Create New Site using Command Line
stsadm -o extendvs -url "http://sps:16333" -ownerlogin "serverpsp\trushar" -owneremail "trushar@sps.com" -dn "SP_test" -apcreatenew -apidname "TEST1" -apidtype configurableid -apidlogin "serverpsp\trushar" -apidpwd "trushar"
:: Copy WebConfig,DLL,Pages
copy /Y *.dll "%inetpub%\Inetpub\wwwroot\wss\VirtualDirectories\16333\bin\"
copy /Y web.config "%inetpub%\Inetpub\wwwroot\wss\VirtualDirectories\16333\"
mkdir "%inetpub%\Inetpub\wwwroot\wss\VirtualDirectories\16333\UserControl"
copy /Y myacc.ascx "%inetpub%\Inetpub\wwwroot\wss\VirtualDirectories\16333\UserControl\"
:: Restore New Site
stsadm -o restore -url "http:// sps:16333" -filename "C:\TestBKP.dat" -overwrite
