Update tool-windows.tmpl

changed "%1%" and %2% to "%~1" and %~2 to allow spaces in paths by surrounding quotes
according to advice at 
http://stackoverflow.com/questions/473117/pass-path-with-spaces-as-parameter-to-bat-file
http://ss64.com/nt/syntax-args.html

test case:
PS C:\Users\bjornr> scala -toolcp "test blank/myJar.jar" "test blank/myJar.jar"

with the suggested fix this test case will NOT print this error msg:
blank/myJar.jar""=="-toolcp" was unexpected at this time.