Hi Macindy
You can use this command that will do the job for you:
"request system storage cleanup"
If you are not sure or if you just want to see what kind of files this command will erase you can use it this way:
"request system storage cleanup dry-run"
Nevertheless if you use it without the dry-run option the router will ask you to confirm if you realy want to erase the files.
On the other hand you will certainly be able do delete only the package file using this comand under the shell with the root permission:
"rm /cf/var/sw/pkg/junos-XYZ.tgz"
Finally to answer to your last question the file is here I believe, only to have a clear way to tidy files and to be able to recover it easily.
HTH
Regards
Alain