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If Yummy gets launched as a result of an FTP Alias being used, Yummy should automatically quit after the transfer is complete. There are two exceptions: If Yummy was already running it will not quit. Similarly, if Yummy was launched as a result of an FTP Alias being used but other tasks were performed afterwards, such as opening another connection manually, then Yummy will not quit.
You have the option to create both Standard and Secure FTP Aliases. The newer variant, Secure FTP Alias, contains a mini version of Yummy FTP itself but capable only of uploading, and as such it works independently of Yummy FTP so it doesn't have to be launched at all. Additionally, the Secure FTP Alias can be copied to other computers and used used without Yummy FTP installed. The name "secure" comes from the fact that the connection details embedded in them cannot be read or edited once created, even by you, so it's safe to distribute around.