For security reasons FlashFXP will not save your application password anywhere. You must enter it every time you start FlashFXP.
When you start a new instance from FlashFXP it passes some special information to the new FlashFXP, This special information is used to authenticate the new FlashFXP and bypass the prompt. This can only be done if you start a new FlashFXP from within FlashFXP.
Your other suggestion will be considered for future releases.
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