The visibility of a file or folder is determined by the server configuration.
When using FTP there are the normal listing and an advanced listing that includes files that are hidden by default. To see these files you need to use the LIST command and set the list parameter to "show hidden files".
By default FlashFXP will use the MLSD command because this format has many advantages over the old LIST style format which was never intended to be machine parsed by FTP clients. However the MLSD command does not support the same parameters as the LIST command.
Almost all FTP servers can be configured to show hidden files (all files) when using MLSD or regular list, however since this is not the typical behavior, most FTP servers do not use this setting as default.
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