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Keep Remote Directory Up To Date Dialog
In the dialog you select options for function Keep Remote Directory Up To Date. To display the dialog go to Commands > Keep Remote Directory Up To Date or click respective toolbar button.
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Directories
Enter root directories for the synchronization into the two boxes. By default the current working directories will be used. In Explorer interface, where there is no local working directory, it will be the last local directory used.
Synchronize Options
The Delete files checkbox makes WinSCP delete files and subdirectories in remote directory that you delete in a corresponding local directory. Before using this, learn how it works, so you know what you are doing.
The Existing files only checkbox makes WinSCP not to consider files and subdirectories not existing in remote directory as new. Such files and subdirectories will be ignored.
The Update subdirectories checkbox will make WinSCP watch for changes in subdirectories as well.
The Selected files only checkbox makes WinSCP synchronize only files and directories selected in any file panel. The option is not available, if no file or directory is selected.
Check Use same options next time if you want to make your options be default next time you use function Keep remote directory up to date. This will not save transfer settings. You can change default transfer settings in preferences. Note that defaults affect function Synchronize as well.
Check Synchronize on start to perform full synchronization of remote directory on start (recommended). Initially the checkbox is in undefined (grayed) state, making WinSCP ask you explicitly.
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Transfer Settings
Transfer settings box shows current transfer settings.
To change the settings, use Transfer settings button. It will reveal drop down menu with list of configured presets. Use special command Custom to configure ad hoc transfer settings (alternatively you may double-click Transfer settings box). Command Configure opens Preferences dialog on Presets tab.
You may want to change transfer settings particularly to exclude certain files and subdirectories from synchronization.