You can set each sync item to exclude specific files. Excluded files are simply ignored: they are neither copied, nor overwritten, nor removed (unless the option „Remove excluded files“ is enabled). However, excluded files inside directories to be removed are only preserved if they are explicitly included (i.e. they appear in the „Following files“ section described afterwards).
In the Exclude tab of a sync item’s settings you will find the following options.
Exclude hidden files
Files or directories which start with a dot are hidden in the Finder. Most of the times these files are used to cache data and can be recreated by macOS if necessary. For example, .DS_STORE files are created by the Finder when opening a directory and are used for example to store information about the position of icons. The .Spotlight-V100 directory is created whenever a volume is indexed by Spotlight, the search engine on the Mac, and can also be safely excluded.
After enabling the check box „Filenames containing any of the following words“, you can enter a list of tokens which are checked against each filename in order to determine if it should be excluded or not. After typing an expression, you have to press Return in order to tokenise it. Starting from version 2.2, you can then turn a token into a regular expression by clicking on the small triangle on its right. Starting from version 2.6, you can turn a token from exclusive to inclusive. Tokens at the start of the text field have higher priority, meaning that if a file is matched by an inclusive token but also by a following exclusive token, it will be included.
Be careful when using inclusive tokens in combination with explicitly excluded directories: since inclusive tokens always cause excluded directories to be scanned, this could lead to higher than normal scanning time.
Exclude a specific file
Add a file to the list under the „Following files“ check box by clicking on the „+“ button. Starting from version 2.2, files inside excluded directories will be included, and vice versa; you can alternate as many excluded and included files as you want. Excluded and included files apply for both source and destination. Files contained in included directories can still be excluded and files contained in excluded directories can still be included by the above filters.
You may want to exclude the source directory itself and include some of the contained directories as a means of grouping together many sync items with a common parent directory and the same settings.