When using Sublime Text 3 on my Mac I noticed that it was showing all hidden files and folders in the left-hand folder/file navigation pane. This can become quite annoying in a large project with tens of files and folders, specially when it shows all of the ._ files for each and every file in the project. To stop this from happening all you need to do is edit your .sublime-project file so it looks similar to the following.

{
    "folders":
    [
        {
            "path": ".",
            "folder_exclude_patterns": [".*"],
            "file_exclude_patterns": [".*"]
        }
    ]
}

As soon as you save the project file the hidden files and folders will instantly vanish from the left-hand pane.