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Cookies, web extension and custom URI handlers were initialized in ephy_embed_shell_init(), so they were always called even for secondary instances. All other initializations were in ephy_shell_startup so that it only happens for the primary instance. Move all the code to ephy_embed_shell_startup to make sure everything happens at the same time and only for the primary instance. https://bugzilla.gnome.org/show_bug.cgi?id=696020
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