Only "body" changed to the theme

[Frexuz]

Using latest Sublime 3 on Ubuntu 14.04LTS

My settings

{
    "always_show_minimap_viewport": true,
    "animation_enabled": false,
    "binary_file_patterns":
    [
        "*.min.js",
        "*jquery*.js"
    ],
    "bold_folder_labels": true,
    "color_scheme": "Packages/ayu/ayu.tmTheme",
    "draw_minimap_border": true,
    "ensure_newline_at_eof_on_save": true,
    "file_exclude_patterns":
    [
        "*.pyc",
        "*.pyo",
        "*.exe",
        "*.dll",
        "*.obj",
        "*.o",
        "*.a",
        "*.lib",
        "*.so",
        "*.dylib",
        "*.ncb",
        "*.sdf",
        "*.suo",
        "*.pdb",
        "*.idb",
        ".DS_Store",
        "*.class",
        "*.psd",
        "*.db",
        "*.sublime-workspace",
        "*.log"
    ],
    "folder_exclude_patterns":
    [
        ".svn",
        ".git",
        ".hg",
        "CVS",
        "tmp",
        "coverage",
        "public/assets"
    ],
    "font_size": 12,
    "highlight_line": true,
    "highlight_modified_tabs": true,
    "ignored_packages":
    [
        "SublimeLinter",
        "Vintage"
    ],
    "index_exclude_patterns":
    [
        "*.log"
    ],
    "index_files": true,
    "index_workers": 2,
    "match_brackets_angle": true,
    "scroll_speed": 10.0,
    "show_encoding": true,
    "show_line_endings": true,
    "tab_size": 2,
    "translate_tabs_to_spaces": true,
    "tree_animation_enabled": false,
    "trim_trailing_white_space_on_save": true
}

[dempfi]

You missed to add theme entry. Check out readme.