Ah okay so I recreated the Library/Application\ Support/Sublime/User directory as well as the Preferences.sublime-settings, and the ignored packaged populated themselves.
Console output here:
[details=Summary]startup, version: 3126 osx x64 channel: stable
executable: /Applications/Sublime Text.app/Contents/MacOS/Sublime Text
working dir: /
packages path: /Users/User/Library/Application Support/Sublime Text 3/Packages
state path: /Users/User/Library/Application Support/Sublime Text 3/Local
zip path: /Applications/Sublime Text.app/Contents/MacOS/Packages
zip path: /Users/User/Library/Application Support/Sublime Text 3/Installed Packages
ignored_packages: [“Alignment”, “AutoFileName”, “BracketHighlighter”, “BufferScroll”, “C++ Snippets”, “C++ Starting Kit”, “C++11”, “Cobalt2 Flat Theme”, “CSS3”, “Emmet”, “GitGutter”, “JavaScript & NodeJS Snippets”, “Javatar”, “Keymaps”, “Markdown Preview”, “Numix Theme”, “Sass”, “Select Quoted”, “SideBarEnhancements”, “Theme - Cobalt2”, “Vintage”]
pre session restore time: 0.27174
using gpu buffer for window
first paint time: 0.332757
using gpu buffer for window
startup time: 0.378139
reloading plugin Default.auto_indent_tag
reloading plugin Default.block
reloading plugin Default.comment
reloading plugin Default.convert_syntax
reloading plugin Default.copy_path
reloading plugin Default.delete_word
reloading plugin Default.detect_indentation
reloading plugin Default.duplicate_line
reloading plugin Default.echo
reloading plugin Default.exec
reloading plugin Default.fold
reloading plugin Default.font
reloading plugin Default.goto_line
reloading plugin Default.history_list
reloading plugin Default.indentation
reloading plugin Default.install_package_control
reloading plugin Default.kill_ring
reloading plugin Default.mark
reloading plugin Default.new_templates
reloading plugin Default.open_context_url
reloading plugin Default.open_in_browser
reloading plugin Default.pane
reloading plugin Default.paragraph
reloading plugin Default.paste_from_history
reloading plugin Default.profile
reloading plugin Default.quick_panel
reloading plugin Default.run_syntax_tests
reloading plugin Default.save_on_focus_lost
reloading plugin Default.scroll
reloading plugin Default.set_unsaved_view_name
reloading plugin Default.settings
reloading plugin Default.show_scope_name
reloading plugin Default.side_bar
reloading plugin Default.sort
reloading plugin Default.swap_line
reloading plugin Default.switch_file
reloading plugin Default.symbol
reloading plugin Default.transform
reloading plugin Default.transpose
reloading plugin Default.trim_trailing_white_space
reloading plugin CSS.css_completions
reloading plugin Diff.diff
reloading plugin HTML.encode_html_entities
reloading plugin HTML.html_completions
reloading plugin 0_package_control_loader.00-package_control
reloading plugin 0_package_control_loader.01-pygments
reloading plugin 0_package_control_loader.50-markupsafe
reloading plugin 0_package_control_loader.50-python-markdown
reloading plugin 0_package_control_loader.50-pyyaml
reloading plugin 0_package_control_loader.51-python-jinja2
reloading plugin 0_package_control_loader.55-mdpopups
reloading plugin Package Control.1_reloader
reloading plugin Package Control.2_bootstrap
reloading plugin Package Control.Package Control
plugins loaded
Package Control: Skipping automatic upgrade, last run at 2017-08-23 22:16:48, next run at 2017-08-23 23:16:48 or after[/details]