My Atom settings - automatic update by http://atom.io/packages/sync-settings

init.coffee

# initialization file (not found)

keymap.cson

'atom-text-editor':
  'cmd-shift-l':'window:toggle-bottom-dock'
  'cmd-.':'window:toggle-bottom-dock'

packages.json

{
	"about": {
		"version": "1.9.1"
	},
	"archive-view": {
		"version": "0.65.2"
	},
	"atom-beautify": {
		"version": "0.33.4"
	},
	"atom-brackets-glow": {
		"version": "0.6.0"
	},
	"atom-dark-syntax": {
		"version": "0.29.1",
		"theme": "syntax"
	},
	"atom-dark-ui": {
		"version": "0.53.3",
		"theme": "ui"
	},
	"atom-html-preview": {
		"version": "0.2.6"
	},
	"atom-light-syntax": {
		"version": "0.29.1",
		"theme": "syntax"
	},
	"atom-light-ui": {
		"version": "0.46.3",
		"theme": "ui"
	},
	"atom-mermaid": {
		"version": "3.5.4"
	},
	"atom-ternjs": {
		"version": "0.20.0"
	},
	"auto-indent": {
		"version": "0.5.0"
	},
	"auto-update-packages": {
		"version": "1.0.1"
	},
	"autocomplete-atom-api": {
		"version": "0.10.7"
	},
	"autocomplete-css": {
		"version": "0.17.5"
	},
	"autocomplete-html": {
		"version": "0.8.8"
	},
	"autocomplete-modules": {
		"version": "2.3.0"
	},
	"autocomplete-plus": {
		"version": "2.42.3"
	},
	"autocomplete-snippets": {
		"version": "1.12.1"
	},
	"autoflow": {
		"version": "0.29.4"
	},
	"autosave": {
		"version": "0.24.6"
	},
	"background-tips": {
		"version": "0.28.0"
	},
	"base16-tomorrow-dark-theme": {
		"version": "1.6.0",
		"theme": "syntax"
	},
	"base16-tomorrow-light-theme": {
		"version": "1.6.0",
		"theme": "syntax"
	},
	"better-git-blame": {
		"version": "0.5.0"
	},
	"bookmarks": {
		"version": "0.46.0"
	},
	"bracket-matcher": {
		"version": "0.91.2"
	},
	"busy-signal": {
		"version": "2.0.1"
	},
	"cobalt2-syntax": {
		"version": "0.5.3",
		"theme": "syntax"
	},
	"command-palette": {
		"version": "0.43.5"
	},
	"css-declaration-sorter": {
		"version": "2.0.0"
	},
	"custom-window-title": {
		"version": "1.0.4"
	},
	"dalek": {
		"version": "0.2.2"
	},
	"deprecation-cop": {
		"version": "0.56.9"
	},
	"dev-live-reload": {
		"version": "0.48.1"
	},
	"editorconfig": {
		"version": "2.6.1"
	},
	"emmet": {
		"version": "2.4.3"
	},
	"emmet-jsx-css-modules": {
		"version": "1.0.0"
	},
	"encoding-selector": {
		"version": "0.23.9"
	},
	"exception-reporting": {
		"version": "0.43.1"
	},
	"file-icons": {
		"version": "2.1.42"
	},
	"find-and-replace": {
		"version": "0.219.3"
	},
	"fonts": {
		"version": "3.12.0"
	},
	"fuzzy-finder": {
		"version": "1.14.2"
	},
	"git-blame": {
		"version": "1.8.0"
	},
	"git-diff": {
		"version": "1.3.9"
	},
	"git-diff-details": {
		"version": "1.4.0"
	},
	"git-log": {
		"version": "0.4.1"
	},
	"github": {
		"version": "0.34.2"
	},
	"go-to-line": {
		"version": "0.33.0"
	},
	"grammar-selector": {
		"version": "0.50.1"
	},
	"highlight-selected": {
		"version": "0.17.0"
	},
	"Hydrogen": {
		"version": "2.14.4"
	},
	"hyperclick": {
		"version": "0.1.5"
	},
	"image-view": {
		"version": "0.64.0"
	},
	"import-cost-atom": {
		"version": "1.0.9"
	},
	"incompatible-packages": {
		"version": "0.27.3"
	},
	"intentions": {
		"version": "1.1.5"
	},
	"jshint": {
		"version": "1.8.6"
	},
	"keybinding-resolver": {
		"version": "0.39.0"
	},
	"keymap-control": {
		"version": "1.2.0"
	},
	"language-babel": {
		"version": "2.85.0"
	},
	"language-c": {
		"version": "0.60.19"
	},
	"language-clojure": {
		"version": "0.22.8"
	},
	"language-coffee-script": {
		"version": "0.50.0"
	},
	"language-csharp": {
		"version": "1.1.0"
	},
	"language-css": {
		"version": "0.44.4"
	},
	"language-gfm": {
		"version": "0.90.7"
	},
	"language-git": {
		"version": "0.19.1"
	},
	"language-go": {
		"version": "0.47.2"
	},
	"language-haml": {
		"version": "0.32.1"
	},
	"language-html": {
		"version": "0.53.1"
	},
	"language-hyperlink": {
		"version": "0.17.1"
	},
	"language-java": {
		"version": "0.31.5"
	},
	"language-javascript": {
		"version": "0.134.1"
	},
	"language-json": {
		"version": "1.0.5"
	},
	"language-less": {
		"version": "0.34.3"
	},
	"language-make": {
		"version": "0.23.0"
	},
	"language-mdx": {
		"version": "0.1.0"
	},
	"language-mermaid": {
		"version": "0.6.0"
	},
	"language-mustache": {
		"version": "0.14.5"
	},
	"language-objective-c": {
		"version": "0.16.0"
	},
	"language-perl": {
		"version": "0.38.1"
	},
	"language-php": {
		"version": "0.44.4"
	},
	"language-property-list": {
		"version": "0.9.1"
	},
	"language-python": {
		"version": "0.53.4"
	},
	"language-ruby": {
		"version": "0.72.23"
	},
	"language-ruby-on-rails": {
		"version": "0.25.3"
	},
	"language-rust-bundled": {
		"version": "0.1.0"
	},
	"language-sass": {
		"version": "0.62.1"
	},
	"language-shellscript": {
		"version": "0.28.2"
	},
	"language-source": {
		"version": "0.9.0"
	},
	"language-sql": {
		"version": "0.25.10"
	},
	"language-text": {
		"version": "0.7.4"
	},
	"language-todo": {
		"version": "0.29.4"
	},
	"language-toml": {
		"version": "0.20.0"
	},
	"language-typescript": {
		"version": "0.6.2"
	},
	"language-vue": {
		"version": "0.26.0"
	},
	"language-vue-component": {
		"version": "0.5.0"
	},
	"language-xml": {
		"version": "0.35.3"
	},
	"language-yaml": {
		"version": "0.32.0"
	},
	"line-ending-selector": {
		"version": "0.7.7"
	},
	"lines": {
		"version": "0.13.1"
	},
	"link": {
		"version": "0.31.6"
	},
	"linter": {
		"version": "2.3.1"
	},
	"linter-coffeelint": {
		"version": "2.0.54"
	},
	"linter-eslint": {
		"version": "8.5.5"
	},
	"linter-phpcs": {
		"version": "1.7.6"
	},
	"linter-rubocop": {
		"version": "2.5.7"
	},
	"linter-ruby": {
		"version": "1.3.1"
	},
	"linter-sass-lint": {
		"version": "1.9.0"
	},
	"linter-stylelint": {
		"version": "4.5.1"
	},
	"linter-tslint": {
		"version": "1.10.43"
	},
	"linter-ui-default": {
		"version": "1.8.1"
	},
	"markdown-preview": {
		"version": "0.160.2"
	},
	"markdown-preview-plus": {
		"version": "4.5.0"
	},
	"merge-conflicts": {
		"version": "1.4.5"
	},
	"metrics": {
		"version": "1.8.1"
	},
	"native-ui": {
		"version": "0.27.0",
		"theme": "ui"
	},
	"notifications": {
		"version": "0.71.0"
	},
	"one-dark-syntax": {
		"version": "1.8.4",
		"theme": "syntax"
	},
	"one-dark-ui": {
		"version": "1.12.5",
		"theme": "ui"
	},
	"one-light-syntax": {
		"version": "1.8.4",
		"theme": "syntax"
	},
	"one-light-ui": {
		"version": "1.12.5",
		"theme": "ui"
	},
	"open-on-github": {
		"version": "1.3.2"
	},
	"package-generator": {
		"version": "1.3.0"
	},
	"path-copy": {
		"version": "0.14.0"
	},
	"pigments": {
		"version": "0.40.2"
	},
	"platformio-ide-terminal": {
		"version": "2.10.0"
	},
	"prettier-atom": {
		"version": "0.60.1"
	},
	"rails-open-rspec": {
		"version": "1.2.0"
	},
	"ruby-test": {
		"version": "1.0.2"
	},
	"settings-view": {
		"version": "0.261.4"
	},
	"snippets": {
		"version": "1.5.1"
	},
	"solarized-dark-syntax": {
		"version": "1.3.0",
		"theme": "syntax"
	},
	"solarized-light-syntax": {
		"version": "1.3.0",
		"theme": "syntax"
	},
	"spell-check": {
		"version": "0.76.1"
	},
	"status-bar": {
		"version": "1.8.17"
	},
	"styleguide": {
		"version": "0.49.12"
	},
	"Sublime-Style-Column-Selection": {
		"version": "1.7.5"
	},
	"swackets": {
		"version": "0.35.0"
	},
	"symbols-view": {
		"version": "0.118.4"
	},
	"sync-settings": {
		"version": "4.3.8"
	},
	"tabs": {
		"version": "0.110.0"
	},
	"tasks": {
		"version": "2.10.1"
	},
	"timecop": {
		"version": "0.36.2"
	},
	"tool-bar": {
		"version": "1.3.0"
	},
	"tool-bar-almighty": {
		"version": "0.9.0"
	},
	"tree-view": {
		"version": "0.228.0"
	},
	"update-package-dependencies": {
		"version": "0.13.1"
	},
	"wakatime": {
		"version": "9.0.2"
	},
	"welcome": {
		"version": "0.36.9"
	},
	"whitespace": {
		"version": "0.37.7"
	},
	"wrap-guide": {
		"version": "0.41.0"
	}
}

settings.json

{
	"*": {
		"atom-beautify": {
			"cpp": {
				"beautify_on_save": true
			},
			"general": {
				"_analyticsUserId": "5a53a5b0-55f0-442e-837a-88aed72addb1"
			},
			"html": {
				"end_with_newline": true,
				"indent_inner_html": true
			},
			"php": {
				"cs_fixer_path": "/usr/local/bin/php-cs-fixer"
			},
			"ruby": {
				"rubocop_path": "/Users/leonardo/.rvm/gems/ruby-2.1.2@thinkific/bin/rubocop"
			},
			"sass": {
				"beautify_on_save": true
			},
			"scss": {
				"align_assignments": true
			}
		},
		"better-git-blame": {
			"searchInLayerEnabled": false
		},
		"core": {
			"disabledPackages": [
				"markdown-preview",
				"busy-signal",
				"path-copy",
				"autocomplete-modules",
				"linter-phpcs",
				"tool-bar",
				"keybinding-resolver",
				"jshint"
			],
			"ignoredNames": [
				".git",
				".hg",
				".svn",
				".DS_Store",
				"._*",
				"Thumbs.db",
				"desktop.ini",
				".sass-cache"
			],
			"packagesWithKeymapsDisabled": [
				"platformio-ide-terminal"
			],
			"telemetryConsent": "no",
			"themes": [
				"native-ui",
				"cobalt2-syntax"
			]
		},
		"css-declaration-sorter": {
			"sortOrder": "smacss"
		},
		"custom-title": {
			"template": "<%= projectName %> • <%= fileName %> • <%= filePath %>"
		},
		"custom-window-title": {
			"template": "<%= projectName %> • <%= fileName %> • <%= relativeFilePath %>"
		},
		"editor": {
			"fontFamily": "FiraCode-light, Menlo, Consolas, DejaVu Sans Mono, monospace",
			"fontSize": 16,
			"preferredLineLength": 100,
			"softWrap": true
		},
		"exception-reporting": {
			"userId": "9e525c74-6ffc-46e1-af2c-336307ccb06c"
		},
		"fonts": {
			"fontFamily": "FiraCode Light"
		},
		"fuzzy-finder": {},
		"git-blame": {
			"columnWidth": -187
		},
		"git-diff": {
			"showIconsInEditorGutter": true
		},
		"glowing-cursor": {
			"cursorWidth": 8,
			"glowColor": "#ffffff",
			"glowDistance": 10,
			"innerColor": "#ffffff",
			"transitionDuration": 900
		},
		"jshint": {
			"onlyConfig": true
		},
		"linter-eslint": {
			"autofix": {
				"fixOnSave": true
			}
		},
		"linter-phpcs": {
			"codeStandardOrConfigFile": "Wordpress",
			"executablePath": "/usr/local/bin/phpcs"
		},
		"linter-rubocop": {
			"command": "/Users/leonardo/.rvm/gems/ruby-2.3.4@thinkific/bin/rubocop",
			"disableWhenNoConfigFile": true
		},
		"linter-ruby": {
			"rubyExecutablePath": "/Users/leonardo/.rvm/gems/ruby-2.3.4@thinkific/bin/rubocop"
		},
		"linter-ui-default": {
			"alwaysTakeMinimumSpace": true,
			"panelHeight": 152,
			"showPanel": true,
			"showProviderName": true,
			"statusBarRepresents": "Current File",
			"useBusySignal": false
		},
		"markdown-preview-plus": {
			"previewConfig": {
				"previewSplitPaneDir": "down"
			},
			"syntaxThemeName": "atom-dark-syntax",
			"useGitHubStyle": true
		},
		"platformio-ide-terminal": {
			"core": {
				"mapTerminalsTo": "Folder"
			}
		},
		"prettier-atom": {
			"formatOnSaveOptions": {
				"showInStatusBar": true
			}
		},
		"ruby-test": {
			"rspecAllCommand": "docker exec rails bash -lc \"bin/rspec --tty spec\"",
			"rspecFileCommand": "docker exec rails bash -lc \"bin/rspec --tty {relative_path}\"\t",
			"rspecSingleCommand": "docker exec rails bash -lc \"bin/rspec --tty {relative_path}:{line_number}\"",
			"specFramework": "rspec"
		},
		"sync-settings": {
			"gistDescription": "My Atom settings - automatic update by http://atom.io/packages/sync-settings",
			"hiddenSettings": {}
		},
		"tasks": {
			"useTouchbar": true
		},
		"tool-bar": {
			"fullWidth": false,
			"iconSize": "16px"
		},
		"tool-bar-almighty": {
			"override": true
		},
		"tree-view": {
			"hideIgnoredNames": true
		},
		"wakatime": {
			"apikey": "Saved in your $WAKATIME_HOME/.wakatime.cfg file"
		},
		"welcome": {
			"showOnStartup": false
		}
	}
}

snippets.cson

# snippets file (not found)

styles.less

.file-info,
.line-ending-tile {
  display: none;
}

atom-panel-container.left .inset-panel,
atom-panel-container.bottom .inset-panel {
  display: none;
}

.linter-status-count {
  border-radius: 4px;
  padding: 0 !important;

  a {
    border-radius: 0;
    font-weight: bold;
    margin-right: 0 !important;
    padding: 4px 6px;
  }

  a:nth-child(1) {
    background-color: @background-color-error;
    color: #fff;
    border-top-left-radius: 4px;
    border-bottom-left-radius: 4px;
  }

  a:nth-child(2) {
    background-color: @background-color-warning;
    color: #fff;
  }

  a:nth-child(3) {
    background-color: @background-color-info;
    color: #fff;
    border-top-right-radius: 4px;
    border-bottom-right-radius: 4px;
  }

  .icon {
    display: none;
  }
}

atom-text-editor {
  text-rendering: optimizeLegibility;

  &.editor .syntax--string.syntax--quoted,
  &.editor .syntax--string.syntax--regexp {
    -webkit-font-feature-settings: "liga" off, "calt" off;
  }
}

// atom-text-editor.editor {
//   /*
//     Transform selected text into alternative font for elegant touch:
//     - this
//     - HTML and JSX attributes
//     - JS functions (except arrow function)
//     - JS undefined
//     - JS storage (const/let/async)
//     - EX constants
//     - Ruby (nil/self/block)
//     - Ruby hash keys
//   */
//   .syntax--variable.syntax--language.syntax--this,
//   .syntax--html > .syntax--attribute-name,
//   .syntax--JSXAttrs > .syntax--attribute-name,
//   .syntax--storage.syntax--type.syntax--js:not(.syntax--function):not(.syntax--arrow),
//   .syntax--constant.syntax--language.syntax--undefined.syntax--js,
//   .syntax--constant.syntax--other.syntax--object.syntax--key.syntax--js,
//   .syntax--variable.syntax--other.syntax--constant.syntax--elixir,
//   .syntax--constant.syntax--language.syntax--elixir,
//   .syntax--constant.syntax--language.syntax--nil.syntax--ruby,
//   .syntax--variable.syntax--language.syntax--self.syntax--ruby,
//   .syntax--constant.syntax--other.syntax--symbol.syntax--hashkey.syntax--ruby,
//   .syntax--variable.syntax--other.syntax--block.syntax--ruby {
//     vertical-align: baseline;
//     font-size: 100%;
//     font-style: italic !important;
//     height: inherit;
//     line-height: 100%;
//   }
// }

// Uncomment this to show the tab names
// Useful when the Keybinding resolver tab hides the linter tab
// atom-dock .tab-bar {
//   display: block !important;
// }

Muito boa sua configuração!
Qual é o seu esquema de cores?

@bryandidur desculpe a demora em responder: UI Theme: Native, Syntax Theme: Cobalt 2