chrome.storage.local.get(['pattern', 'case_insensitive', 'color', 'opacity'], function(items) {
  var pattern, case_insensitive, color, opacity;
  var re, flags;

  pattern = items.pattern;
  if (!pattern) {
    pattern = 'WIP';
  }

  case_insensitive = !!items.case_insensitive;
  if (case_insensitive) {
    flags = 'i';
  } else {
    flags = '';
  }

  re = new RegExp(pattern, flags);

  color   = items.color   || 'lightgray';
  opacity = items.opacity || 0.7;

  var unhighlighter = function(element, re, color, opacity) {
    var items = element.querySelectorAll('.Box-row-link');
    Array.prototype.filter.call(items, function(item) {
      if (item.innerText.match(re)) {
        element.style.backgroundColor = color;
        element.style.opacity = opacity;
      }
    })
  };

  var walk = function(re, color, opacity) {
    var elements = document.querySelectorAll('.js-issue-row');
    Array.prototype.forEach.call(elements, function(element) {
      unhighlighter(element, re, color, opacity);
    });
  }

  var target = document.querySelector('body');
  var config = {
    childList: true,
    subtree: true
  };

  var observer = new MutationObserver(function(mutations, self) {
    mutations.forEach(function(mutation) {
      if (mutation.type === 'childList') {
        walk(re, color, opacity);
      }
    });
  });

  observer.observe(target, config);
  walk(re, color, opacity);
});

chrome.storage.local.get(['pattern', 'case_insensitive', 'color', 'opacity'], function(items) {
  var pattern, case_insensitive, color, opacity;
  var re, flags;

  pattern = items.pattern;
  if (!pattern) {
    pattern = 'WIP';
  }

  case_insensitive = !!items.case_insensitive;
  if (case_insensitive) {
    flags = 'i';
  } else {
    flags = '';
  }

  re = new RegExp(pattern, flags);

  color   = items.color   || 'lightgray';
  opacity = items.opacity || 0.7;

  var unhighlighter = function(element, re, color, opacity) {
    var items = element.querySelectorAll('.Box-row-link');
    Array.from(items).filter(function(item) {
      if (item.innerText.match(re)) {
        element.style.backgroundColor = color;
        element.style.opacity = opacity;
      }
    });
  };

  var walk = function(re, color, opacity) {
    var elements = document.querySelectorAll('.js-issue-row');
    Array.from(elements).forEach(function(element) {
      unhighlighter(element, re, color, opacity);
    });
  }

  var target = document.querySelector('body');
  var config = {
    childList: true,
    subtree: true
  };

  var observer = new MutationObserver(function(mutations, self) {
    mutations.forEach(function(mutation) {
      if (mutation.type === 'childList') {
        walk(re, color, opacity);
      }
    });
  });

  observer.observe(target, config);
  walk(re, color, opacity);
});

Use Array.from instead of Array.prototype