Filter out all test and tests folders

Prevent all test/tests folders from ending up in the built
app instead of an explicit and ever-growing list
Filter example files from built app
Uncomment grunt.task.run call
Don't include .cc files from native modules
Don't include .h files from native modules
Update comment with .h files
Don't include jasmine-node/spec files
Remove unused replication fixture
Don't include more build files
Don't include .travis.yml and .npmignore files
Don't include atom-shell's default_app folder
Make e optional in test regex
Remove unused package fixtures
Specify regex directly as filter
Upgrade to dev-live-reload@0.32
Don't include benchmark folders
Don't include bootstrap site files
Don't include target.mk or linker.lock files
Don't include binding.gyp files
Don't include nan