Fix misuse of coffeescript existential operator

for path in project.paths? was being transpiled to
_ref = project.paths != null;
Use atom.config.set for each project setting
Instead of extending atom.config.settings and run
atom.config.emit('updated')
Fix failing test
Add test for getCurrentPath bug
Use atom.config.setRawValue instead of atom.config.set

atom.config.set was writting to the user config file
Also, use _.union to preserve existing array setting values
Use underscore plus in flattenSettings
Load project settings when opening a project with project manager toggle
Use getPaths (getPath is deprecated)
Add settings tests, bug tests, fix existing tests
Merge remote-tracking branch 'upstream/master' into bugfix/settings-broken

Conflicts:
	lib/project-manager.coffee
Merge branch 'pr/53' into dev
Opening a project should not load its settings into current project
Fix length of line
Updated
Prepare 1.13.0 release