Catch and log deactivate errors

Closes #3538

spec/atom-spec.coffee

@@ -350,7 +350,7 @@ describe "the `atom` global", ->
             atom.packages.deactivatePackage("package-that-throws-on-activate")
             expect(badPack.mainModule.serialize).not.toHaveBeenCalled()
 
-        it "absorbs exceptions that are thrown by the package module's serialize methods", ->
+        it "absorbs exceptions that are thrown by the package module's serialize method", ->
           spyOn(console, 'error')
 
           waitsForPromise ->
@@ -365,6 +365,16 @@ describe "the `atom` global", ->
             expect(atom.packages.packageStates['package-with-serialization']).toEqual someNumber: 1
             expect(console.error).toHaveBeenCalled()
 
+        it "absorbs exceptions that are thrown by the package module's deactivate method", ->
+          spyOn(console, 'error')
+
+          waitsForPromise ->
+            atom.packages.activatePackage("package-that-throws-on-deactivate")
+
+          runs ->
+            expect(-> atom.packages.deactivatePackage("package-that-throws-on-deactivate")).not.toThrow()
+            expect(console.error).toHaveBeenCalled()
+
         it "removes the package's grammars", ->
           waitsForPromise ->
             atom.packages.activatePackage('package-with-grammars')

spec/fixtures/packages/package-that-throws-on-deactivate/index.coffee

@@ -0,0 +1,4 @@
+module.exports =
+  activate: ->
+  deactivate: -> throw new Error('Top that')
+  serialize: ->

src/package.coffee

@@ -273,7 +273,11 @@ class Package
     @unsubscribeFromActivationEvents()
     @deactivateResources()
     @deactivateConfig()
-    @mainModule?.deactivate?() if @mainActivated
+    if @mainActivated
+      try
+        @mainModule?.deactivate?()
+      catch e
+        console.error "Error deactivating package '#{@name}'", e.stack
     @emit 'deactivated'
     @emitter.emit 'did-deactivate'