Never load config settings from disk when a save is pending

Fixes #5771

We load the user’s settings from disk when we detect a change to their
config.cson file. However, if there’s a save pending, doing this will
end up blowing away the values we intend to save.

spec/config-spec.coffee

@@ -486,6 +486,7 @@ describe "Config", ->
 
       atom.config.set('foo.bar.baz', "value 1")
       expect(observeHandler).toHaveBeenCalledWith("value 1")
+      advanceClock(100) # complete pending save that was requested in ::set
 
       observeHandler.reset()
       atom.config.loadUserConfig()
@@ -789,6 +790,22 @@ describe "Config", ->
           expect(warnSpy).toHaveBeenCalled()
           expect(warnSpy.mostRecentCall.args[0]).toContain "foo.int"
 
+      describe "when there is a pending save", ->
+        it "does not change the config settings", ->
+          fs.writeFileSync atom.config.configFilePath, "'*': foo: bar: 'baz'"
+
+          atom.config.set("foo.bar", "quux")
+          atom.config.loadUserConfig()
+          expect(atom.config.get("foo.bar")).toBe "quux"
+
+          advanceClock(100)
+          expect(atom.config.save.callCount).toBe 1
+
+          expect(atom.config.get("foo.bar")).toBe "quux"
+          atom.config.loadUserConfig()
+          expect(atom.config.get("foo.bar")).toBe "baz"
+
+
     describe ".observeUserConfig()", ->
       updatedHandler = null
 

src/config.coffee

@@ -332,9 +332,16 @@ class Config
     @configFilePath = fs.resolve(@configDirPath, 'config', ['json', 'cson'])
     @configFilePath ?= path.join(@configDirPath, 'config.cson')
     @transactDepth = 0
+    @savePending = false
 
-    @debouncedSave = _.debounce(@save, 100)
-    @debouncedLoad = _.debounce(@loadUserConfig, 100)
+    @requestLoad = _.debounce(@loadUserConfig, 100)
+    @requestSave = =>
+      @savePending = true
+      debouncedSave.call(this)
+    save = =>
+      @savePending = false
+      @save()
+    debouncedSave = _.debounce(save, 100)
 
   ###
   Section: Config Subscription
@@ -605,7 +612,7 @@ class Config
     else
       @setRawValue(keyPath, value)
 
-    @debouncedSave() if source is @getUserConfigPath() and shouldSave and not @configFileHasErrors
+    @requestSave() if source is @getUserConfigPath() and shouldSave and not @configFileHasErrors
     true
 
   # Essential: Restore the setting at `keyPath` to its default value.
@@ -635,7 +642,7 @@ class Config
           _.setValueForKeyPath(settings, keyPath, undefined)
           settings = withoutEmptyObjects(settings)
           @set(null, settings, {scopeSelector, source, priority: @priorityForSource(source)}) if settings?
-          @debouncedSave()
+          @requestSave()
       else
         @scopedSettingsStore.removePropertiesForSourceAndSelector(source, scopeSelector)
         @emitChangeEvent()
@@ -757,9 +764,10 @@ class Config
       CSON.writeFileSync(@configFilePath, {})
 
     try
-      userConfig = CSON.readFileSync(@configFilePath)
-      @resetUserSettings(userConfig)
-      @configFileHasErrors = false
+      unless @savePending
+        userConfig = CSON.readFileSync(@configFilePath)
+        @resetUserSettings(userConfig)
+        @configFileHasErrors = false
     catch error
       @configFileHasErrors = true
       message = "Failed to load `#{path.basename(@configFilePath)}`"
@@ -776,7 +784,7 @@ class Config
   observeUserConfig: ->
     try
       @watchSubscription ?= pathWatcher.watch @configFilePath, (eventType) =>
-        @debouncedLoad() if eventType is 'change' and @watchSubscription?
+        @requestLoad() if eventType is 'change' and @watchSubscription?
     catch error
       @notifyFailure """
         Unable to watch path: `#{path.basename(@configFilePath)}`. Make sure you have permissions to