Include remote paths, but skip normalization in the save/restore execution flow

src/atom.coffee

@@ -763,8 +763,7 @@ class Atom extends Model
   # Notify the browser project of the window's current project path
   watchProjectPath: ->
     @disposables.add @project.onDidChangePaths =>
-      @constructor.updateLoadSetting('initialPaths',
-        @project.getPaths().filter((projectPath) -> fs.existsSync(projectPath)))
+      @constructor.updateLoadSetting('initialPaths', @project.getPaths())
 
   exit: (status) ->
     app = remote.require('app')

src/browser/atom-application.coffee

@@ -369,7 +369,12 @@ class AtomApplication
   #   :windowDimensions - Object with height and width keys.
   #   :window - {AtomWindow} to open file paths in.
   openPaths: ({pathsToOpen, pidToKillWhenClosed, newWindow, devMode, safeMode, apiPreviewMode, windowDimensions, profileStartup, window}={}) ->
-    pathsToOpen = (fs.normalize(pathToOpen) for pathToOpen in pathsToOpen)
+    pathsToOpen = pathsToOpen.map (pathToOpen) ->
+      if fs.existsSync(pathToOpen)
+        fs.normalize(pathToOpen)
+      else
+        pathToOpen
+
     locationsToOpen = (@locationForPathToOpen(pathToOpen) for pathToOpen in pathsToOpen)
 
     unless pidToKillWhenClosed or newWindow
@@ -517,6 +522,8 @@ class AtomApplication
     new AtomWindow({bootstrapScript, @resourcePath, exitWhenDone, isSpec, specDirectory, devMode})
 
   locationForPathToOpen: (pathToOpen) ->
+    {protocol} = url.parse(pathToOpen)
+    return {pathToOpen} if protocol?
     return {pathToOpen} unless pathToOpen
     return {pathToOpen} if fs.existsSync(pathToOpen)
 

src/default-directory-provider.coffee

@@ -1,6 +1,7 @@
 {Directory} = require 'pathwatcher'
 fs = require 'fs-plus'
 path = require 'path'
+url = require 'url'
 
 module.exports =
 class DefaultDirectoryProvider
@@ -21,7 +22,13 @@ class DefaultDirectoryProvider
     else
       projectPath
 
-    new Directory(directoryPath)
+    # TODO: Stop normalizing the path in pathwatcher's Directory.
+    directory = new Directory(directoryPath)
+    if (url.parse(directoryPath).protocol)
+      directory.path = directoryPath;
+      if (fs.isCaseInsensitive())
+        directory.lowerCasePath = directoryPath.toLowerCase();
+    directory
 
   # Public: Create a Directory that corresponds to the specified URI.
   #

src/window-event-handler.coffee

@@ -23,12 +23,12 @@ class WindowEventHandler
             if pathToOpen? and needsProjectPaths
               if fs.existsSync(pathToOpen)
                 atom.project.addPath(pathToOpen)
+              else if fs.existsSync(path.dirname(pathToOpen))
+                atom.project.addPath(path.dirname(pathToOpen))
               else
-                dirToOpen = path.dirname(pathToOpen)
-                if fs.existsSync(dirToOpen)
-                  atom.project.addPath(dirToOpen)
+                atom.project.addPath(pathToOpen)
 
-            unless fs.isDirectorySync(pathToOpen)
+            if fs.isFileSync(pathToOpen)
               atom.workspace?.open(pathToOpen, {initialLine, initialColumn})
 
           return