diff --git a/spec/git-spec.coffee b/spec/git-spec.coffee
index f29f71397..3774f14c4 100644
--- a/spec/git-spec.coffee
+++ b/spec/git-spec.coffee
@@ -223,7 +223,7 @@ describe "GitRepository", ->
     [editor] = []
 
     beforeEach ->
-      atom.project.setPath(copyRepository())
+      atom.project.setPaths([copyRepository()])
 
       waitsForPromise ->
         atom.workspace.open('other.txt').then (o) -> editor = o
@@ -232,7 +232,7 @@ describe "GitRepository", ->
       editor.insertNewline()
 
       statusHandler = jasmine.createSpy('statusHandler')
-      atom.project.getRepo().onDidChangeStatus statusHandler
+      atom.project.getRepositories()[0].onDidChangeStatus statusHandler
       editor.save()
       expect(statusHandler.callCount).toBe 1
       expect(statusHandler).toHaveBeenCalledWith {path: editor.getPath(), pathStatus: 256}
@@ -241,7 +241,7 @@ describe "GitRepository", ->
       fs.writeFileSync(editor.getPath(), 'changed')
 
       statusHandler = jasmine.createSpy('statusHandler')
-      atom.project.getRepo().onDidChangeStatus statusHandler
+      atom.project.getRepositories()[0].onDidChangeStatus statusHandler
       editor.getBuffer().reload()
       expect(statusHandler.callCount).toBe 1
       expect(statusHandler).toHaveBeenCalledWith {path: editor.getPath(), pathStatus: 256}
@@ -252,7 +252,7 @@ describe "GitRepository", ->
       fs.writeFileSync(editor.getPath(), 'changed')
 
       statusHandler = jasmine.createSpy('statusHandler')
-      atom.project.getRepo().onDidChangeStatus statusHandler
+      atom.project.getRepositories()[0].onDidChangeStatus statusHandler
       editor.getBuffer().emitter.emit 'did-change-path'
       expect(statusHandler.callCount).toBe 1
       expect(statusHandler).toHaveBeenCalledWith {path: editor.getPath(), pathStatus: 256}
@@ -266,7 +266,7 @@ describe "GitRepository", ->
       project2?.destroy()
 
     it "subscribes to all the serialized buffers in the project", ->
-      atom.project.setPath(copyRepository())
+      atom.project.setPaths([copyRepository()])
 
       waitsForPromise ->
         atom.workspace.open('file.txt')
@@ -283,7 +283,7 @@ describe "GitRepository", ->
         buffer.append('changes')
 
         statusHandler = jasmine.createSpy('statusHandler')
-        project2.getRepo().onDidChangeStatus statusHandler
+        project2.getRepositories()[0].onDidChangeStatus statusHandler
         buffer.save()
         expect(statusHandler.callCount).toBe 1
         expect(statusHandler).toHaveBeenCalledWith {path: buffer.getPath(), pathStatus: 256}
diff --git a/spec/project-spec.coffee b/spec/project-spec.coffee
index 06e3ee29d..324772459 100644
--- a/spec/project-spec.coffee
+++ b/spec/project-spec.coffee
@@ -9,7 +9,7 @@ BufferedProcess = require '../src/buffered-process'
 
 describe "Project", ->
   beforeEach ->
-    atom.project.setPath(atom.project.resolve('dir'))
+    atom.project.setPaths([atom.project.resolve('dir')])
 
   describe "serialization", ->
     deserializedProject = null
@@ -41,8 +41,8 @@ describe "Project", ->
   describe "when an editor is saved and the project has no path", ->
     it "sets the project's path to the saved file's parent directory", ->
       tempFile = temp.openSync().path
-      atom.project.setPath(undefined)
-      expect(atom.project.getPath()).toBeUndefined()
+      atom.project.setPaths([])
+      expect(atom.project.getPaths()[0]).toBeUndefined()
       editor = null
 
       waitsForPromise ->
@@ -50,7 +50,7 @@ describe "Project", ->
 
       runs ->
         editor.saveAs(tempFile)
-        expect(atom.project.getPath()).toBe path.dirname(tempFile)
+        expect(atom.project.getPaths()[0]).toBe path.dirname(tempFile)
 
   describe ".open(path)", ->
     [absolutePath, newBufferHandler] = []
@@ -164,7 +164,7 @@ describe "Project", ->
 
     describe "when the project has no path", ->
       it "returns undefined for relative URIs", ->
-        atom.project.setPath()
+        atom.project.setPaths([])
         expect(atom.project.resolve('test.txt')).toBeUndefined()
         expect(atom.project.resolve('http://github.com')).toBe 'http://github.com'
         absolutePath = fs.absolute(__dirname)
@@ -173,33 +173,33 @@ describe "Project", ->
   describe ".setPath(path)", ->
     describe "when path is a file", ->
       it "sets its path to the files parent directory and updates the root directory", ->
-        atom.project.setPath(require.resolve('./fixtures/dir/a'))
-        expect(atom.project.getPath()).toEqual path.dirname(require.resolve('./fixtures/dir/a'))
+        atom.project.setPaths([require.resolve('./fixtures/dir/a')])
+        expect(atom.project.getPaths()[0]).toEqual path.dirname(require.resolve('./fixtures/dir/a'))
         expect(atom.project.getRootDirectory().path).toEqual path.dirname(require.resolve('./fixtures/dir/a'))
 
     describe "when path is a directory", ->
       it "sets its path to the directory and updates the root directory", ->
         directory = fs.absolute(path.join(__dirname, 'fixtures', 'dir', 'a-dir'))
-        atom.project.setPath(directory)
-        expect(atom.project.getPath()).toEqual directory
+        atom.project.setPaths([directory])
+        expect(atom.project.getPaths()[0]).toEqual directory
         expect(atom.project.getRootDirectory().path).toEqual directory
 
     describe "when path is null", ->
       it "sets its path and root directory to null", ->
-        atom.project.setPath(null)
-        expect(atom.project.getPath()?).toBeFalsy()
+        atom.project.setPaths([])
+        expect(atom.project.getPaths()[0]?).toBeFalsy()
         expect(atom.project.getRootDirectory()?).toBeFalsy()
 
     it "normalizes the path to remove consecutive slashes, ., and .. segments", ->
-      atom.project.setPath("#{require.resolve('./fixtures/dir/a')}#{path.sep}b#{path.sep}#{path.sep}..")
-      expect(atom.project.getPath()).toEqual path.dirname(require.resolve('./fixtures/dir/a'))
+      atom.project.setPaths(["#{require.resolve('./fixtures/dir/a')}#{path.sep}b#{path.sep}#{path.sep}.."])
+      expect(atom.project.getPaths()[0]).toEqual path.dirname(require.resolve('./fixtures/dir/a'))
       expect(atom.project.getRootDirectory().path).toEqual path.dirname(require.resolve('./fixtures/dir/a'))
 
   describe ".replace()", ->
     [filePath, commentFilePath, sampleContent, sampleCommentContent] = []
 
     beforeEach ->
-      atom.project.setPath(atom.project.resolve('../'))
+      atom.project.setPaths([atom.project.resolve('../')])
 
       filePath = atom.project.resolve('sample.js')
       commentFilePath = atom.project.resolve('sample-with-comments.js')
@@ -332,7 +332,7 @@ describe "Project", ->
 
       it "works on evil filenames", ->
         platform.generateEvilFiles()
-        atom.project.setPath(path.join(__dirname, 'fixtures', 'evil-files'))
+        atom.project.setPaths([path.join(__dirname, 'fixtures', 'evil-files')])
         paths = []
         matches = []
         waitsForPromise ->
@@ -387,7 +387,7 @@ describe "Project", ->
           fs.removeSync(projectPath) if fs.existsSync(projectPath)
 
         it "excludes ignored files", ->
-          atom.project.setPath(projectPath)
+          atom.project.setPaths([projectPath])
           atom.config.set('core.excludeVcsIgnoredPaths', true)
           resultHandler = jasmine.createSpy("result found")
           waitsForPromise ->
@@ -399,7 +399,7 @@ describe "Project", ->
 
       it "includes only files when a directory filter is specified", ->
         projectPath = path.join(path.join(__dirname, 'fixtures', 'dir'))
-        atom.project.setPath(projectPath)
+        atom.project.setPaths([projectPath])
 
         filePath = path.join(projectPath, 'a-dir', 'oh-git')
 
@@ -419,7 +419,7 @@ describe "Project", ->
         projectPath = temp.mkdirSync()
         filePath = path.join(projectPath, '.text')
         fs.writeFileSync(filePath, 'match this')
-        atom.project.setPath(projectPath)
+        atom.project.setPaths([projectPath])
         paths = []
         matches = []
         waitsForPromise ->
diff --git a/spec/spec-helper.coffee b/spec/spec-helper.coffee
index cc5f05c1f..199959f19 100644
--- a/spec/spec-helper.coffee
+++ b/spec/spec-helper.coffee
@@ -62,7 +62,7 @@ beforeEach ->
   Grim.clearDeprecations() if isCoreSpec
   $.fx.off = true
   projectPath = specProjectPath ? path.join(@specDirectory, 'fixtures')
-  atom.project = new Project(path: projectPath)
+  atom.project = new Project(paths: [projectPath])
   atom.workspace = new Workspace()
   atom.keymaps.keyBindings = _.clone(keyBindingsToRestore)
   atom.commands.setRootNode(document.body)
diff --git a/spec/window-spec.coffee b/spec/window-spec.coffee
index 5f12a51fe..0a60c302f 100644
--- a/spec/window-spec.coffee
+++ b/spec/window-spec.coffee
@@ -8,7 +8,7 @@ describe "Window", ->
 
   beforeEach ->
     spyOn(atom, 'hide')
-    initialPath = atom.project.getPath()
+    initialPath = atom.project.getPaths()[0]
     spyOn(atom, 'getLoadSettings').andCallFake ->
       loadSettings = atom.getLoadSettings.originalValue.call(atom)
       loadSettings.initialPath = initialPath
@@ -16,7 +16,7 @@ describe "Window", ->
     atom.project.destroy()
     windowEventHandler = new WindowEventHandler()
     atom.deserializeEditorWindow()
-    projectPath = atom.project.getPath()
+    projectPath = atom.project.getPaths()[0]
 
   afterEach ->
     windowEventHandler.unsubscribe()
@@ -263,19 +263,19 @@ describe "Window", ->
 
     describe "when the project does not have a path", ->
       beforeEach ->
-        atom.project.setPath()
+        atom.project.setPaths([])
 
       describe "when the opened path exists", ->
         it "sets the project path to the opened path", ->
           $(window).trigger('window:open-path', [{pathToOpen: __filename}])
 
-          expect(atom.project.getPath()).toBe __dirname
+          expect(atom.project.getPaths()[0]).toBe __dirname
 
       describe "when the opened path does not exist but its parent directory does", ->
         it "sets the project path to the opened path's parent directory", ->
           $(window).trigger('window:open-path', [{pathToOpen: path.join(__dirname, 'this-path-does-not-exist.txt')}])
 
-          expect(atom.project.getPath()).toBe __dirname
+          expect(atom.project.getPaths()[0]).toBe __dirname
 
     describe "when the opened path is a file", ->
       it "opens it in the workspace", ->
diff --git a/spec/workspace-spec.coffee b/spec/workspace-spec.coffee
index a175245a6..9e4ea2b7c 100644
--- a/spec/workspace-spec.coffee
+++ b/spec/workspace-spec.coffee
@@ -5,7 +5,7 @@ describe "Workspace", ->
   workspace = null
 
   beforeEach ->
-    atom.project.setPath(atom.project.resolve('dir'))
+    atom.project.setPaths([atom.project.resolve('dir')])
     atom.workspace = workspace = new Workspace
 
   describe "::open(uri, options)", ->
diff --git a/spec/workspace-view-spec.coffee b/spec/workspace-view-spec.coffee
index f47b75e85..f2abe04f5 100644
--- a/spec/workspace-view-spec.coffee
+++ b/spec/workspace-view-spec.coffee
@@ -10,7 +10,7 @@ describe "WorkspaceView", ->
   pathToOpen = null
 
   beforeEach ->
-    atom.project.setPath(atom.project.resolve('dir'))
+    atom.project.setPaths([atom.project.resolve('dir')])
     pathToOpen = atom.project.resolve('a')
     atom.workspace = new Workspace
     atom.workspaceView = atom.workspace.getView(atom.workspace).__spacePenView
@@ -49,7 +49,7 @@ describe "WorkspaceView", ->
 
           expect(atom.workspaceView.getEditorViews().length).toBe 2
           expect(atom.workspaceView.getActivePaneView()).toBe atom.workspaceView.getPaneViews()[1]
-          expect(atom.workspaceView.title).toBe "untitled - #{atom.project.getPath()}"
+          expect(atom.workspaceView.title).toBe "untitled - #{atom.project.getPaths()[0]}"
 
     describe "when there are open editors", ->
       it "constructs the view with the same panes", ->
@@ -106,7 +106,7 @@ describe "WorkspaceView", ->
           expect(editorView3).not.toHaveFocus()
           expect(editorView4).not.toHaveFocus()
 
-          expect(atom.workspaceView.title).toBe "#{path.basename(editorView2.getEditor().getPath())} - #{atom.project.getPath()}"
+          expect(atom.workspaceView.title).toBe "#{path.basename(editorView2.getEditor().getPath())} - #{atom.project.getPaths()[0]}"
 
     describe "where there are no open editors", ->
       it "constructs the view with no open editors", ->
@@ -144,7 +144,7 @@ describe "WorkspaceView", ->
   describe "window title", ->
     describe "when the project has no path", ->
       it "sets the title to 'untitled'", ->
-        atom.project.setPath(undefined)
+        atom.project.setPaths([])
         expect(atom.workspaceView.title).toBe 'untitled'
 
     describe "when the project has a path", ->
@@ -155,25 +155,25 @@ describe "WorkspaceView", ->
       describe "when there is an active pane item", ->
         it "sets the title to the pane item's title plus the project path", ->
           item = atom.workspace.getActivePaneItem()
-          expect(atom.workspaceView.title).toBe "#{item.getTitle()} - #{atom.project.getPath()}"
+          expect(atom.workspaceView.title).toBe "#{item.getTitle()} - #{atom.project.getPaths()[0]}"
 
       describe "when the title of the active pane item changes", ->
         it "updates the window title based on the item's new title", ->
           editor = atom.workspace.getActivePaneItem()
           editor.buffer.setPath(path.join(temp.dir, 'hi'))
-          expect(atom.workspaceView.title).toBe "#{editor.getTitle()} - #{atom.project.getPath()}"
+          expect(atom.workspaceView.title).toBe "#{editor.getTitle()} - #{atom.project.getPaths()[0]}"
 
       describe "when the active pane's item changes", ->
         it "updates the title to the new item's title plus the project path", ->
           atom.workspaceView.getActivePaneView().activateNextItem()
           item = atom.workspace.getActivePaneItem()
-          expect(atom.workspaceView.title).toBe "#{item.getTitle()} - #{atom.project.getPath()}"
+          expect(atom.workspaceView.title).toBe "#{item.getTitle()} - #{atom.project.getPaths()[0]}"
 
       describe "when the last pane item is removed", ->
         it "updates the title to contain the project's path", ->
           atom.workspaceView.getActivePaneView().remove()
           expect(atom.workspace.getActivePaneItem()).toBeUndefined()
-          expect(atom.workspaceView.title).toBe atom.project.getPath()
+          expect(atom.workspaceView.title).toBe atom.project.getPaths()[0]
 
       describe "when an inactive pane's item changes", ->
         it "does not update the title", ->
@@ -188,7 +188,7 @@ describe "WorkspaceView", ->
         workspace2 = atom.workspace.testSerialization()
         workspaceView2 = workspace2.getView(workspace2).__spacePenView
         item = atom.workspace.getActivePaneItem()
-        expect(workspaceView2.title).toBe "#{item.getTitle()} - #{atom.project.getPath()}"
+        expect(workspaceView2.title).toBe "#{item.getTitle()} - #{atom.project.getPaths()[0]}"
         workspaceView2.remove()
 
   describe "window:toggle-invisibles event", ->
diff --git a/src/atom.coffee b/src/atom.coffee
index 688bec833..1dc2fedea 100644
--- a/src/atom.coffee
+++ b/src/atom.coffee
@@ -577,7 +577,7 @@ class Atom extends Model
     Project = require './project'
 
     startTime = Date.now()
-    @project ?= @deserializers.deserialize(@state.project) ? new Project(path: @getLoadSettings().initialPath)
+    @project ?= @deserializers.deserialize(@state.project) ? new Project(paths: [@getLoadSettings().initialPath])
     @deserializeTimings.project = Date.now() - startTime
 
   deserializeWorkspaceView: ->
@@ -619,7 +619,7 @@ class Atom extends Model
   # Notify the browser project of the window's current project path
   watchProjectPath: ->
     onProjectPathChanged = =>
-      ipc.send('window-command', 'project-path-changed', @project.getPath())
+      ipc.send('window-command', 'project-path-changed', @project.getPaths()[0])
     @subscribe @project, 'path-changed', onProjectPathChanged
     onProjectPathChanged()
 
diff --git a/src/project.coffee b/src/project.coffee
index e57969436..9f0f3dbfe 100644
--- a/src/project.coffee
+++ b/src/project.coffee
@@ -10,6 +10,7 @@ Q = require 'q'
 Serializable = require 'serializable'
 TextBuffer = require 'text-buffer'
 {Directory} = require 'pathwatcher'
+Grim = require 'grim'
 
 TextEditor = require './text-editor'
 Task = require './task'
@@ -33,14 +34,16 @@ class Project extends Model
   Section: Construction and Destruction
   ###
 
-  constructor: ({path, @buffers}={}) ->
+  constructor: ({path, paths, @buffers}={}) ->
     @buffers ?= []
 
     for buffer in @buffers
       do (buffer) =>
         buffer.onDidDestroy => @removeBuffer(buffer)
 
-    @setPath(path)
+    Grim.deprecate("Pass 'paths' array instead of 'path' to project constructor") if path?
+    paths ?= _.compact([path])
+    @setPaths(paths)
 
   destroyed: ->
     buffer.destroy() for buffer in @getBuffers()
@@ -70,21 +73,30 @@ class Project extends Model
   Section: Accessing the git repository
   ###
 
-  # Public: Returns the {GitRepository} if available.
-  getRepo: -> @repo
+  # Public: Get an {Array} of {GitRepository}s associated with the project's
+  # directories.
+  getRepositories: -> _.compact([@repo])
+  getRepo: ->
+    Grim.deprecate("Use ::getRepositories instead")
+    @repo
 
   ###
   Section: Managing Paths
   ###
 
-  # Public: Returns the project's {String} fullpath.
+
+  # Public: Get an {Array} of {String}s containing the paths of the project's
+  # directories.
+  getPaths: -> _.compact([@rootDirectory?.path])
   getPath: ->
+    Grim.deprecate("Use ::getPaths instead")
     @rootDirectory?.path
 
-  # Public: Sets the project's fullpath.
+  # Public: Set the paths of the project's directories.
   #
-  # * `projectPath` {String} path
-  setPath: (projectPath) ->
+  # * `projectPaths` {Array} of {String} paths.
+  setPaths: (projectPaths) ->
+    [projectPath] = projectPaths
     projectPath = path.normalize(projectPath) if projectPath
     @path = projectPath
     @rootDirectory?.off()
@@ -100,9 +112,15 @@ class Project extends Model
       @rootDirectory = null
 
     @emit "path-changed"
+  setPath: (path) ->
+    Grim.deprecate("Use ::setPaths instead")
+    @setPaths([path])
 
-  # Public: Returns the root {Directory} object for this project.
+  # Public: Get an {Array} of {Directory}s associated with this project.
+  getDirectories: ->
+    [@rootDirectory]
   getRootDirectory: ->
+    Grim.deprecate("Use ::getDirectories instead")
     @rootDirectory
 
   # Public: Given a uri, this resolves it relative to the project directory. If
@@ -120,7 +138,7 @@ class Project extends Model
     else
       if fs.isAbsolute(uri)
         path.normalize(fs.absolute(uri))
-      else if projectPath = @getPath()
+      else if projectPath = @getPaths()[0]
         path.normalize(fs.absolute(path.join(projectPath, uri)))
       else
         undefined
diff --git a/src/text-editor-component.coffee b/src/text-editor-component.coffee
index 8519ac21d..5b2dd61d4 100644
--- a/src/text-editor-component.coffee
+++ b/src/text-editor-component.coffee
@@ -500,7 +500,7 @@ TextEditorComponent = React.createClass
         'editor:fold-at-indent-level-9': -> editor.foldAllAtIndentLevel(8)
         'editor:toggle-line-comments': -> editor.toggleLineCommentsInSelection()
         'editor:log-cursor-scope': -> editor.logCursorScope()
-        'editor:checkout-head-revision': -> atom.project.getRepo()?.checkoutHeadForEditor(editor)
+        'editor:checkout-head-revision': -> atom.project.getRepositories()[0]()?.checkoutHeadForEditor(editor)
         'editor:copy-path': -> editor.copyPathToClipboard()
         'editor:move-line-up': -> editor.moveLineUp()
         'editor:move-line-down': -> editor.moveLineDown()
diff --git a/src/text-editor.coffee b/src/text-editor.coffee
index 1e3eba11b..2bd07102a 100644
--- a/src/text-editor.coffee
+++ b/src/text-editor.coffee
@@ -133,8 +133,8 @@ class TextEditor extends Model
   subscribeToBuffer: ->
     @buffer.retain()
     @subscribe @buffer.onDidChangePath =>
-      unless atom.project.getPath()?
-        atom.project.setPath(path.dirname(@getPath()))
+      unless atom.project.getPaths()[0]?
+        atom.project.setPaths([path.dirname(@getPath())])
       @emit "title-changed"
       @emitter.emit 'did-change-title', @getTitle()
       @emit "path-changed"
diff --git a/src/workspace-view.coffee b/src/workspace-view.coffee
index 255ec3b5b..52898a0d4 100644
--- a/src/workspace-view.coffee
+++ b/src/workspace-view.coffee
@@ -136,7 +136,7 @@ class WorkspaceView extends View
     if process.platform is 'darwin'
       @command 'window:install-shell-commands', => @installShellCommands()
 
-    @command 'window:run-package-specs', -> ipc.send('run-package-specs', path.join(atom.project.getPath(), 'spec'))
+    @command 'window:run-package-specs', -> ipc.send('run-package-specs', path.join(atom.project.getPaths()[0], 'spec'))
 
     @command 'window:focus-next-pane', => @focusNextPaneView()
     @command 'window:focus-previous-pane', => @focusPreviousPaneView()
@@ -367,7 +367,7 @@ class WorkspaceView extends View
   # Updates the application's title and proxy icon based on whichever file is
   # open.
   updateTitle: ->
-    if projectPath = atom.project.getPath()
+    if projectPath = atom.project.getPaths()[0]
       if item = @getModel().getActivePaneItem()
         title = "#{item.getTitle?() ? 'untitled'} - #{projectPath}"
         @setTitle(title, item.getPath?())