Show staged status of files, and don't commit any files that aren't checked

If a file is staged outside of Unity, this makes sure the check box is checked
automatically when listing changed files. If the user unchecks a file that has
been staged for commit outside of Unity, we remove the file from the index
right before commiting all the (other) checked files, to make sure
WICIWIC (What Is Checked Is What Is Commited)

Author: shana

src/GitHub.Api/Git/TreeData.cs

@@ -7,6 +7,7 @@ public interface ITreeData
     {
         string Path { get; }
         bool IsActive { get; }
+        bool IsChecked { get; }
     }
 
     [Serializable]
@@ -64,6 +65,7 @@ public bool Equals(GitBranchTreeData other)
 
         public string Path => GitBranch.Name;
         public bool IsActive => isActive;
+        public bool IsChecked => false;
     }
 
     [Serializable]
@@ -73,11 +75,13 @@ public struct GitStatusEntryTreeData : ITreeData
 
         public GitStatusEntry gitStatusEntry;
         public bool isLocked;
+        public bool isChecked;
 
         public GitStatusEntryTreeData(GitStatusEntry gitStatusEntry, bool isLocked = false)
         {
             this.isLocked = isLocked;
             this.gitStatusEntry = gitStatusEntry;
+            isChecked = gitStatusEntry.Staged;
         }
 
         public override int GetHashCode()
@@ -127,5 +131,6 @@ public bool Equals(GitStatusEntryTreeData other)
         public GitStatusEntry GitStatusEntry => gitStatusEntry;
         public GitFileStatus FileStatus => gitStatusEntry.Status;
         public bool IsLocked => isLocked;
+        public bool IsChecked => isChecked;
     }
-}
+}

src/GitHub.Api/UI/TreeBase.cs

@@ -118,7 +118,7 @@ public void Load(IEnumerable<TData> treeDatas)
                         {
                             isActive = treeData.IsActive;
                             treeNodeTreeData = treeData;
-                            isChecked = isCheckable && checkedFiles.Contains(nodePath);
+                            isChecked = isCheckable && (checkedFiles.Contains(nodePath) || treeData.IsChecked);
                         }
 
                         isSelected = selectedNodePath != null && nodePath == selectedNodePath;

src/UnityExtension/Assets/Editor/GitHub.Unity/UI/ChangesView.cs

@@ -478,19 +478,26 @@ private void Commit()
         {
             isBusy = true;
             var files = treeChanges.GetCheckedFiles().ToList();
-            ITask addTask;
+            ITask addTask = null;
 
             if (files.Count == gitStatusEntries.Count)
             {
                 addTask = Repository.CommitAllFiles(commitMessage, commitBody);
             }
             else
             {
-                addTask = Repository.CommitFiles(files, commitMessage, commitBody);
+                ITask commit = Repository.CommitFiles(files, commitMessage, commitBody);
+
+                // if there are files that have been staged outside of Unity, but they aren't selected for commit, remove them
+                // from the index before commiting, otherwise the commit will take them along.
+                var filesStagedButNotChecked = gitStatusEntries.Where(x => x.Staged).Select(x => x.Path).Except(files).ToList();
+                if (filesStagedButNotChecked.Count > 0)
+                    addTask = GitClient.Remove(filesStagedButNotChecked);
+                addTask = addTask == null ? commit : addTask.Then(commit);
             }
 
             addTask
-                .FinallyInUI((success, exception) => 
+                .FinallyInUI((success, exception) =>
                     {
                         if (success)
                         {

src/tests/UnitTests/UI/TreeBaseTests.cs

@@ -35,6 +35,7 @@ public struct TestTreeData : ITreeData
 
         public string Path { get; set; }
         public bool IsActive { get; set; }
+        public bool IsChecked { get; set; }
 
         public override string ToString()
         {