IDEA-191309 git: update staging area using "git add -A" on commit

Unify logic for deleted, new, modified, renamed, etc files.
This prevents possible "Deleted-Unversioned" file status when
we expected file to be removed, but it is actually a modification on disk.
(ex: because pre-commit hook recreated a file that was deleted before)

Use "-A" as a parameter for "addPaths", to unify logic between git versions.
(This flag is set by default since git 2.0.0)

plugins/git4idea/src/git4idea/checkin/GitCheckinEnvironment.java

@@ -646,26 +646,17 @@ public class GitCheckinEnvironment implements CheckinEnvironment {
                                      final Collection<FilePath> added,
                                      final Collection<FilePath> removed,
                                      final List<VcsException> exceptions) {
-    boolean rc = true;
-    if (!added.isEmpty()) {
-      try {
-        GitFileUtils.addPaths(project, root, added);
-      }
-      catch (VcsException ex) {
-        exceptions.add(ex);
-        rc = false;
-      }
+    try {
+      List<FilePath> files = new ArrayList<>();
+      files.addAll(added);
+      files.addAll(removed);
+      GitFileUtils.addPaths(project, root, files);
+      return true;
     }
-    if (!removed.isEmpty()) {
-      try {
-        GitFileUtils.delete(project, root, removed, "--ignore-unmatch", "--cached");
-      }
-      catch (VcsException ex) {
-        exceptions.add(ex);
-        rc = false;
-      }
+    catch (VcsException ex) {
+      exceptions.add(ex);
+      return false;
     }
-    return rc;
   }
 
   /**

plugins/git4idea/src/git4idea/util/GitFileUtils.java

@@ -23,7 +23,10 @@ import com.intellij.openapi.vcs.VcsException;
 import com.intellij.openapi.vfs.VirtualFile;
 import com.intellij.vcsUtil.VcsFileUtil;
 import git4idea.GitUtil;
-import git4idea.commands.*;
+import git4idea.commands.Git;
+import git4idea.commands.GitBinaryHandler;
+import git4idea.commands.GitCommand;
+import git4idea.commands.GitLineHandler;
 import git4idea.repo.GitRepository;
 import org.jetbrains.annotations.NotNull;
 
@@ -126,7 +129,7 @@ public class GitFileUtils {
         continue;
       }
       GitLineHandler handler = new GitLineHandler(project, root, GitCommand.ADD);
-      handler.addParameters("--ignore-errors");
+      handler.addParameters("--ignore-errors", "-A");
       handler.endOptions();
       handler.addParameters(paths);
       Git.getInstance().runCommand(handler).getOutputOrThrow();