fix files not being committed

Author: zeapo

app/src/main/java/com/zeapo/pwdstore/PasswordStore.java

@@ -573,13 +573,13 @@ private void commitChange(final String message) {
             public void execute(boolean finishOnEnd) {
                 Log.d(TAG, "Commiting with message " + message);
                 Git git = new Git(this.repository);
-                GitAsyncTask tasks = new GitAsyncTask(activity, false, true, this);
+                GitAsyncTask tasks = new GitAsyncTask(activity, finishOnEnd, true, this);
                 tasks.execute(
                         git.add().addFilepattern("."),
-                        git.commit().setMessage(message)
+                        git.commit().setAll(true).setMessage(message)
                 );
             }
-        }.execute(true);
+        }.execute(false);
     }
 
     protected void onActivityResult(int requestCode, int resultCode,

app/src/main/java/com/zeapo/pwdstore/git/GitAsyncTask.java

@@ -64,7 +64,8 @@ protected String doInBackground(GitCommand... commands) {
             try {
                 if (command instanceof StatusCommand) {
                     // in case we have changes, we want to keep track of it
-                    nbChanges = ((StatusCommand) command).call().getChanged().size();
+                    org.eclipse.jgit.api.Status status = ((StatusCommand) command).call();
+                    nbChanges = status.getChanged().size() + status.getMissing().size();
                 } else if (command instanceof CommitCommand) {
                     // the previous status will eventually be used to avoid a commit
                     if (nbChanges == null || nbChanges > 0)

app/src/main/java/com/zeapo/pwdstore/git/SyncOperation.java

@@ -41,7 +41,7 @@ public SyncOperation setCommands() {
         Git git = new Git(repository);
         this.addCommand = git.add().addFilepattern(".");
         this.statusCommand = git.status();
-        this.commitCommand = git.commit().setMessage("[Android Password Store] Sync");
+        this.commitCommand = git.commit().setAll(true).setMessage("[Android Password Store] Sync");
         this.pullCommand = git.pull().setRebase(true).setRemote("origin");
         this.pushCommand = git.push().setPushAll().setRemote("origin");
         return this;