What am I doing wrong with this REBASE command?

I recently submitted another pull request and my team lead came back with a couple of changes and at one point he hinted at the fact that I may have done my rebase incorrectly.

As it turns out, the last time I ensured that my current branch was up to date with the newest and coolest was a couple of weeks ago.

So, here's what I did:

Made a copy of my current branch (final-activity-stream), just to make sure that I had copy of everything I had worked on
checkout out "code-cleanup" and did a "git pull" to make sure that branch was up to date with the remote repository
checked out "final-activity-stream" and did "git rebase code-cleanup"

At this point, I get a number of prompts that has me using my Merge Tool and I repair the conflicts.

It's here where I start getting a little concerned, because I repair them, save the file and get routed back to my Command Line. I type in "git rebase --continue" and I get another round of conflicts that I have to fix.

It seems like I would get the prompt to repair a bunch of conflicts only once, no?

In any event, I'm at the end of this odyssey and I see this:

b.gust@AHA-DT-BGUST2 MINGW64 /c/wamp64/www/bsmart (final-activity-stream|REBASE 28/32)
$ git status
rebase in progress; onto 6139829
You are currently rebasing branch 'final-activity-stream' on '6139829'.
  (all conflicts fixed: run "git rebase --continue")

Untracked files:
  (use "git add <file>..." to include in what will be committed)
       .vs/VSWorkspaceState.json.orig
        .vs/bsmart/v16/.suo.orig
        .vs/slnx.sqlite.orig
        public/assets/js/cams.js.orig
        public/assets/js/dashboard.js.orig
        server/lib/object-models.js.orig
        server/routes/companies.js.orig
        server/services/activity.js.orig
        views/partials/company-slide-out/history-tab.html.twig.orig
        views/pipeline.html.twig.orig
        views/reporting.html.twig.orig
        yarn.lock.orig

nothing added to commit but untracked files present (use "git add" to track)

checked out final-activity-stream,  

There's two things about the files that I have in bold that bug me.

First of all, every one of them has the "orig" file type attached to it. What is that? I've got a couple of those in my directory and I made the mistake of pushing them up to my remote branch. I would expect that all of the changes I've made as far as the merge tool that I used (P4 Merge), would be applied to the files themselves and not an ".orig" version.

What do I need to do based on the way I've described this scenario to complete the REBASE correctly?

Thanks!