git rebase merge conflict

I forked a github repo and worked on my github repo.
I have made pull-requests and it was completed.

After that the upstream had some more commits so now I want to rebase, I guess thats what I have to do.
But I'm getting these merge conflicts:

First, rewinding head to replay your work on top of it...
Applying: Issue 135 homepage refresh
Using index info to reconstruct a base tree...
<stdin>:17: trailing whitespace.
      %h4 
warning: 1 line adds whitespace errors.
Falling back to patching base and 3-way merge...
Auto-merging app/views/layouts/application.html.haml
CONFLICT (content): Merge conflict in app/views/layouts/application.html.haml
Auto-merging app/views/home/index.html.haml
CONFLICT (content): Merge conflict in app/views/home/index.html.haml
Auto-merging app/views/home/_group_projects.html.haml
CONFLICT (content): Merge conflict in app/views/home/_group_projects.html.haml
Failed to merge in the changes.
Patch failed at 0001 Issue 135 homepage refresh

When you have resolved this problem run "git rebase --continue".
If you would prefer to skip this patch, instead run "git rebase --skip".
To check out the original branch and stop rebasing run "git rebase --abort".

I don't know how to fix these, please help.

Rebasing can be a real headache. You have to resolve the merge conflicts and continue rebasing. For example you can use the merge tool (which differs depending on your settings)

git mergetool

Then add your changes and go on

git rebase --continue

Good luck

If you have a lot of commits to rebase, and some part of them are giving conflicts, that really hurts. But I can suggest a less-known approach how to "squash all the conflicts".

First, checkout temp branch and start standard merge

git checkout -b temp
git merge origin/master

You will have to resolve conflicts, but only once and only real ones. Then stage all files and finish merge.

git commit -m "Merge branch 'origin/master' into 'temp'"

Then return to your branch (let it be alpha) and start rebase, but with automatical resolving any conflicts.

git checkout alpha
git rebase origin/master -X theirs

Branch has been rebased, but project is probably in invalid state. That's OK, we have one final step. We just need to restore project state, so it will be exact as on branch 'temp'. Technically we just need to copy its tree (folder state) via low-level command git commit-tree. Plus merging into current branch just created commit.

git merge --ff $(git commit-tree temp^{tree} -m "Fix after rebase" -p HEAD)

And delete temporary branch

git branch -D temp

That's all. We did a rebase via hidden merge.

Also I wrote a script, so that can be done in a dialog manner, you can find it here.