Git merge with beyond compare

Question

I've recently purchased beyond compare pro to merge code shared with git (of which I have a very limited understanding). I now have two branches, a master and a feature. I recently pulled the master from remote so that now the master is a few commits ahead of the common ancestor between master and feature.

Since my branch feature has mostly deletions I want to merge master into feature and not the reverse (does this make sense?). So I basically did

git checkout master
git pull origin master
git push origin master

So at this point my feature is a few commits behind and a few commits ahead of master. To merge the commits of master into feature I did:

git checkout feature
git merge master
git mergetool

Now I'm prompted with a series of messages like

Deleted merge conflict for 'ED/build/make/rules.mk':
  {local}: deleted
  {remote}: modified file
Use (m)odified or (d)eleted file, or (a)bort? m

Normal merge conflict for 'ED/src/driver/ed_model.F90':
  {local}: modified file
  {remote}: modified file
merge of ED/src/driver/ed_model.F90 failed
Continue merging other unresolved paths [y/n]? y

All other files give a failed merge error without even opening the beyondcompare mergetool to do the merge.

The first prompt says (m)odified or (d)eleted, does this mean that I have to choose which file to select between local and remote as a result of the merge?
The second prompt tells me that the merge failed, why is this happening?

EDIT

The relevant part of my .gitconfig is

[diff]
    tool = bc3
[difftool]
        prompt = false
[difftool "bc3"]
    trustExitCode = true
[core]
    fileMode = false
    symlink = false
    ignorecase = true
[merge]
    tool = bc3
[mergetool "bc3"]
    trustExitCode = true
[alias]
    difftool = difftool --dir-dif --no-symlinks

Git merge with beyond compare

2 Answers