git merge ignores deleted files, existing on merged branch (renamed files)

Question

I've got the branches feature1 and master.
Then in feature1 I renamed a file dir/file.txt into dir2/file2.txt.
After that I altered the file in master and a week later altered the file in feature1 too.

I have 40 files changed like that across the project.
When I try to merge master into feature1 I'm using low renaming threshold. Most of the files are auto-merged correctly. Some files are offered for manual conflict resolution.

But some concrete files neither appear in the merge response as auto-merged,
nor getting merged properly. Under properly I expect one of two outcomes I could resolve:
1. It wouldnt detect renaming and just add me another dir/file.txt into the feature1 branch.
2. It would detect renaming and offer me to manually resolve conflict.

There are many changes when I view them with
git difftool master:dir/file.txt feature1:dir2/file2.txt

Therefore I assume that git recognizes the renaming and decides to keep my version without informing me about what's going on. How can I solve it / debug it ?

This is the command I use

git config merge.renameLimit 9999999999
git merge --no-ff -Xrename-threshold=20 -Xignore-space-change master

Upd1

While working with feature1 branch, I had deleted dir/file.txt.
Maybe git assumes this file should be deleted and therefore ignores it's existence in master.
Renaming detection fails, although the similarity of the files is kept ( levenshtein distance is less than 2% of the content's length )
Another discussion suggests 'manual merge' copying files from branch to branch.

Upd2

Some other files are resolved correctly
CONFLICT (rename/delete): images/ab.gif deleted in master and renamed in HEAD. Version HEAD of cdn/img/ab.gif left in tree.
Files that were removed in master and merged into feature1 are resolved correctly. Files that are deleted (or moved) in feature1 ain't recognized at the merge.
Sugestions?

Upd3

At the moment I'm trying to merge the other way around. Merge feature1 into master and see what files are being added and removed. This way I'll a list of files git fail's to recognize as renames and resort to manual merging.

Answer 1

If you are deleting files from your repo - git is tracking this deletion and the merge is considering this when determining what to do.

This is probably not all that you have going on, but it is part of it. You can try git add'ing them again.