Unstaged type changes and deletions are misrecognized as staged changes

[mlell]

Hi, thank you for maintaining this script, it helps me every day!

I am using git annex, so my repository contains a lot of symlinks (git-annex maintains a separate storage of large files in .git/ and commits symlinks to these files instead of the big files themselves). The files that are annexed are results of a scientific pipeline, so when the computation is executed, it will replace the committed version (i.e., the symlinks) by a regular file with the new content. Executing git annex add will move these files to the annex storage and create new symlinks in their place. This means that I get a lot of "typechange" git status outputs:

$ git status
On branch master
Changes not staged for commit:
  (use "git add/rm <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
        modified:   .doit.db.db
        deleted:    data/03 Merge genomic and phenotypic/BLUEs/blues_across.qs
        deleted:    data/03 Merge genomic and phenotypic/BLUEs/blues_within.qs
        typechange: data/03 Merge genomic and phenotypic/Match genotype names/ARGV.rds
        typechange: data/03 Merge genomic and phenotypic/Match genotype names/genotypes.fst

or when using git status -s:

$ git status -s
 M .doit.db.db
 D "data/03 Merge genomic and phenotypic/BLUEs/blues_across.qs"
 D "data/03 Merge genomic and phenotypic/BLUEs/blues_within.qs"
 T "data/03 Merge genomic and phenotypic/Match genotype names/ARGV.rds"
 T "data/03 Merge genomic and phenotypic/Match genotype names/genotypes.fst"

• Expectation: bash-git-prompt shows [master L|✚ 5]
• Actual behaviour: bash-git-prompt shows [master L|●2✚ 3]
• Version of bash-git-prompt: 5cf208c` (2023-10-12)

So it shows my deletions and typechanges are staged changes.