This may or may not be considered a bug, given the empty file, but I thought it would be prudent to report it just in case. When moving/renaming a tracked file, and then creating a new file with the original name, stash loses/deletes the new file. Below is the full transaction to reproduce the behavior.
-- Quin Hoxie
[quin@qmbp /tmp] $ mkdir repo [quin@qmbp /tmp] $ cd repo [quin@qmbp /tmp/repo] $ git init Initialized empty Git repository in /private/tmp/repo/.git/ [quin@qmbp /tmp/repo] $ echo "hello world" > foo [quin@qmbp /tmp/repo] $ git add foo [quin@qmbp /tmp/repo] $ git commit -m "added foo" [master (root-commit)]: created 9ed55f1: "added foo" 1 files changed, 1 insertions(+), 0 deletions(-) create mode 100644 foo [quin@qmbp /tmp/repo] $ git mv foo bar [quin@qmbp /tmp/repo] $ git status # On branch master # Changes to be committed: # (use "git reset HEAD <file>..." to unstage) # # renamed: foo -> bar # [quin@qmbp /tmp/repo] $ touch foo [quin@qmbp /tmp/repo] $ git status # On branch master # Changes to be committed: # (use "git reset HEAD <file>..." to unstage) # # renamed: foo -> bar # # Untracked files: # (use "git add <file>..." to include in what will be committed) # # foo [quin@qmbp /tmp/repo] $ git stash Saved working directory and index state "WIP on master: 9ed55f1... added foo" HEAD is now at 9ed55f1 added foo (To restore them type "git stash apply") [quin@qmbp /tmp/repo] $ git stash apply # On branch master # Changes to be committed: # (use "git reset HEAD <file>..." to unstage) # # new file: bar # # Changed but not updated: # (use "git add/rm <file>..." to update what will be committed) # (use "git checkout -- <file>..." to discard changes in working directory) # # deleted: foo # [quin@qmbp /tmp/repo] $ ls bar [quin@qmbp /tmp/repo] $