Git untracked files list is wrong

Question

Somehow, git got it in its head that I have an untracked file (A directory that has been in my repository for quite some time, ~17 months). At any rate, I can't seem to convince git that this is not an untracked file. Furthermore, I can't re-add the file(s) in question. Any idea how I can fix this?

Example:

➜ git status # On branch master # Untracked files: #   (use "git add <file>..." to include in what will be committed) # #   rosetta_tests/profile/tests/docking/ nothing added to commit but untracked files present (use "git add" to track) 

I try to add the directory and re-check the status.

➜ git add rosetta_tests/profile/tests/docking/ ➜ git status # On branch master # Untracked files: #   (use "git add <file>..." to include in what will be committed) # #   rosetta_tests/profile/tests/docking/ nothing added to commit but untracked files present (use "git add" to track) 

Just to be sure (from the root of my source tree)

➜ git add . ➜ git status # On branch master # Untracked files: #   (use "git add <file>..." to include in what will be committed) # #   rosetta_tests/profile/tests/docking/ nothing added to commit but untracked files present (use "git add" to track) 

What is going on here? How can I convince git to fix itself?

EDIT

A few more details:

-The files are not in the .gitignore

-There are three tracked files in the folder in question, so it's not empty

-After even more digging, it seems something like this could arise from changing the case of a tracked folder. This, unfortunately, is not the case (pun!). The folder name has never changed case.

-Contents of the docking directory:

➜ ls -lA rosetta_tests/profile/tests/docking/. total 16 -rw-r--r--  1 tim  staff  2209 Jul 17 10:47 command -rw-r--r--  1 tim  staff   260 Jul 17 10:47 flags drwxr-xr-x  3 tim  staff   102 Jul 17 10:47 input 

Answer 1

The . in the git add . command refers to the "current directory". So, running git add . will add all the files in the current directory and its subdirectories. You should ensure that you are in the correct directory before running git add.

git add -A is what you want. It will add everything.

Answer 2

I solved this by running

git clean -f