Normally, you should see the file unless
- the folder holding the file is not yet added to the repo (in that case, you'll see only the folder when typing 
git status) 
- the file is contained in a 
.gitignore present in the folder holding the file 
- the file is contained in 
.gitignore 
- the file is contained in 
.git/info/exclude 
- the file is contained in your global 
.gitignore file (check with
git config --global core.excludesfile) 
To check whether your file is ignored by one of the ignore files, type 
git status --ignored
This will also show ignored files.
Solutions for the five cases:
- when the folder is not yet versioned, add it with 
git add folder_name. This will add the folder and all of it's files (unless they are ignored) to the index. 
- when the file is filtered by a 
.gitignore, modify that file so that your file to be added shows up when typing git status.