Git keeps forgetting the current directory

Question

I've got a git repository, call it myscripts/. Within myscripts/ are subdirectories perl/, python/, and ruby/. For some reason, when I edit code in one of the subdirectories, Git forgets that the subdirectory is part of the repository.

$ cd myscripts/
$ cd perl/
$ vi hello.pl
...
$ git commit -a
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#   ./
$ git add .
$ git commit -a

I have to do this over and over, and I don't know why.

Answer 1

When you run git commit, Git creates a new commit with the contents of the index. The index contains the current HEAD, plus any changes you have made using git add or git rm.

However, git commit does accept the -a switch. The man page says about this switch:

Tell the command to automatically stage files that have been modified and deleted, but new files you have not told git about are not affected.

This means that when you run git commit -a, Git will only commit changes to files that exist in the current HEAD.

Therefore, you must run git add at least once on each file or directory you want to track:

$ cd myscripts/
$ cd perl/
$ vi hello.pl
...
$ git add .               # Add each file in this directory to the index
$ git commit              # Commit this version of hello.pl
$ vi hello.pl             # Edit hello.pl some more
... edit some more ...
$ git commit -a           # Commits the changes to hello.pl