added update-index and ls-files

README.md

@@ -603,6 +603,48 @@ checkout
   were just on. This is probably the most likely way you'll create a branch,
   when you use them.
 
+update-index and ls-files
+--------------------------
+
+  These are two very useful commands when you're writing scripts
+  and storing them in git. I have often seen students commit a
+  script to git, and then ask why it's not running when I am doing
+  a grading pass. The reason is that they haven't told git that the
+  script file should be executable. If you set the execute bit
+  before adding the file to a commit for the first time, git will
+  pick this up automatically. If, however, you add and commit it
+  before making it executable, you have to go back and tell git to
+  record the executable bit for the file.
+
+  Fortunately, this is easy to do using `git update-index`. This
+  command tells git that you want to change some of the metadata
+  about one or more files, as opposed to modifying the contents of
+  the file. Let's say we have `foo.sh`, but git doesn't (yet) know
+  that it should be an executable bash script. We can fix this by
+  running
+
+    git update-index --chmod=+x foo.sh
+
+  This behaves like the standard Posix `chmod` (change mode) command,
+  which is used to change permissions on a file or directory. In
+  particular, we're telling it to add the executable (x) bit. This
+  also adds the file to a commit, so you'll then just need to do
+  the actual commit (and push, if necessary.
+
+  Let's say you're not sure if the executable bit is set. That's where
+  `git ls-files` comes in. If you run
+
+    git ls-files --stage foo.sh
+
+  it will show you the index entry for the file. The first column
+  will be an octal number like `100644` or `100755`. The last three
+  digits tell you (respectively) the owner, group, and other
+  permissions. The first bit is whether the file is readable, the
+  second writable, and the third exectuable.  That means `100644`
+  means the owner can read and write the file, and everyone   else
+  can only read it. `100755` means the executable bit is set for
+  everyone.
+
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