Suppose the project looks like this when clean:<p><pre><code>  README.txt
  src&#x2F;
  include&#x2F;
  doc&#x2F;
  TODO.oo3
</code></pre>
In the midst of development, I may end up with files in some of these directories that are not supposed to go into the repository. There may be output files from test runs that I&#x27;m keeping around temporarily while I debug, notes (that will be incorporated into commit messages which is why the notes files do not belong in the repository), short-lived alternative versions of some of the source or include files, and so on.<p>I don&#x27;t want to &quot;git add&quot; on the project directory, or any of the subdirectories other than TODO.oo3 because I don&#x27;t want to pick up those files. For everywhere except TODO.oo3, &quot;git add -u&quot; is what I (think I) want. It&#x27;s only with TODO.oo3 that I want &quot;git add&quot; instead of (or in addition to) &quot;git add -u&quot;.