How do I preserve custom files in my Drupal configuration across minor core upgrades? When I do a minor upgrade of the core, my custom .htaccess and robots.txt are overwritten.

How do I prevent that?
You can build a site totally with git to help manage this process. The process is basically

Git clone into your DOCROOT:

git clone --branch 7.x http://git.drupal.org/project/drupal.git /var/www/mysite/docroot


Rename the remote:

git remote rename origin drupal


Checkout the latest tag, and make a site branch for your site:

git checkout 7.26
git branch -b mysite


Now, you can build your site and customize robots.txt and .htaccess to your needs.

When there is a core update, you can:

git fetch drupal


and then use the normal git methods for merging your changes in, eg:

git merge 7.27


or you can preview what will happen, check for conflicts, etc.

If you do this, you need to make sure you don't do a plain:

drush pm-update drupal


as this will then mess things up. I do not think that drush pm-update --lock=drupal works to prevent this.