To control what files are searched for in what order in a directory, edit `/etc/apache2/mods-available/dir.conf`
and modify the line
```
DirectoryIndex index.html index.cgi index.pl index.php index.xhtml index.htm
```
to e.g.
```
DirectoryIndex index.php index.html index.cgi index.pl index.xhtml index.htm
```
if you want `index.php` to take preference over `index.html`. Apache searches for the 
first file in this list that it finds, and serves that.