Wa Alaykumassalam,
They are Velocity files. Velocity is: a Java-based template engine. It
permits anyone to use a simple yet powerful template language to
reference objects defined in Java code.
If you are familiar with scripting languages like PHP, ASP or JSP, you
can think of .vm files like one of them, letting a developer to define
the UI template on runtime.
In Zekr .vm files are used to generate output Quran/translation HTML
files. You can see that any of themes have a separate set of .vm and
.css files. A theme designer can then customize Zekr UI either through
.vm or .css files.
Mohsen.