Assume these lines are set in a Doxyfile

ALIASES  = "myalias=@if FOO"
ALIASES += "endmyalias=@endif"

Now given the file, foo.md, with the following contents:



Here is some documentation that contains a documented C enum
~~~{.c}
typedef enum {
    ONE = 1,  /* First number */
    TWO = 2  
} Numbers;
~~~

@myalias

A bunch of  commands support by an external tool that looks for "@myalias"
@dofoo
@dobar
@dobaz

@endmyalias



Running doxygen gives the following warnings:
warning: Documentation block ended in the middle of a conditional section!
warning: Found unknown command `\myalias'
warning: Found unknown command `\dofoo'
warning: Found unknown command `\dobar'
warning: Found unknown command `\dobaz'
warning: Found unknown command `\endmyalias'

Doxygen has appeared to discard it's set of known aliases.
Oddly, all other normal command processing works, i.e. I can still use @if and @endif normally

It all happens because a "*/" is encountered in the markdown file. I would of assumed doxygen is parsing the file as markdown, not C/C++ or some other supported programming language.

Also, changing ~~~{.c} to <pre> (and </pre>) prevents the first warning from being generated, but the following 5 still do.