Created attachment 226931 [details]
Source and Doxifile file showing the problem

When we have a '(single quote) or " (double quote) in a normal Fortran comment (odd number of quotes), the Doxygen comment convert parser is broken.
When we have the source code (aa.f):
!  A normal comment line with a ' (single quote) in it.

!> just a comment
!> \MY_ALIAS
         SUBROUTINE TST
         END

And the alias MY_ALIAS defined as MY_ALIAS=some text one would expect the text
"just a comment some text" in the output, but just the text "just a comment" is shown and the error messages in the console output (twice): aa.f:4: warning: Found unknown command `\MY_ALIAS'

Some investigation lead to the statement:
<Scan>[^"'!\/\n\\#\\-]*           { /* eat anything that is not " / or \n */
in commentcnv.l on line 264, here all characters are skipped till a quote (start of a string) in case of a non-comment line, but the normal Fortran comments are not recognized properly, only Doxygen Fortran comments are recognized.

In Fortran there is of course the problem that we have the ! comments, but in the fixed format also th C,c,*,! in column 1 (and excluding the ! in columns 6 as continuation character, but this is quite rare that this is used and error prone so we can forget this one in my opinion)