So to add to the following comment from a related thread:

I did find that if I explicitly set the language for the \code command, “\code 
{.c}”, I do not get the line numbers, but I do get color coding. Seems that 
someone figured this out about which formatters are used for which languages: 
http://stackoverflow.com/questions/21406101/doxygen-code-line-numbers.)
And depending on whether I’m documenting a regular function (in a .c file) or a 
member function in a typedef struct (in a .h file), the \code command’s output 
is opposite with respect to line numbers and color-coding:
* In the .c file: With NO language qualifier, I get line numbers but no 
color-coding. WITH the {.c} qualifier, I get color coding but no line numbers.
* In the .h file: With NO language qualifier, I get color coding but no line 
numbers. WITH the {.unparsed} qualifier, I get line numbers but no 
color-coding. 
Other than the OPTIMIZE_OUTPUT_FOR_C = YES config option, I’m not sure if any 
other config options might be relevant?
So again, I can work with this, but I have to ask whether this is by design or 
a bug?
-Monique
 
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