If you want to do this reliably, you need a full C front end, and the ability to modify parsed code.
Our DMS Software Reengineering Toolkit with its C Front End can probably do what you want. DMS can parse, build ASTs, and carry out custom transformations on source text, either procedural or as a surface syntax transform.
There are some issues with macros and preprocessor directives; if you parse and retain these, it can do so in many cases but it expandis such directives where they are not "structured". Retention means you don't get a symbol table. If you expand all the directives, after parsing you can get a symbol table with the same content that a C compiler produces.
For OP's specific task, he'd like write a source to source transform something like the following:
rule decorate_function_definition_with_pragma(fh:function_head, b: block): declaration -> declaration
= " fh " ->
" fh
#pragma my_pragma
"
if some_condiiton(fh);
where "my_pragma" is replace essentially by the pragma text he wants, and some_condition is custom predicate that filters matched function_headers for which the pragma should be inserted.
The pattern matches against the syntax tree, so it cannot mismatch like sed or a regex might. The secret to this is that the pattern variables reference to grammar rules in the C Front End; a pattern variable of type function_head can only match those trees that the function_head grammar rule(s) can satisfy.
One needs some trivial control logic to run this transformation just once for each encountered function definition.
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