gcc-4.4.0-15 and later in rawhide should allow this.

This is still failing for htmldoc. Here is a modified fam.c, with a structure that is failing in htmldoc (from ps-pdf.cxx):


#include <stdio.h>
#include <stdlib.h>
#include <string.h>

typedef struct render_str		/**** Render entity structure ****/
{
  struct render_str	*prev;		/* Previous rendering entity */
  struct render_str	*next;		/* Next rendering entity */
  int	type;				/* Type of entity */
  float	x,				/* Position in points */
	y,				/* ... */
	width,				/* Size in points */
	height;				/* ... */
  union
  {
    struct
    {
      int	typeface,		/* Typeface for text */
		style;			/* Style of text */
      float	size;			/* Size of text in points */
      float	spacing;		/* Inter-character spacing */
      float	rgb[3];			/* Color of text */
      unsigned char	buffer[1];		/* String buffer */
    }   	text;
    void	*image;			/* Image pointer */
    float	box[3];			/* Box color */
    unsigned char	link[1];		/* Link URL */
  }	data;
} fam_t;

int main( void )
{

    char test_string[] = "Toto je testovaci string.";


    size_t size = 0;
    size = sizeof( fam_t ) + (strlen(test_string)-1)*sizeof(char);

    fam_t* fam = NULL;
    fam = (fam_t*)malloc(size);
    strcpy( fam->data.text.buffer, test_string );
    printf("%s\n", fam->data.text.buffer);

    free(fam);

    return 0;
}

That's nested too much, sorry, this isn't going to work with -D_FORTIFY_SOURCE=2.
Either build with -D_FORTIFY_SOURCE=1, or rearrange the struct.

Or use memcpy instead of strcpy.

Another bug/problem/nasty thing with flexible array member. It seems that code is work perfectly. Valgrind said there isn't any memory leaks. Give only echo if it will be fixed. Easy solution is use memcpy.

#include <stdio.h>
#include <stdlib.h>
#include <string.h>


typedef int *ClientData;


typedef struct VarTrace {
    ClientData clientData;	/* Argument to pass to proc. */
    int flags;			/* What events the trace procedure is
				 * interested in: OR-ed combination of
				 * TCL_TRACE_READS, TCL_TRACE_WRITES,
				 * TCL_TRACE_UNSETS and TCL_TRACE_ARRAY. */
    struct VarTrace *nextPtr;	/* Next in list of traces associated with a
				 * particular variable. */
} VarTrace;

typedef struct {
    int flags;			/* Operations for which Tcl command is to be
				 * invoked. */
    size_t length;		/* Number of non-NUL chars. in command. */
    char command[4];		/* Space for Tcl command to invoke. Actual
				 * size will be as large as necessary to hold
				 * command. This field must be the last in the
				 * structure, so that it can be larger than 4
				 * bytes. */
} TraceVarInfo;

typedef struct {
    VarTrace traceInfo;
    TraceVarInfo traceCmdInfo;
} CombinedTraceVarInfo;


int main( void )
{

    char test_string[] = "This is testing string for flexible member array";

    CombinedTraceVarInfo* ctvi;
    size_t size = sizeof( CombinedTraceVarInfo) + strlen(test_string) +1 - sizeof( ctvi->traceCmdInfo.command);
    ctvi = malloc( size );
//    strcpy( ctvi->traceCmdInfo.command, test_string );
    memcpy(ctvi->traceCmdInfo.command, test_string, sizeof(test_string ));
    printf("%s\n", ctvi->traceCmdInfo.command);
    free(ctvi);

    return 0;
}

That's definitely nothing close to the standard flexible array member definition.
Fix up the code.  Easy fix is to put what is meant to be a flexible array member as a flexible array member (i.e. as last, array, field into CombinedTraceVarInfo).