First of all, the command you have specified in the question is for compiling c/c++ files and instrumenting them for getting coverage generated later at the time of execution.
That command can be used as following too:
gcc --coverage
g++ --coverage
Note: you must specify the same flag for linking too.
Now about the question, if your question is about compiling multiple files then there are a lot ways for building projects, no matter how complex. You can use automated builds for it.
If your question is about generating coverage report for multiple files then:
You can use gcovr for generating report in various forms just by specifying root directory (directory above src and obj ) with "-r or --root=ROOT" flags.
Refer to this user guide.
Answers given by others works too if you really want to use only gcov and nothing else. But in my opinion gcovr meets every purpose that can be fulfilled with gcov(except function level detail, you can get line level details though).