You can see the `build.sh` scrip here https://github.com/google/oss-fuzz/pull/5279/files which is used to build the fuzzer. This may help clarify the structure of the set up.
We simple indicate where to find `parse_uri.c` by way of `-I`. Perhaps it would be smarter to change it to `#include "core/parser/parse_uri.c"`. In either case we can place the fuzzer wherever we like and I am happy to put it in the location that you prefer.
Yes, this is just the beginning and it would be great to add more. Similar files will have to be added for other parts of the code.