Fix misuse of SYSTEM include flag to suppress warnings only for third-party headers

- Previously, SYSTEM was incorrectly applied to normal includes as well
- Adjusted CMake to restrict SYSTEM usage to external dependencies (e.g., FlatBuffers)
- Ensures project headers remain subject to warning checks and fixed all
  the warnings

Signed-off-by: Yuvaraj Venkatesh <yuvaraj.venkatesh@arm.com>
Change-Id: I16a5c0e6b9ab4db5e623516210dbf9bddaea7be0