C Binary Data CLI Tool

I need a small, self-contained command-line utility written purely in C that reads binary input, performs the required data processing, and writes the transformed output either to STDOUT or a specified file. The exact processing steps are straightforward: parse the byte stream, apply my algorithmic rules (I will share the specification and test vectors after we start), then preserve the original file structure where untouched and update only the flagged sections.

Portability matters, so please target ANSI C with no external dependencies beyond the standard library; the code must compile cleanly with gcc on Linux and clang on macOS. Clear, well-named functions, concise documentation blocks, and a Makefile that supports release and debug targets are part of the deliverable.

Once the tool meets the test vectors, send me the source, executable, and a brief README explaining build instructions, command-line flags, and examples.