Refactor: Remove dependency on shell commands for file operations

[A-006]

This PR replaces usages of std::system for file system operations (like creating directories, checking file existence, and copying files) with C++ standard library functions or POSIX system calls (mkdir, stat, rmdir, std::ifstream/std::ofstream). This improves portability and removes the dependency on a shell environment.

Changes:

• Replaced system("mkdir ...") with mkdir() in Global_File::make_dir_out, GlobalFunc::MAKE_DIR, and Exx_Lip::write_q_pack.
• Replaced system("test -d ...") with stat() in ReadInput::create_directory and GlobalFunc::MAKE_DIR.
• Replaced system("cp ...") with std::ifstream/std::ofstream in Exx_Lip::write_q_pack.
• Updated unit tests in global_function_test.cpp to use stat and rmdir instead of system.
• Fixed a template instantiation syntax error in
  ctrl_runner_lcao.cpp