Remove unused -F, -O, -I and -R options

[wegank]

Fixes #301.

Summary

The -F, -O, -I/--isolate and -R options were added in early 2023 (adc7198, 5c1b905, 456ccf2) for an experimental mode that isolated real roots from precomputed parametrizations, read from binary (-F) or text files. That code path was removed from main() in 50b812e ("several bug fixes (seg faults) + code cleaning"), but the options stayed:

• -F FILE only set files->bin_file, which nothing reads. It also left files->in_file as NULL, so get_data_from_file(NULL, ...) crashed. For example, msolve -F input_files/bug-68.ms exits with SIGSEGV.
• -O, -I and -R were parsed into variables or fields that nothing used. -I was still listed in the help text.
• Nothing ever wrote the binary parametrization format, so there was no way to produce a valid -F input.

This PR removes:

• the four options: help text, the short and long option tables, and their getoptions handling, along with the unused refine and isolate variables;
• the bin_file and bin_out_file fields of files_gb;
• the parametrization readers in iofiles.c that had no callers (get_params_from_file_bin, get_params_from_file and their helpers).

Since -f is now the only way to give an input file, the input-file check in main() just opens files->in_file.

msolve -F ... now prints invalid option -- F and the usage text instead of crashing.

isolate_real_roots_lparam and display_arrays_of_real_roots in msolve.c are also unused now, but they have external linkage, so I left them for a separate decision.

Testing

• make check: all 68 tests pass (macOS, LLVM clang).

AI disclosure

I investigated this issue and wrote the changes with the help of Claude Code (generative AI). I reviewed and tested them.

Co-authored-by: Claude Opus 5.5 noreply@anthropic.com

🤖 Generated with Claude Code