refactor: remove ID count from offsets

[spacer07]

Description

This completes the binary format cleanup started in #410. It:

• bumps the fraction binary data version to V6;
• stops writing the legacy ID count placeholder to the offsets section;
• keeps V0–V5 fractions readable by skipping the legacy field for old versions;

Fixes #409

---

• I have read and followed all requirements in CONTRIBUTING.md;
• I used LLM/AI assistance to make this pull request;