chore(flexus-bot-dev): remove obsolete files and migrate skill to bob

- Delete check_bot_install.sh, FLEXUS_BOT_REFERENCE.md, and legacy SKILL.md
- Add updated flexus-bot-dev skill to bob/skills/ covering classic, manifest, and integration bots
- Update bob prompts to reference flexus-bot-dev skill and modern patterns
- Add FETCH_SKILL_TOOL handler and auto IDE overlay detection to bob_bot.py

Author: JegernOUTT