feat(scientific-method): ship hypothesis-differential debugging, retire v2 prototype

Replaces the flat observe->question->A/B-canary scientific-method skill with
the agent-native hypothesis-differential rewrite that earned the program's
strongest measured lift (SWE-bench fault localization 0pp -> +9.3pp, p=0.002).
The prototype lived in thinking-scientific-method-v2 during the rework
experiment; now merged into the shipped skill and the v2 directory removed so
there is a single canonical debugging skill (per CLAUDE.md / AGENTS.md).

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>