Investigate PhysicsIntern Run

You are auditing a PhysicsIntern workspace run. Three sources:

1. The workspace at $workspace_path — files, git history, and the actual skills/agents and methodology file the run was operating under (.claude/ + CLAUDE.md for Claude Code, .pi/ + AGENTS.md for Pi, .codex/ + AGENTS.md for Codex, .opencode/ + AGENTS.md for OpenCode).
2. The session record — every prompt, response, and tool call from the run. Single JSONL for Claude Code; main-agent JSONL plus per-skill sub-agent JSONLs for Pi; main-agent JSONL plus per-spawned-agent JSONLs for Codex; a single SQLite database (rows keyed by session, not files) for OpenCode (see Host detection and session locations below).
3. The methodology contract — the workspace's own methodology file and (.claude|.pi|.codex)/agents/ or .opencode/agents/, and (.claude/skills|skills|.agents/skills|.opencode/commands)/. These are the rules the run is being audited against. (Optional: the canonical templates in the parent commons/ and hosts/<host>/ dirs for cross-reference.)
4. Reference solution (if available) — the known-correct answer to the problem, if it exists, can be documented in references/. This is a quality check, not a methodology requirement; the audit should be honest about whether the run produced a correct, partially correct, or incorrect answer, but the main focus is on the process rather than the outcome.

The methodology promises: