Fix Pi extension package-root resolution

[rochecompaan]

Summary

• Added a shared nearest-ancestor package-root resolver with fail-fast filesystem semantics.
• Migrated fixture lookup, version lookup, and Patchmill-owned Pi extension paths to the shared resolver.
• Validated source, compiled, npm-packed, and Nix-installed extension resolution, including missing and non-file todos-extension failures.

Validation

• node --test src/package-root.test.ts src/pi/resource-profiles.test.ts src/pi/resource-profiles.compiled.test.ts src/cli/commands/setup-test-repo/fixtures.test.ts src/cli/commands/version/main.test.ts — 24/24 passed
• npm test — 1,136/1,136 passed
• npm run lint — passed
• npm run build — passed
• npm-packed install verification — passed (all extension paths exist in the packed install)
• nix build .#patchmill --no-link --print-build-logs — passed
• diff/status checks — passed; clean worktree

Reviews

• Final Codex full-worktree review: pass after accepted fixes.
• Final thermo-nuclear full-worktree review: pass.
• Final validation-readiness review: pass.

Closes #121

Patchmill run cost

Stage	Model	Prompt tokens	Output tokens	Estimated cost (USD)
Development environment	gpt-5.5	355,890	1,889	$0.5551
Implementation	gpt-5.5	2,688,053	15,110	$2.2975
Implementation	gpt-5.6-sol	2,112,747	34,061	$3.7566
Implementation	gpt-5.6-terra	3,588,605	15,335	$1.9048
Implementation subtotal		8,389,405	64,506	$7.9589
Total		8,745,295	66,395	$8.5140

Prompt tokens include uncached input, cache reads, and cache writes. Cost is an estimate based on Pi's recorded model pricing and includes parent and subagent sessions.