feat(agent): add counterfactual reasons to decision snapshots

[bitloi]

Summary

Closes #284

• Adds structured counterfactualReasons to repo decisions and decision actions so snapshots can explain why obvious alternatives were rejected.
• Threads scoped counterfactuals into agent context snapshots as grouped rejectedAlternatives per selected repo.
• Keeps counterfactual public summaries deterministic, advisory, and sanitized.

Scope

• This PR is focused and does not mix unrelated backend, UI, MCP, docs, dependency, and deploy changes.
• This follows CONTRIBUTING.md and does not reintroduce GitHub Pages, VitePress, site/, or CNAME.
• I linked an issue, or this is small enough that the summary explains why an issue is not needed.

Validation

• git diff --check
• npm run actionlint
• npm run typecheck
• npm run test:coverage locally; global coverage stays at or above 97% for lines, statements, functions, and branches (aim for 98%+ branch coverage locally so CI variance does not fail near the threshold)
• npm run test:workers
• npm run build:mcp
• npm run test:mcp-pack
• npm run ui:openapi:check
• npm run ui:lint
• npm run ui:typecheck
• npm run ui:build
• npm audit --audit-level=moderate
• New or changed behavior has unit/integration tests for new branches, fallback paths, and sanitizer boundaries

If any required check was skipped, explain why:

• npm run test:coverage / npm run validate was attempted locally, but this shell is on Node 24 while .nvmrc requires Node 22. The unrelated test/unit/local-scorer-adapter.test.ts external-command fixtures fail locally with scorer_failed fallback results before coverage can complete. Focused feat(agent): add counterfactual reasons to decision snapshots #284 tests pass with npx vitest run test/unit/decision-pack.test.ts test/unit/agent-orchestrator.test.ts (59 tests), and CI should run the full Node 22 gate.
• Partial focused coverage was also attempted with npx vitest run --coverage test/unit/decision-pack.test.ts test/unit/agent-orchestrator.test.ts; the tests pass, but the repo-wide 97% global threshold fails as expected for a partial suite.
• GitHub Actions validate passed on this PR after submission.

Safety

• No secrets, wallet details, hotkeys, coldkeys, user PATs, private keys, raw trust scores, private rankings, or private maintainer evidence are exposed.
• Public GitHub text stays sanitized, low-noise, and does not imply compensation guarantees or optimization tactics.
• Auth, cookie, CORS, GitHub App, Cloudflare, or session changes include negative-path tests. — N/A, no auth/session/GitHub App behavior changed.
• API/OpenAPI/MCP behavior is updated and tested where needed. — no API schema change; existing generic decision/snapshot payloads carry the new structured data, and npm run ui:openapi:check passed.
• UI changes use live API data or real empty/error/loading states, not production mock/demo fallbacks. — N/A, no UI changes.
• Visible UI changes include screenshots or a short recording. — N/A, no visible UI changes.
• Public docs/changelogs are updated where needed; changelogs are only edited for release-prep PRs. — N/A, no docs/changelog change needed.

Notes

• This intentionally avoids feat(agent): persist snapshot provenance counterfactuals and replay #311's broader migration, replay endpoint, OpenAPI, and package-lock scope.
• Counterfactual entries separate facts from assumptions and include sanitized publicSummary text for public-safe downstream summaries.

[JSONbored]

@bitloi this is ready from this pass.

A few notes:

• Adding structured counterfactual reasons to repo decisions and scoped snapshots improves explainability without exposing raw private scoring context.
• The implementation keeps facts, assumptions, and public summaries separated.
• The focused decision-pack/orchestrator tests cover the new behavior, and CI validate is green.

No code changes are requested from this review pass.

[JSONbored]

@bitloi this remains merge-ready.

A few notes:

• The counterfactual reason additions are scoped to the decision snapshot behavior.
• The current branch is locally merge-clean against main.
• No code changes requested.

Validation expected:

• Keep the current green CI run after any required branch update.