fix(core): honor reset-only workspace hooks

[christso]

Closes #1058

Summary

• honor reset-only before_each hooks during eval execution instead of silently ignoring them
• allow reset hooks to operate on the shared/static workspace root when no nested repos are declared
• refresh the file-change baseline after before_each setup scripts so setup artifacts do not leak into file_changes

Red/Green E2E

Red on main:

• Command: bun apps/cli/src/cli.ts eval run D:\GitHub\christso\agentv-e2e-1058\repro.eval.yaml --output D:\GitHub\christso\agentv-e2e-1058-out-main --workers 1
• Evidence: D:\GitHub\christso\agentv-e2e-1058-out-main\repro\case-1\grading.json reported workspace_changes.diff_summary for setup.txt, even though that file was written by the before_each hook rather than the agent.

Green on this branch:

• Command: bun apps/cli/dist/cli.js eval run D:\GitHub\christso\agentv-e2e-1058\repro.eval.yaml --output D:\GitHub\christso\agentv-e2e-1058-out-fix --workers 1
• Evidence: D:\GitHub\christso\agentv-e2e-1058-out-fix\repro\case-1\grading.json no longer contains workspace_changes; the before_each setup file is excluded from file_changes as intended.

Verification

• bun test packages/core/test/evaluation/orchestrator.test.ts packages/core/test/evaluation/validation/eval-validator.test.ts
• bun run build
• bun run test still has one unrelated timeout in pipeline grade > writes code_grader_results/<name>.json with score

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