fix(agent): recover timeout and rate-limited runs - #4952
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Timeout and rate-limit failures currently make checkpointed runs terminal, preventing recovery after a restart.
Allow Resume, ResumeStreamAsk and ResumePending to recover these runs using the original run ID, saved input and completed tool results. Canceled and expired runs remain terminal. Document fresh contexts, backoff and configurable timeouts.
Validation: targeted fake-provider regression tests cover both statuses across all three resume paths after recreating the agent, and assert completed tools are not repeated. Repository build and golangci-lint pass. Full tests run in CI; the local full-suite attempt was previously blocked by automatic approval review because an existing test makes an external Atlas request.
Closes #4935