Fix shell tool output replay consistency

[ScriptSmith]

No description provided.

[greptile-apps]

Greptile Summary

This PR fixes two interrelated bugs in shell tool output replay: shell_call and shell_call_output items that share the same id were being collapsed (one silently dropped from persistence) and ordered incorrectly (output before call), causing previous_response_id replay to break on Anthropic-family models.

• output_pos / item_index key fix (runner.rs): Both maps now key on a (type, id) qualified key for shell items, so the paired items each get their own persistence slot and live-stream output_index. Delta events still key on bare id since they never carry a type field.
• Ordering fix (shell_tool.rs, responses_pipeline.rs): New order_shell_outputs_after_calls function stably reorders the collected output array to call-before-output; both the streaming (StreamRewriter::ordered_output_items) and buffered (collect_streaming_response_to_json) paths call it, keeping the wire order intact while persisting a replayable transcript.

Confidence Score: 5/5

Safe to merge — both the streaming and buffered paths are fixed consistently and covered by focused regression tests.

The changes are tightly scoped to the two broken maps (output_pos, item_index) and the missing reorder step. The qualified-key logic for shell items is isolated to index_for and record_output_item, with a clear fallback for all other item types. order_shell_outputs_after_calls is deterministic, handles all edge cases (already-ordered input, orphaned outputs, multi-call interleaving), and is exercised by both new and existing tests. The previous reviewer concern about item_index being unpatched is fully addressed here.

No files require special attention.

Important Files Changed

Filename	Overview
src/services/server_tools/runner.rs	Fixes output_pos and item_index to key on qualified (type, id) for shell items; adds ordered_output_items() to the terminal-event path. New unit tests cover both the distinct-slot and correct-persistence invariants.
src/services/shell_tool.rs	Adds order_shell_outputs_after_calls to stably reorder output-before-call pairs; handles already-ordered input, orphaned outputs, and multi-call interleaving. Well-tested.
src/services/responses_pipeline.rs	Applies order_shell_outputs_after_calls in the buffered (non-streaming) collection path so the persisted transcript matches the streaming path.

Sequence Diagram

sequenceDiagram
    participant U as Upstream
    participant SR as StreamRewriter
    participant DB as Persisted transcript

    U->>SR: "output_item.added shell_call id=toolu_1 -> slot 0"
    U->>SR: "output_item.added shell_call_output id=toolu_1 -> slot 1"
    Note over SR: index_for uses qualified key per type
    U->>SR: "output_item.done shell_call_output -> output_items[0]"
    U->>SR: "output_item.done shell_call -> output_items[1]"
    Note over SR: output_pos uses (type,id) - no collision
    U->>SR: response.completed
    SR->>SR: ordered_output_items() reorders to call-before-output
    SR->>DB: "output[0]=shell_call output[1]=shell_call_output"

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[ScriptSmith]

@greptile-apps