[Feature]: structured output from shell steps (opt-in output_format: json)

### Problem Statement

No workflow step that runs external code can hand a **typed** value to a later step. Shell steps expose only `{exit_code, stdout, stderr}` (`src/specify_cli/workflows/steps/shell/__init__.py:42-44`), command steps the same (and their stdout streams, so it's empty in run state — see SK-style discussions around streaming), and workflow inputs are scalar-only (`string`/`number`/`boolean`). The practical consequence: a `fan-out` can never consume a dynamically-computed collection — there is no end-to-end path from "a script computed a list" to "`items:` receives a list".

#2960 (`from_json` filter) covers the consumption side for shell stdout, but a structural opt-in on the step itself would make the contract explicit and also benefit steps whose stdout isn't reliably capturable.

### Proposed Solution

An **opt-in** `output_format: json` on shell steps:

```yaml
- id: emit
type: shell
run: "python extract.py"
output_format: json
```

When set, stdout is parsed and exposed under `output.data` (raw `stdout`/`stderr`/`exit_code` keys unchanged — no merge/clobber ambiguity), so later steps can use `{{ steps.emit.output.data.items }}`. A parse failure **fails the step** with a clear error — declaring the format is a contract, and silence would hide wiring bugs. Fully backward-compatible: without the key, behavior is byte-identical.

This is a **proposal with a reference implementation** — happy to rework toward whichever direction you prefer.

### Alternatives Considered

- `output_file: ` — the step writes JSON to a file the engine reads into `output.*`; better for large payloads and streaming-stdout steps, slightly more machinery.
- A declared named-`outputs:` schema (map output names to JSON paths) — the most expressive, biggest API surface.
- Status quo + `#2960`'s `from_json` — works for shell stdout only, and leaves the contract implicit.

### Component

Workflow engine (shell step)

### AI Agent (if applicable)

n/a

### Use Cases

- Fan-out over runtime-computed items (extract → `items: {{ steps.emit.output.data.items }}`).
- Conditions/args consuming structured tool results without string hacks.

---

**Coordination note:** I'm aware open PR #2443 also touches `steps/shell/__init__.py` (security opt-in) — this change is isolated to the structured-output addition and I'm happy to rebase/coordinate in whichever order suits.

**AI disclosure (per CONTRIBUTING.md):** this issue and the accompanying reference PR were authored with AI assistance (Claude); verified by running the repo's test suite locally.

Start with src/specify_cli/workflows/steps/shell/__init__.py at lines 42-44, then trace how shell step outputs are consumed by later steps and by fan-out items. Review the related #2960 from_json work and the existing workflow output contract. Done means opt-in JSON stdout is exposed under output.data, parse failures fail clearly, and behavior without output_format remains unchanged.

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