test: cover pipeline input-set override merge regressions (PR #532)

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Description

Adds missing regression tests for the pipeline input-set + inline override fix in PR #532 (substituteInputsIntoBaseYaml, resolveRuntimeInputsWithBaseYaml, and harness_execute combined path).

Risky behavior now covered

• Variable identity by name: overrides update the correct pipeline variable when base YAML variable order differs from the runtime template, and append missing variables instead of writing by template list index.
• Base input-set preservation: optional <+input>.default(...) placeholders are treated as covered when the materialized input set already supplies a value.
• Fail-closed pre-flight with input sets: harness_execute blocks execution when input_set_ids + inline overrides still leave required fields uncovered (no execute API call).
• Resolution metadata: successful combined runs expose _inputResolution.mode = "input_set_with_overrides".

Test files added/updated

• tests/utils/runtime-input-resolver.test.ts — 7 new cases for substituteInputsIntoBaseYaml and resolveRuntimeInputsWithBaseYaml
• tests/tools/tool-handlers.test.ts — 2 new harness_execute integration cases

Why these tests materially reduce regression risk

The original bug shipped because the combined input-set + override path skipped materialization and validation. These tests lock in the corrected merge semantics (name-based variable updates, base-value retention, and pre-flight blocking) at both the utility and public tool boundary.

Type of Change

• Bug fix
• New feature
• Refactor
• Documentation
• Other — test coverage

Checklist

• pnpm test passes (focused: 198 tests in touched files)
• pnpm typecheck passes
• pnpm build passes
• pnpm standards:check passes
• pnpm docs:check passes

  

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