Fix remote pipeline branch context for input resolution

[cursor]

Description

Fixes remote pipeline execution branch propagation so supporting input-resolution calls read from the same intended Git context as the run:

• Runtime input template fetch now falls back to pipeline_branch when callers omit branch, preventing feature-branch runs from resolving against the default-branch template.
• Remote input-set GETs now prefer explicit branch over pipeline_branch, while still falling back to pipeline_branch when no branch is supplied.
• Object-form runtime YAML (inputs: { pipeline: ... }) now participates in CI codebase branch/repo extraction, matching YAML-string behavior before input-set materialization.

Impact: the old behavior could execute a feature-branch remote pipeline with runtime inputs or saved input-set values loaded from the wrong branch, causing silent wrong deployment configuration.

Type of Change

• Bug fix
• New feature
• Refactor
• Documentation
• Other

Checklist

• pnpm test passes
• pnpm typecheck passes
• pnpm build passes
• pnpm standards:check passes (architecture guardrails — see docs/coding-standards.md)
• pnpm docs:check passes (if registry/tool counts changed)

Coding Standards (registry-driven MCP model)

If this PR adds or changes Harness API coverage:

• No new server.registerTool() calls — only toolset definitions in src/registry/toolsets/
• Toolset registered in ALL_TOOLSETS and ToolsetName union
• operationPolicy on every new/changed endpoint
• Shared response extractors from src/registry/extractors.ts (no raw passthrough on real endpoints)
• identifierFields and scope declared on new resources
• No console.log() in src/ (stdio JSON-RPC safety)

  

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