Move setup check/doctor JSON assembly into Python

[codeforester]

Goal

Move structured setup/check/doctor JSON assembly out of shell argument construction and into Python-owned code while preserving the current JSON schema and command behavior.

Background

#1570 split the coherent shell ownership domains out of setup_common.sh: Linux/Debian platform setup, macOS/Homebrew setup, Base runtime venv/bootstrap, and setup/check profiles. The remaining structured JSON path is a different cleanup boundary. It is schema and serialization work, not another shell helper split.

Keeping JSON payload assembly in shell makes schema changes harder to test and increases quoting/escaping risk. Python is already the owner for structured project data, manifest parsing, artifact decisions, workspace data, and stable JSON serialization.

Scope

• Inventory the JSON payloads currently coordinated by setup_common.sh, including setup_run_check_json(), project virtualenv check/doctor snippets, and Base finding metadata.
• Add Python-owned assembly/serialization for the structured check and doctor payloads.
• Keep shell responsible for command dispatch, process orchestration, human text rendering, exit-status handling, and pre-runtime fallback routing.
• Preserve current JSON keys, value types, ordering expectations where tests depend on them, and exit behavior.
• Add focused tests that compare representative before/after payloads for base, profile, project, and pre-venv failure paths.

Acceptance Criteria

• setup_common.sh no longer owns general JSON argument assembly for setup check/doctor payloads.
• Current JSON output shape is preserved for existing tested setup/check/doctor paths.
• Shell remains the thin orchestrator for dispatch and fallback paths.
• Python owns schema construction and serialization for structured payloads.
• Documentation records the new boundary between shell orchestration and Python JSON ownership.

Validation

• Focused Python tests for the new JSON assembly surface.
• Existing setup/check/doctor JSON tests.
• Focused BATS coverage for shell dispatch into the Python JSON surface.
• Shell syntax checks for touched shell files.
• ShellCheck at the repository standard for touched shell files where practical.
• git diff --check.

Non-Goals

• Do not change user-visible setup/check/doctor JSON schema in this issue.
• Do not rewrite top-level setup/check/doctor orchestration in Python.
• Do not move platform install bodies out of their current domain helpers.
• Do not use this issue to continue splitting shell files by line count.

Project Fields

• Priority: P2
• Status: Backlog
• Size: M
• Area: Setup
• Initiative: Contract Hardening

Agent Assignment

• Recommended next slice after Plan staged setup_common.sh domain decomposition #1570 close-out.
• Keep the first PR schema-preserving and test-first.

[codeforester]

Progress update:

• Merged Move Base check metadata into diagnostics renderer #1593: moved Base check finding IDs and display names into base_setup.diagnostics as the primary metadata owner.
• Added the internal base-check-metadata diagnostics command for shell consumers.
• Updated doctor text rendering to consume Python metadata in one batch while preserving a shell fallback for pre-runtime text diagnostics.
• Updated focused tests and the setup ownership map.

Remaining #1591 work:

• Reduce setup_run_check_json() so shell passes raw collected check facts to a Python-owned assembly surface instead of building the command-specific JSON argument shape itself.
• Decide whether the project virtualenv pre-runtime JSON helpers should remain as thin shell wrappers around Python or move behind the same Python assembly surface.
• Preserve current JSON shape, embedded profile_checks / project_checks, check-record writing, stdout/stderr behavior, and exit codes.

[codeforester]

Completed by #1593, #1594, and #1595.

Summary:

• Move Base check metadata into diagnostics renderer #1593 moved Base finding metadata and display names into Python diagnostics, keeping only a pre-runtime shell fallback.
• Move check JSON assembly to result records #1594 moved check and doctor JSON item assembly to Python by having shell pass raw check-result records instead of per-item JSON argument tuples.
• Document Python diagnostics JSON ownership #1595 updated the ownership map so the documented boundary matches the implemented Python diagnostics JSON ownership.

Validation included focused Python/BATS/syntax/ShellCheck/pylint checks, full local ./bin/base-test for the implementation slice, and green CI for all three PRs.