fix(setup): run merge-config with uv

[ColumbusLabs]

What

Run the dependency-bearing merge-config.py setup helper through uv, including its documented help command. Keep the dependency-free CSV helper on python3.

Why

Bare python3 does not provision the script's PEP 723 pyyaml dependency, so setup can fail on otherwise valid uv-managed installations.

Fixes #259
Related #287

How

• changed both documented merge-config.py invocations to uv run
• added a focused guard preventing those commands from drifting back to bare Python

Testing

• exact uv run .../merge-config.py --help command
• uv run pytest -q tests/test_setup_cleanup_scripts.py (11 passed)
• uv run pytest -q (2938 passed, 29 skipped)
• trunk check
• git diff --check

Summary by CodeRabbit

• Documentation

  • Updated setup instructions to run the configuration merge through the project’s managed command environment.
  • Consolidated usage and help guidance for the merge scripts in the setup workflow.
  • Preserved existing behavior for JSON output, error handling, and legacy configuration.

• Tests

  • Added regression coverage to verify the documented setup command uses the correct execution method.

[coderabbitai]

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Review details

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 301c73d6-dd6e-4ddf-a772-a8c7b5399693

📥 Commits

Reviewing files that changed from the base of the PR and between 3007ad2 and bac941e.

📒 Files selected for processing (1)

• tests/test_setup_cleanup_scripts.py

Walkthrough

The setup skill documentation now runs the dependency-bearing merge-config.py through uv run, while retaining python3 for merge-help-csv.py. A regression test verifies the documented merge-config command appears twice and the legacy invocation is absent.

Changes

Setup script execution

Layer / File(s)	Summary
Document and test merge command execution src/bmad_loop/data/skills/bmad-loop-setup/SKILL.md, tests/test_setup_cleanup_scripts.py	The setup instructions use uv run for merge-config.py, and a regression test validates both occurrences and rejects the previous python3 invocation.

Estimated code review effort: 1 (Trivial) | ~5 minutes

Possibly related PRs

• bmad-code-org/bmad-loop#285: Updates the related merge-config.py TOML layout and script behavior.

Suggested reviewers: pbean

Poem

I’m a bunny with a setup command,
Hopping through uv as planned.
The old path sleeps, the tests now say,
“Run the merge script the proper way!”
Two checks thump their paws today.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title is concise and matches the main change: switching merge-config to uv run in setup docs.
Linked Issues check	✅ Passed	The PR updates bmad-loop-setup docs/tests to use uv run for merge-config, matching issue #259.
Out of Scope Changes check	✅ Passed	The changes stay focused on setup docs and regression coverage for merge-config invocation.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@tests/test_setup_cleanup_scripts.py`:
- Around line 292-296: Update
test_setup_skill_uses_uv_for_dependency_bearing_merge_config to also assert that
“python3 ./scripts/merge-help-csv.py” appears exactly twice, while preserving
the existing uv invocation and exclusion assertions.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Organization UI

Review profile: CHILL

Plan: Pro Plus

Run ID: beddbde5-d917-4286-b371-744446c1e114

📥 Commits

Reviewing files that changed from the base of the PR and between d4d1764 and 3007ad2.

📒 Files selected for processing (2)

• src/bmad_loop/data/skills/bmad-loop-setup/SKILL.md
• tests/test_setup_cleanup_scripts.py

[pbean]

closed as duplicate of #297 and already resolved