Preserve user MCP env block; unify home resolution across the bridge #30

	name: CI

	on:
	push:
	branches: [main]
	pull_request:
	branches: [main]

	jobs:
	r-cmd-check:
	name: R CMD check
	runs-on: ubuntu-latest
	env:
	_R_CHECK_FORCE_SUGGESTS_: false
	steps:
	- uses: actions/checkout@v4
	- uses: r-lib/actions/setup-r@v2
	with:
	use-public-rspm: true
	- uses: r-lib/actions/setup-r-dependencies@v2
	with:
	dependencies: '"hard"'
	extra-packages: any::rcmdcheck
	- uses: r-lib/actions/check-r-package@v2
	with:
	error-on: '"warning"'
	args: 'c("--no-manual")'

	r-checks:
	name: R parse + functional checks
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: r-lib/actions/setup-r@v2
	with:
	use-public-rspm: true
	- name: Install check dependencies
	run: Rscript -e 'install.packages(c("jsonlite", "xml2", "zip"))'
	- name: Run checks
	run: Rscript .github/scripts/checks.R

	bridge-smoke:
	name: MCP bridge build + stdio handshake
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: astral-sh/setup-uv@v5
	- name: Bridge copies must be identical
	run: diff clauder-mcp/src/clauder_mcp/server.py inst/scripts/persistent_r_mcp.py
	- name: Build wheel
	run: uv build
	working-directory: clauder-mcp
	- name: Install wheel
	run: \|
	uv venv smoke
	uv pip install --python smoke/bin/python clauder-mcp/dist/*.whl pytest
	- name: Unit tests
	run: smoke/bin/python -m pytest clauder-mcp/tests -q
	- name: stdio initialize + tools/list handshake
	run: timeout 60 python3 .github/scripts/handshake.py smoke/bin/clauder-mcp

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