Address PR review feedback: fix indentation, update configuration paths, replace archived server#169
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d-morrison merged 2 commits intotest-mcpfrom Jan 8, 2026
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…al Brave Search server Co-authored-by: d-morrison <2474437+d-morrison@users.noreply.github.com>
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[WIP] Fix pkgdown website rendering issues
Address PR review feedback: fix indentation, update configuration paths, replace archived server
Jan 8, 2026
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Applies code review suggestions from PR #163 to fix workflow syntax errors, improve configurability, and update deprecated dependencies.
Workflow Fixes
Configuration Updates
R-4.1.0paths with placeholderR-x.y.zand added comments instructing Windows users to update for their R version$commentfield documenting that hardcoded paths (/home/runner/work/serodynamics/serodynamics) are CI-specific and must be updated for local useDependency Updates
@modelcontextprotocol/server-brave-searchwith official@brave/brave-search-mcp-serverThe GitHub MCP server respects token permissions and branch protection rules - it cannot bypass protected branch restrictions on main.
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