fix: add CROSSREF_MAILTO env var and bump to 2.0.2

chore: bump manuscript-tools to 2.0.1

fix: add portable MCP runner script and fix semantic-scholar-mcp missing main()

feat: register ty-lsp in marketplace and update docs

feat: add ty LSP plugin for Python

docs: clarify Air install options

chore: ignore local claude files

docs: expand visual-sync checks

feat: add R LSP plugin with Air fallback

fix: convert semantic-scholar-mcp from submodule to tracked files

docs: make CrossRef email configuration prominent

docs: expand token usage note with project-specific option

fix: add mcpServers configuration to plugin.json

fix: remove unsupported mcps key from plugin.json

fix: update marketplace.json with correct name and homepage