You're building an internal tool for your company's HR department using Claude Code with MCP integrations. Your team needs three integrations:
- a shared Jira server (everyone uses this)
- a personal Notion workspace (each person has their own)
- an experimental scratch server you're prototyping
Where should each be configured?
Why did you pick that answer? Two or three sentences. The act of articulating it is what builds the judgment — not the click that follows.
Project-scoped configuration (.mcp.json) is for shared team infrastructure that everyone needs and that should be version-controlled. User-scoped configuration (~/.claude.json) is for personal or experimental setups that shouldn't be imposed on teammates. Jira fits the first category — it's shared team tooling. Personal Notion workspaces and experimental scratch servers fit the second — they're individual, and committing them to the project would either expose private workspaces or pollute the team's environment with half-finished experiments. Use environment variable expansion (e.g., ${JIRA_TOKEN}) for credentials so the project file can be committed safely.
Putting personal Notion workspaces in the project repo would mean every team member sees and potentially attempts to authenticate against everyone else's personal workspace. And the experimental scratch server probably shouldn't exist for teammates yet. "Version-controlled and consistent" applies to shared infrastructure, not personal tools.
Putting Jira in user-scoped config means every team member has to set up Jira independently, with no shared standard, and a new hire has nothing to pull from. Shared infrastructure belongs in shared configuration.
Git branches isolate code changes, not runtime configurations. Multiple users can't be on different branches simultaneously to get different MCP servers — that's not how branches work.