Audit and correct package documentation

[aezell]

Summary

• align Git installation and package-filter examples with the unpublished npm state
• clarify configuration precedence, session reset behavior, checkpoint activation, and service routing
• distinguish HTTP JSON requests from the internal Pi JSONL RPC transport
• repair manual and automated test instructions, including remote paths and cleanup boundaries
• remove a stale reference to a nonexistent heavy e2e option

Verification

• npm run check
• npm run pack:check
• git diff --check
• all local Markdown links resolve
• upstream Pi and Sprites documentation reviewed for current behavior