docs: Clarify ii-commons CLI usage

[liujuanjuan1984]

Summary

• Makes ii-commons the primary command surface across the README, skill guide, API reference, and OpenAI agent prompt.
• Keeps the human-facing cold-start prompt concise while avoiding source-path-oriented usage examples.
• Aligns documentation around npm/npx CLI usage and global PATH diagnostics.
• Deduplicates search payload option construction and adds PubMed filter coverage.

Why

The npm CLI is the expected retrieval interface. The docs should help humans cold-start an agent with the skill while guiding agents toward ii-commons ... instead of internal script paths.

Validation

• Temporary-lockfile npm audit: 0 vulnerabilities
• npm test
• npm run pack:dry