Highlight Plan Mode and Interactive Q&A as core approaches in quickstart

Condense project CLAUDE.md to match global version

Remove 21 optional skills and 8 optional Cursor extensions

Switch default mode to sandbox, remove Zotero/paper-search MCP from core

Add Marp slide deck: Coding Agents for Academic Research

Incorporate colleague feedback: beginner-friendly README overhaul

Automate plugin installation and improve prerequisite guidance

Update installation instructions for Claude Code CLI

Update installation command for Claude Code CLI

Improve quickstart prompts with realistic research examples

Add Useful Commands section with CLI, session, and keyboard references

Merge docs into README, switch to bypassPermissions, add quickstart

Switch to permissive defaults, add plugin URLs, improve Phase 3 and tips

Restructure into core/optional with workflow-driven README

Fix Codex review findings: README count math, lit-review tool names