feat: restore security validation and add unified download tools

[erphenheimer]

Summary

v3.0.0 simplified the architecture but removed all input validation (security.ts was deleted entirely). This PR restores security protections while preserving v3's lean design:

• Restore src/utils/security.ts with validateProjectId, validateArxivId, validateDoi, ensureWithinDirectory
• Apply validation in CLI (research.ts) and commands (commands.ts) to prevent path traversal
• Add unified paper_download tool (merges arxiv-download + unpaywall-download, validates all identifiers)
• Add paper_browser tool for paginated reading of large papers
• Remove unsafe bash template skill (skills/paper-download/) — replaced by typed tool with input validation
• Update SKILL.md references and documentation

Motivation

The v3.0.0 refactor deleted src/utils/security.ts which contained critical protections against:

• Path traversal: LLM-generated project IDs like ../../etc could escape the workspace
• Shell injection: bash templates in SKILL.md passed unvalidated arXiv IDs to shell commands
• Identifier injection: No validation on arXiv IDs or DOIs before use in HTTP requests

This PR adds ~350 lines of focused security + tooling code without reverting v3's architectural simplification (~7500 lines removed).

Test plan

• npm run build passes with no TypeScript errors
• validateProjectId rejects ../../etc, accepts my-project-1
• validateArxivId rejects ; rm -rf /, accepts 2401.12345
• ensureWithinDirectory blocks path traversal attempts
• paper_download tool validates IDs before making HTTP requests

[erphenheimer]

对不起，我第一次搞这个不太懂，我回去研究研究，抱歉