Improve SDK integration, add multi-instance support and plugin loading

[EON-LEE]

Title: Improve SDK integration, add multi-instance support and plugin loading

Body:

Summary

• Replace MCP-based permission server with in-process canUseTool callback for simpler, more
  reliable tool approval
• Add settingSources support so Claude Code plugins and settings work through the bot
  automatically
• Support running multiple bot instances from a single codebase via ENV_FILE
• Add configurable slash commands, bot display name, and system prompt customization
• Add BASE_DIRECTORY fallback in working directory resolution
• Update Slack app manifest with additional required scopes (channels:read, groups:read,
  mpim:read, interactivity)
• Update README with comprehensive documentation

Key Changes

Permission handling (permission-mcp-server.ts)

Replaced the standalone MCP stdio server with simple exported functions (requestSlackApproval,
resolveApproval). The canUseTool SDK callback handles permission requests in-process instead of
spawning a separate MCP server.

Configuration (config.ts)

Added settingSources, systemPromptAppend, botDisplayName, slashCommand, and ENV_FILE
support.

Claude handler (claude-handler.ts)

Uses canUseTool callback instead of permissionMode + permissionPromptToolName, which avoids
the "MCP tool not found" error.

Test plan

• Bot responds to DMs and channel mentions
• Tool approval buttons work when message starts with plan
• Multiple instances run independently with ENV_FILE=.env.bot2 npm run dev
• Claude Code plugins load via settingSources

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