Improve ingestion reporting and agent setup

[jb-thery]

Summary

• Expand ingestion inventory with unsupported/oversized/secret-like skipped-file reporting and checksum-based stale detection.
• Add broader text/document parsing support, configurable ingestion limits, and tests for skipped files, EPUB, MCP project-root resolution, and stale audit detection.
• Add the bundled mimir-markdown-report skill plus Claude Code and Codex MCP helper snippets generated by kb setup.
• Bump packages to 0.4.7 and regenerate committed dist/ artifacts.

Validation

• pnpm validate
• git diff --cached --check
• staged secret scan for common token patterns