Reorganize markdown documentation into structured doc/ directory

[Copilot]

The root directory contained 9 scattered markdown files with significant redundancy and unclear organization. This consolidates and structures the documentation.

Changes

Root cleanup

• Removed all markdown files except README.md from root
• Updated README.md with organized documentation links

New structure: doc/

• development/ - Build and deployment guides
  • BUILDING.md - Consolidated build instructions
  • DEPLOYING.md - Deployment procedures with DWR integration notes
• technical-notes/ - Implementation details
  • DWR.md - Direct Web Remoting Spring 5 compatibility
  • UPGRADES.md - Consolidated SLF4J, Jersey 2.x, and JUnit 4 migrations (merged from 4 separate files: DEPLOYMENT_FIX_ANALYSIS.md, FIX_SUMMARY.md, JERSEY_2X_UPGRADE.md, JUNIT4_MIGRATION.md)
• archive/ - Deprecated TreeBASE v.1 migration procedures
  • INSTALL.md - Data loading environment (marked deprecated)
  • LOADING.md - Nexus file import (marked deprecated)
• README.md - Navigation guide

Content improvements

• Eliminated duplication across 4 fix/analysis documents
• Added deprecation notices to archived v.1 migration docs
• Updated all internal cross-references
• Removed outdated deployment workaround instructions

Original prompt

In the root there is a proliferation of *.md files. Clean these up:

• only keep README.md in the root
• move all others to doc/
• check the documents for accuracy and consistency
• remove all old, deprecated information
• structure the *.md files in a logical set
• carry info over from one to the other if you have to
• if need be, link between the files

---

✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.