Document search functionality in user-story-01-search.md

[Copilot]

Addresses TODO items in doc/v3/user-story-01-search.md from the v3-ui-ux branch by documenting the existing search functionality based on codebase analysis.

Changes

• Current Pages: Listed 5 main search pages with URL paths
• Navigation Flow: Added mermaid diagram showing user flow from entry points through search tabs, forms, results, detail pages, and downloads
• Searchable Fields: Documented fields and CQL predicates for each data type:
  • Studies (8 fields): ID, author, title, abstract, citation, keywords, DOI
  • Matrices (5 fields): ID, title, type, NTAX, NCHAR
  • Trees (6 fields): ID, title, type, kind, quality, NTAX
  • Taxa (7 fields): ID, NCBI ID, uBio ID, name, label, variant
  • Tree Topologies: form-based topology matching (not CQL)
• Pages Inventory: Complete table of 22+ pages organized by category (main search, secondary, detail, download endpoints, API)

Navigation Flow Diagram

graph TB
    NAV[Navigation Bar] --> STUDY[Study Search]
    NAV --> MATRIX[Matrix Search]
    NAV --> TREE[Tree Search]
    NAV --> TAXON[Taxon Search]
    NAV --> TREETOP[Tree Topology Search]
    
    STUDY --> RESULTS[Search Results]
    RESULTS --> STUDY_DETAIL[Study Summary]
    RESULTS -.->|Project Results| MATRIX

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Documentation derived from JSP search forms, Spring controller mappings, and servlet configuration in treebase-web.

Original prompt

Go into branch v3-ui-ux and address the TODO items in doc/v3/user-story-01-search.md by updating the document in place.

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