feat(ux): reorganize command groups and add Tufte-inspired help styling

- Add semantic coloring to help output (section headers, flags, types)
- Reorganize commands into clearer categories:
  - "Views & Reports" for readonly queries (ready, stats, blocked, etc.)
  - "Maintenance" for health/repair tasks (doctor, validate, migrate, etc.)
  - Merge "Issue Metadata" back into "Working With Issues"
- Highlight "doctor" as primary maintenance entry point with "(start here)"
- Create docs/UI_PHILOSOPHY.md documenting Tufte-inspired design principles
- Add guidance for PR to not include .beads/issues.jsonl

docs/UI_PHILOSOPHY.md

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+# UI/UX Philosophy
+
+Beads CLI follows Tufte-inspired design principles for terminal output.
+
+## Core Principles
+
+1. **Maximize data-ink ratio**: Only color what demands attention
+2. **Respect cognitive load**: Let whitespace and position do most of the work
+3. **Create scannable hierarchy**: Headers mark territory, bold creates scan targets
+
+## Color Usage
+
+| Purpose | Style | When to Use |
+|---------|-------|-------------|
+| Navigation landmarks | Accent (blue) | Section headers, group titles |
+| Scan targets | Bold | Command names, flag names |
+| De-emphasized | Muted (gray) | Types, defaults, closed items |
+| Semantic states | Pass/Warn/Fail | P0/P1 priority, bugs, blocked |
+| Standard text | Plain | Descriptions, prose, examples |
+
+## Anti-Patterns
+
+- Don't highlight everything (defeats the purpose)
+- Don't use color for decoration
+- Don't style closed/completed items (they're done, users don't care)
+- Keep examples plain (copy-paste friendly)
+
+## Help Output Styling
+
+### Main Help (`bd help`)
+
+- **Group headers** (Working With Issues:, Views & Reports:, etc.): Accent color
+- **Command names** in listings: Bold
+- **Command references** in descriptions ('comments add'): Bold
+
+### Subcommand Help (`bd <cmd> --help`)
+
+- **Section headers** (Usage:, Flags:, Examples:): Accent color
+- **Flag names** (-f, --file): Bold
+- **Type annotations** (string, int, duration): Muted
+- **Default values** (default: ...): Muted
+- **Descriptions**: Plain
+- **Examples**: Plain (copy-paste friendly)
+
+## Ayu Theme
+
+All colors use the Ayu theme with adaptive light/dark mode support.
+See `internal/ui/styles.go` for implementation.
+
+| Color | Light Mode | Dark Mode | Usage |
+|-------|------------|-----------|-------|
+| Accent | #399ee6 | #59c2ff | Headers, links |
+| Command | Bold white | Bold white | Command/flag names |
+| Muted | #828c99 | #6c7680 | Types, defaults |
+| Pass | #6cbf43 | #7fd962 | Success states |
+| Warn | #e6ba7e | #ffb454 | Warnings, P1 |
+| Fail | #f07171 | #f26d78 | Errors, bugs, P0 |