[dark-mode] Phase 4.3: Prune outdated documentation

Remove 12 documentation files that became inaccurate after Phase 3-4 changes
(removed ThemeManager methods, color palette redesign, WCAG fixes, test moves).

Deleted (outdated — referenced removed API methods, old color palette):
- CHECKPOINT_REPORT.md, COMPLETION_SUMMARY.md, SESSION_COMPLETION.md
- 1.1-theme-manager-foundation/ (3 files) — referenced onThemeToggle(), toggleTheme()
- 1.2-css-variables-infrastructure/ (3 files) — old VS Code palette colors
- 2.1-2.3-header-toggle-button/ (3 files) — referenced onThemeToggle()

Kept (verified accurate):
- 1.3-app-initialization/, 2.4-2.8 component docs — still correct
- progress-report.md — authoritative doc (paths fixed: e2e/ → src/test/e2e/)
- Requirements.md, Design.md, Tasks.md, README.md — spec docs

Author: Hunta