docs: revise architecture audit and roadmap for v2.6.0

Re-evaluate all architectural recommendations against the actual
codebase as it grew from v1.4.0 (5K lines, 12 modules) to v2.6.0
(17,830 lines, 35 modules).

Architecture audit:
- Reprioritize: dual-function anti-pattern across 15 modules is now #1
  (was analysis/formatting split at #3)
- Downgrade parser plugin system from #1 to #20 (parser.js shrank to
  404 lines after native engine took over)
- Add 3 new recommendations: decompose complexity.js (2,163 lines),
  unified graph model for structure/cochange/communities, pagination
  standardization
- Update all metrics and line counts to current state

Roadmap:
- Add Phase 2.5 (Analysis Expansion) documenting 18 modules shipped
  across v2.0.0-v2.6.0 (complexity, communities, structure, flow,
  cochange, manifesto, boundaries, check, audit, batch, triage,
  hybrid search, owners, snapshot, etc.)
- Mark Phase 5.3 (Hybrid Search) as completed early in Phase 2.5
- Update Phase 3 priorities based on revised architecture analysis
- Update version to 2.6.0, language count to 11, phase count to 10
- Add Phase 8 note referencing check command foundation from 2.5

Author: carlos-alm