Add comprehensive project documentation

Create complete documentation set in doc/ folder:

- index.rst: Main project overview, quickstart, architecture
- philosophy.rst: Design principles, KDL rationale, VCS diversity
- roadmap.rst: Phased development plan (Phase 2.5 current, Phase 3 graphs next)
- history.rst: Development timeline, key decisions, lessons learned
- manifest.rst: Updated to v0.2.0, added Fossil docs, schema upgrade notes

Documentation covers:
- Current state (Phase 2.5)
- Complete roadmap through Phase 4
- Visual dependency graph plans (Phase 3)
- Philosophy and anti-corporate stance
- History from origins to present

All documentation in reStructuredText format for website generation.

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