docs: comprehensive documentation update for post-v0.16.0 features

[bug-ops]

Summary

• Deep documentation update covering all 44 commits since v0.16.0 across specs, mdbook, READMEs, and references
• 36 files changed, +1469 lines across 3 documentation layers
• All stale HandoffContext references removed (reverted in revert(orchestration): remove HandoffContext and validation layer (#2076, #2078) #2082)

Specs (8 files in specs/)

• 004-memory: semantic response caching, anchored summarization, compaction probe, importance scoring
• 012-graph-memory: MAGMA typed edges, SYNAPSE spreading activation
• 006-tools: TAFC, schema filtering, result cache, dependency graph
• 002-agent-loop: HiAgent subgoal-aware compaction
• 009-orchestration: plan template caching (HandoffContext section removed)
• 015-self-learning: multi-language FeedbackDetector (7 languages)
• 007-channels: channel feature parity (16-method trait)
• handoff-skill-system: rewritten to reflect current state (skill-based YAML protocol, no code validation)

mdbook (16 pages in book/src/)

• why-zeph.md fully rewritten with new value proposition sections
• references.md expanded with 7 new research papers (SYNAPSE, MemOS, HiAgent, TAFC, APC, Less is More, Speculative Tool Calls, MAST)
• Updated: concepts (memory, graph-memory, tools, task-orchestration), guides (semantic-memory, self-learning), advanced (context, tools, self-learning, tui), reference (configuration, cli), architecture (crates-overview, token-efficiency), getting-started (wizard)

READMEs (10 files)

• Root README + 9 crate READMEs (memory, tools, core, orchestration, tui, channels, scheduler, skills, sanitizer)

Test plan

• mdbook build book/ passes without errors
• No stale HandoffContext references in any documentation file
• All new config field names verified against source code
• Visual review of rendered mdbook pages