docs: weave exocortex and cognitive mode concepts into platform documentation

[aaronsb]

Context

Issue #331 covers updating MCP tool descriptions with exocortex/System 1/System 2/desire path framing. This companion issue covers the broader documentation surfaces where these concepts should appear.

Problem

The platform documentation (README, guides, ADR index) describes the system technically — what it does, how to install it, what the API looks like. It doesn't describe what the platform is for from the agent's perspective. An agent (or human) reading the docs should understand:

1. This is an exocortex — a persistent external reasoning structure, not a search engine with extra steps
2. Two cognitive modes exist — reflexive exploration (System 1: search/connect/related) and deliberate reasoning (System 2: GraphProgram/Cypher)
3. The graph has desire paths — traversal weight accumulates with use, shaping what connect finds. Young graphs and new edges behave differently than mature ones.

Where to apply

Surface	What to add
README.md project overview	Exocortex framing — what this is and why it exists beyond "knowledge extraction system"
docs/guides/ (new or existing)	Agent user guide — the productive loop (search → details → connect → program → edit → verify), when to switch modes, desire path behavior
ADR index intro	Brief note on the System 1/2 architecture — reflexive tools backed by vector search vs deliberate tools backed by Cypher composition
CLAUDE.md project overview	One-liner: "Agents use this as an exocortex — persistent reasoning that survives across sessions"
CLI --help text	Consider adding cognitive mode hints to kg search --help vs kg program --help

Non-goals

• Not rewriting all docs — just threading these concepts into existing surfaces
• Not changing tool behavior — that's ux: connect tool should indicate structural fallback paths #326, ux: lower label resolution threshold or add fuzzy matching #327, ux: reframe program tool as primary reasoning tool in MCP descriptions #328, ux: default continue_on_error=true for graph edit queue #329, ux: add AGE Cypher syntax examples to program tool description #330
• Not a philosophy paper — keep it concrete and practical

Related

• docs: add exocortex and cognitive mode framing to MCP descriptions #331 (MCP description updates — tool-level framing)
• ux: connect tool should indicate structural fallback paths #326 (connect fallback transparency)
• ux: reframe program tool as primary reasoning tool in MCP descriptions #328 (program tool as primary reasoning tool)
• Agent UX report: /home/aaron/Downloads/knowledge_graph_tool_ux_report.md