refactor: extract kb_framework package, build graph in memory

Scripts become thin CLIs over kb_framework (graph, query, query_tools,
vault, instructions) so the hosted read-only connector shares one
implementation with the stdio server. The MCP server builds the graph
from Markdown on demand and invalidates it on writes; refresh_graph
rebuilds in memory and reports validation problems. Pre-commit hook
validates only; index/graph.json is no longer read, written or staged
(generate-graph.py --write remains for operators). Golden fixtures pin
graph and tool payloads to the previous output. Agent and skill docs
updated to match.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>

tests/fixtures/vault/03_resources/demo/raw/original.md

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+[broken](../missing.md)