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>

scripts/vault_root.py

@@ -1,11 +1,18 @@
-"""Resolve the selected data directory consistently for framework command-line tools."""
+"""Resolve the selected data directory consistently for framework command-line tools.
+
+Also puts the framework root on `sys.path` so every script can import the
+`kb_framework` package from a plain checkout without installing it.
+"""
 
 import argparse
 import os
+import sys
 from pathlib import Path
 
 
 FRAMEWORK_ROOT = Path(__file__).resolve().parents[1]
+if str(FRAMEWORK_ROOT) not in sys.path:
+    sys.path.insert(0, str(FRAMEWORK_ROOT))
 
 
 def parse_vault_args(parser: argparse.ArgumentParser) -> argparse.Namespace: