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/test_mcp_server.py

@@ -40,9 +40,7 @@ class ToolTestCase(unittest.TestCase):
         self._tmp = tempfile.TemporaryDirectory()
         self.root = Path(self._tmp.name).resolve() / "vault"
         self.root.mkdir()
-        self.state = mcp.AppState(
-            root=self.root, graph_path=self.root / "index" / "graph.json"
-        )
+        self.state = mcp.AppState(root=self.root)
         _git(self.root, "init", "-q", "-b", "main")
         _git(self.root, "config", "user.email", "test@example.com")
         _git(self.root, "config", "user.name", "Test")
@@ -440,18 +438,13 @@ class TestGraphSummary(ToolTestCase):
     """
 
     def write_graph(self, nodes: list) -> None:
-        self.state.graph_path.parent.mkdir(parents=True, exist_ok=True)
-        self.state.graph_path.write_text(
-            json.dumps(
-                {
-                    "version": 1,
-                    "generated_at": "2026-09-14T00:00:00Z",
-                    "nodes": nodes,
-                    "edges": [],
-                }
-            ),
-            encoding="utf-8",
-        )
+        # The graph lives in memory; seed the cache the way a build would.
+        self.state.graph_cache = {
+            "version": 1,
+            "generated_at": "2026-09-14T00:00:00Z",
+            "nodes": nodes,
+            "edges": [],
+        }
 
     def node(self, node_id: str, **fields) -> dict:
         base = {