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_external_vault.py

@@ -20,6 +20,8 @@ class ExternalVaultTests(unittest.TestCase):
         self.base = Path(self.tmp.name)
         self.framework = self.base / "framework space"
         shutil.copytree(FRAMEWORK / "scripts", self.framework / "scripts")
+        shutil.copytree(FRAMEWORK / "kb_framework", self.framework / "kb_framework",
+                        ignore=shutil.ignore_patterns("__pycache__"))
         shutil.copy2(FRAMEWORK / "Makefile", self.framework / "Makefile")
         self.vault = self.base / "vault space"
         self.other = self.base / "other"
@@ -115,15 +117,14 @@ class ExternalVaultTests(unittest.TestCase):
                            ("write_note", {"path": "../escape.md", "content": "escape"})]:
             self.assertTrue(self.tool(tool, args).get("isError"))
 
-    def test_refresh_uses_absolute_framework_generator_and_writes_when_validating(self):
+    def test_refresh_validates_in_memory_and_never_runs_vault_tools(self):
         (self.vault / "scripts").mkdir()
         (self.vault / "scripts/generate-graph.py").write_text("raise RuntimeError('vault tool used')\n")
         result = self.tool("refresh_graph", {"validate": True})
         self.assertFalse(result.get("isError"), result)
-        command = result["structuredContent"]["command"]
-        self.assertEqual(command[1], str(self.framework / "scripts/generate-graph.py"))
-        self.assertEqual(command[command.index("--vault-root") + 1], str(self.vault))
-        self.assertTrue((self.vault / "index/graph.json").exists())
+        self.assertEqual(result["structuredContent"]["vault_root"], str(self.vault))
+        self.assertEqual(result["structuredContent"]["node_count"], 1)
+        self.assertFalse((self.vault / "index/graph.json").exists())
         summary = self.tool("graph_summary")
         self.assertFalse(summary.get("isError"), summary)
 
@@ -178,16 +179,17 @@ class ExternalVaultTests(unittest.TestCase):
         def make(*args):
             return subprocess.run(["make", "-C", str(self.framework), f"VAULT_ROOT={self.vault}", *args],
                                   env=self.env, capture_output=True, text=True)
-        proc = make("graph", "install-hooks")
+        proc = make("validate-graph", "install-hooks")
         self.assertEqual(proc.returncode, 0, proc.stdout + proc.stderr)
         hook = self.vault / ".git/hooks/pre-commit"
         self.assertTrue(hook.exists())
-        self.git(self.vault, "add", "index/graph.json")
         proc = subprocess.run([str(hook)], cwd=self.other, env=self.env, capture_output=True, text=True)
         self.assertEqual(proc.returncode, 0, proc.stdout + proc.stderr)
-        (self.vault / "03_resources/new.md").write_text("# new\n")
+        (self.vault / "03_resources/new.md").write_text("# new\n[gone](nowhere)\n")
         proc = subprocess.run([str(hook)], cwd=self.other, env=self.env, capture_output=True, text=True)
         self.assertNotEqual(proc.returncode, 0)
+        self.assertIn("nowhere", proc.stdout + proc.stderr)
+        self.assertFalse((self.vault / "index/graph.json").exists())
         self.assertFalse((self.framework / "index/graph.json").exists())
 
     def test_installer_preserves_unmanaged_hooks_and_reinstalls_managed_hook(self):