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/01_projects/alpha.md

@@ -0,0 +1,15 @@
+---
+id: project-alpha
+title: Project Alpha
+type: project
+status: active
+tags: [alpha, demo]
+repo: alpha
+last_reviewed: 2026-01-01
+---
+
+# Project Alpha
+
+Depends on [Area Ops](area-ops){"type":"depends-on","link-info":"operations area"}.
+See [the demo resource](resource-demo) — resource landing page.
+External: [MCP spec](https://modelcontextprotocol.io/).

tests/fixtures/vault/02_areas/ops.md

@@ -0,0 +1,10 @@
+---
+id: area-ops
+title: Area Ops
+type: area
+tags: [ops]
+---
+
+# Area Ops
+
+Parent hub: [Project Alpha](project-alpha){"type":"part-of"}.

tests/fixtures/vault/03_resources/demo/index.md

@@ -0,0 +1,10 @@
+---
+id: resource-demo
+title: Demo Resource
+type: reference
+tags: [demo]
+---
+
+# Demo Resource
+
+Raw original kept in `raw/`. Related: [Area Ops](02_areas/ops.md).

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

@@ -0,0 +1,2 @@
+not a note
+[broken](../missing.md)

tests/fixtures/vault/README.md

@@ -0,0 +1 @@
+# README