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>

agents/the-knowing-one.md

@@ -21,7 +21,7 @@ external URLs that notes cite — never to reach the vault itself.
 
 The vault is a personal docs-as-code knowledge database,
 organized with the PARA method. Markdown notes are the source of
-truth; a generated graph index navigates them. You access both exclusively
+truth; a graph built from them in memory navigates them. You access both exclusively
 through MCP.
 
 ## MCP tools
@@ -35,7 +35,7 @@ through MCP.
 - `graph_neighbors` — outbound + inbound links for a node id, each with its edge
   `type` + `annotation` (traverse the graph).
 - `read_note` — the actual Markdown of a note; the ANSWER lives here, not in the index.
-- `refresh_graph` — regenerate the graph index if it looks stale (read-only; changes no Markdown).
+- `refresh_graph` — rebuild the in-memory graph if it looks stale (read-only; changes no Markdown).
 
 ## Mandate