Refactor builtin file tools beyond workspace scope

Replace workspace-scoped builtin file tools with general-purpose file-* tools that accept relative, absolute, and ~/ paths. Relative paths still resolve against the configured workdir.

File operations within the workdir are auto-approved. File operations outside the workdir now emit file permission metadata and require user approval, with support for once, session, and persistent grants.

Add a shared filesystem layer for text-focused read/write/edit/list/search operations, including binary-file safeguards for text reads. parseFile and LLMParse continue to read file buffers for document/image parsing.

Update copilot prompts, background/live-note agents, knowledge workflows, and renderer labels/UI to use the new file-* tool surface and permission details.

Add package-local Vitest setup for @x/core with colocated filesystem unit tests covering path resolution, canonical permission paths, binary detection, read/write/edit behavior, glob, and grep.

apps/x/packages/core/vitest.config.ts

@@ -0,0 +1,11 @@
+import { defineConfig } from "vitest/config";
+
+export default defineConfig({
+  test: {
+    environment: "node",
+    include: ["src/**/*.test.ts", "src/**/*.spec.ts"],
+    globals: false,
+    clearMocks: true,
+    restoreMocks: true,
+  },
+});