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/package.json

@@ -5,8 +5,10 @@
   "main": "./dist/index.js",
   "types": "./dist/index.d.ts",
   "scripts": {
-    "build": "rm -rf dist && tsc",
-    "dev": "tsc -w"
+    "build": "rm -rf dist && tsc -p tsconfig.build.json",
+    "dev": "tsc -w -p tsconfig.build.json",
+    "test": "vitest run",
+    "test:watch": "vitest"
   },
   "dependencies": {
     "@ai-sdk/anthropic": "^2.0.63",
@@ -29,8 +31,8 @@
     "express": "^5.2.1",
     "glob": "^13.0.0",
     "google-auth-library": "^10.5.0",
-    "isomorphic-git": "^1.29.0",
     "googleapis": "^169.0.0",
+    "isomorphic-git": "^1.29.0",
     "mammoth": "^1.11.0",
     "node-html-markdown": "^2.0.0",
     "ollama-ai-provider-v2": "^1.5.4",
@@ -48,6 +50,7 @@
     "@types/express": "^5.0.6",
     "@types/node": "^25.0.3",
     "@types/papaparse": "^5.5.2",
-    "@types/pdf-parse": "^1.1.5"
+    "@types/pdf-parse": "^1.1.5",
+    "vitest": "catalog:"
   }
 }