Add read_file skill, session persistence, and update script

- New read_file skill: paginated file reading with line ranges,
  path restricted to /workspace, binary detection, directory listing
- Session persistence via SQLite + FTS5: conversation history survives
  agent restarts, last N messages restored into deque on boot,
  auto-prune to 1000 messages
- Update truncation hint to reference read_file instead of run_command
- New scripts/update.sh for patching rootfs + rebuilding snapshot

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

skills/read_file/SKILL.md

@@ -0,0 +1,17 @@
+---
+name: read_file
+description: Read a file from the workspace with optional line range. Use this to view large tool outputs, logs, or any file in /workspace.
+parameters:
+  path:
+    type: string
+    description: Path to the file to read (must be under /workspace)
+    required: true
+  offset:
+    type: integer
+    description: Start reading from this line number (default 1)
+    required: false
+  limit:
+    type: integer
+    description: Maximum number of lines to return (default 200)
+    required: false
+---