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
+---

skills/read_file/run.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python3
+"""Read a file from /workspace with optional line range."""
+import json
+import os
+import sys
+
+args = json.loads(sys.stdin.read())
+path = args.get("path", "")
+offset = max(int(args.get("offset", 1)), 1)
+limit = max(int(args.get("limit", 200)), 1)
+
+WORKSPACE = os.environ.get("WORKSPACE", "/workspace")
+
+# Resolve to absolute and ensure it stays under /workspace
+resolved = os.path.realpath(path)
+if not resolved.startswith(WORKSPACE + "/") and resolved != WORKSPACE:
+    print(f"[error: path must be under {WORKSPACE}]")
+    sys.exit(0)
+
+if not os.path.exists(resolved):
+    print(f"[error: file not found: {path}]")
+    sys.exit(0)
+
+if os.path.isdir(resolved):
+    entries = sorted(os.listdir(resolved))
+    print(f"Directory listing of {path} ({len(entries)} entries):")
+    for entry in entries[:100]:
+        full = os.path.join(resolved, entry)
+        kind = "dir" if os.path.isdir(full) else "file"
+        print(f"  {entry} ({kind})")
+    if len(entries) > 100:
+        print(f"  ... and {len(entries) - 100} more")
+    sys.exit(0)
+
+# Binary detection — check first 512 bytes
+try:
+    with open(resolved, "rb") as f:
+        chunk = f.read(512)
+    if b"\x00" in chunk:
+        size = os.path.getsize(resolved)
+        print(f"[binary file: {path} ({size} bytes)]")
+        sys.exit(0)
+except Exception as e:
+    print(f"[error reading file: {e}]")
+    sys.exit(0)
+
+# Read with line range
+try:
+    with open(resolved) as f:
+        lines = f.readlines()
+except Exception as e:
+    print(f"[error reading file: {e}]")
+    sys.exit(0)
+
+total = len(lines)
+start_idx = offset - 1  # 0-based
+end_idx = min(start_idx + limit, total)
+
+if start_idx >= total:
+    print(f"[file has {total} lines — offset {offset} is beyond end of file]")
+    sys.exit(0)
+
+for i in range(start_idx, end_idx):
+    print(f"{i + 1}\t{lines[i]}", end="")
+
+if end_idx < total:
+    print(f"\n[showing lines {offset}-{end_idx} of {total} — use offset={end_idx + 1} to read more]")