feat: add core file tools (read_file, write_file, search_files, patch)

Four new built-in tools replacing shell-only file operations:

- read_file: line-numbered output, pagination (offset/limit), binary
  detection, 2000-line cap
- write_file: create/overwrite with auto parent directory creation
- search_files: two modes — regex content search (with file_glob filter)
  and glob file search (sorted by mtime)
- patch: find-and-replace with first-only or replace_all, returns diff

All tools implement the kode.Tool interface with full JSON Schema.

28 TDD tests + race detector clean.

Author: jkyberneees