Refactor: Enforce Read prerequisite for patch/replace tools

[alvis-HaoH]

Related Issue

Resolve #(174)

Description

• Introduce a session-scoped FileOpsWindow that tracks which files have been read via ReadFile.
• Inject the shared window through the agent runtime so every file tool instance shares the same state.
• Update ReadFile to mark files as read after a successful call, and make PatchFile/StrReplaceFile refuse edits unless
  the file was read earlier in the session.
• Refine user-facing docs to call out the new “read before edit” requirement and expand pytest coverage for both happy-path and failure scenarios.

Testing

• uv run pytest tests/test_patch_file.py tests/test_str_replace_file.py -vv