docs: Update PythonClientLibrary.md for v2.0.0

- Adds documentation for `get_all_note_paths`.
- Updates `get_active_note_content` docs for `return_format`.
- Adds new section "Handling Settings Discovery (`--get-settings-json`)"
  explaining the recommended script structure (`define_settings`,
  `_handle_cli_args`) and the consequences of not using it
  (API calls blocked in discovery mode). Emphasizes this structure
  is recommended, not strictly mandatory for basic execution, but
  crucial for settings and avoiding discovery-mode errors.
- Updates Initialization section to mention discovery mode check.
- Updates Error Handling section to mention discovery mode errors.
- General consistency checks and minor clarifications.

Author: mathe00