finish removing 3 zone

[jpn--]

This pull request removes support for "three-zone" (TAP-level) systems from the codebase and documentation, simplifying the model to only support one-zone (TAZ) and two-zone (MAZ/TAZ) systems. The changes include code cleanup, documentation updates, and removal of TAP-related configuration options and references.

Codebase cleanup and removal of TAP support:

• Removed the is_tap attribute from the MatrixSettings and related logic in trip_matrices.py, eliminating TAP-specific matrix writing and configuration. [1] [2] [3] [4]

Documentation updates:

• Removed all references to three-zone and TAP-based systems from the user and core documentation, including the detailed explanation and API documentation for the Transit Virtual Path Builder (TVPB). [1] [2] [3]
• Updated example scripts to remove TAP assignments and references, reflecting the removal of TAP-level modeling. [1] [2]