Docs update file i/o

[mgcooper]

This request includes updates to the documentation related to file input/output in the data.rst and quickstart.rst files. The changes provide more detailed information to users. A follow up request will propose to move the File I/O section out of data.rst to a dedicated configuration.rst file and add a new "Configuration and File I/O" section to the docs, including updating the TOC and anything needed to compile. The changes to the actual content are proposed here first by updating data.rst for easier comparison with existing content, before moving it to a dedicated section in the docs. Double check the updated file and parameter descriptions, especially the new Output File table at the end of data.rst.

Changes Include:

• File I/O Section Rewrite: Added more details, updated parameter definitions tables and JSON entries, and included tree diagrams of input and output directories.
• Separation of Configuration Files from Data Inputs: Introduced distinction between configuration files inputs and flowline / boundary JSON files inputs.
• New Output File Definitions Table: Added a table defining all output files so users understand what files the model produces especially the final flowline and mesh files.
• Quickstart Guide: Rewrote some bullet points to make it more readable.

These updates aim to make the examples and docs more user-friendly especially for new users to understand the file inputs and outputs and how to setup the example configuration.

The branch name for these changes is docs-update-file-i/o.