Refactor nexus writer

[Modularius]

Summary of changes

• The structure of the nexus file is reflected in the directory structure of the nexus_structure module.
• Made error handling more robust
• Added Readme.rm in docs giving summary of source file structure.
• Calls hdf5 flush on each message rathe rather close and reopen
• Consolidates some tracing data into a single span for each message
• Added some docstrings

Closes Refactor Code in Nexus Writer to Follow Structure of Nexus Format, nexus-writer: address unpopulated values, and nexus-wrter: HDF5 version identifier is hardcoded.

Instruction for review/testing

General Code Review
Tested on Simulated Data and HiFi

[DanNixon]

From an initial look.

There are also a lot of violations of these style rules throughout:

• https://github.com/STFC-ICD-Research-and-Design/supermusr-data-pipeline/blob/main/docs/style.md#crab-no-empty-lines-in-use-statements
• https://github.com/STFC-ICD-Research-and-Design/supermusr-data-pipeline/blob/main/docs/style.md#crab-one-empty-line-between-fn-impl-and-mod-block