Update documentation for SIST 1.0.0

[harryswift01]

Summary

This PR updates the SIST documentation for the 1.0.0 release, providing a clearer user-facing structure for installation, usage, source-level operation, development, testing, and citation.

The documentation retains the existing scientific guidance while reflecting the maintained Conda packaging, installed sist command, regression testing, and CCPBioSim maintenance workflow.

Changes

Documentation structure

• Reorganised the documentation into dedicated pages for the user guide, installation, source usage, development and testing, and citation.
• Updated the main documentation index and navigation order.

Installation and usage

• Added the Conda installation route for SIST.
• Documented the installed sist command as the primary user interface.
• Added examples for melting, Z-DNA, cruciform, and competition calculations.
• Documented input requirements, command-line options, output behaviour, and IRF-dependent calculations.
• Retained the recommended scientific parameter ranges and algorithm limitations.

Source and development documentation

• Documented the source components, including master.pl, IR_finder.pl, trans_three, and trans_compete.
• Retained instructions for building and running the C++ components directly.
• Added guidance for source-tree testing and the maintained scientific regression baselines.
• Documented the Conda package build and test workflow.
• Added an overview of the release workflow and package validation process.

Citation and maintenance

• Added guidance for citing the SIST software and associated scientific methods.
• Retained the original SIST scientific references.
• Identified CCPBioSim as the current maintainer and development organisation.
• Retained the original contact information separately from current maintenance information.

Impact

• Provides a clearer and more maintainable documentation structure for SIST 1.0.0.
• Gives users a supported installation and usage path through Conda and the sist command.
• Preserves the scientific guidance and source-level information from the original SIST documentation.
• Documents the validation and release processes used to maintain reproducible scientific behaviour.
• No changes are made to the scientific implementation or numerical behaviour.

[jimboid]

A comprehensive treatment of the documentation for the starting release of SIST as it will stand at 1.0.0. This will enable existing users and new users to pick up and run with the code in its new home. Thanks for this!