[Docs]: Document SIST 1.0.0 Migration to Conda Release

[harryswift01]

Documentation Update

Update the SIST documentation for the maintained 1.0.0 release, with clear instructions for installing, running, and developing SIST.

Why Is This Needed?

SIST now has a maintained Conda packaging and release workflow, including managed runtime dependencies and regression testing against the installed package.

The existing documentation still reflects the older source-based workflow, including manual compilation, direct use of master.pl, and manual IRF setup.

The documentation should now reflect the supported 1.0.0 workflow so that users can install and run SIST without needing to understand the internal repository layout.

Suggested Changes

Document:

• Installing SIST with Conda.
• Required Conda channels.
• Verifying a successful installation.
• Running SIST through the installed sist command.
• Supported calculation modes:
  • melting/SIDD
  • Z-DNA
  • cruciform
  • competition
• Input file requirements.
• Output options and common examples.
• Command-line options and known CLI behaviour.
• Scientific parameter limitations and recommended ranges.
• IRF usage for cruciform and competition calculations.
• Building and running SIST directly from source.
• Source build requirements.
• Running the scientific regression suite.
• Building and testing the Conda package.
• The maintained scientific regression baselines.
• Citation information for SIST.

Clearly distinguish normal user installation and usage from development and source-build workflows.