Add uv environment and miRNA case-study workflow

[zacharopoulou]

Main changes

• Added pyproject.toml for the shared uv environment.
• Added Jupyter support for Simulation experiments.ipynb.
• Added case_study_for_mirna/ with the miRNA case-study scripts.
• Added run_mirna_auprc_table.py for the manuscript miRNA table runs.
• Updated the README files with installation and run instructions.

Notes

• The main src/ implementation is kept aligned with devel.
• The miRNA workflow uses miRBench for dataset access during execution.