chore(claude): Remove unused commands and agents

Remove legacy commands and agents that are no longer needed:
- docs/ commands (start-project, next-task, update-task-documentation)  
- Nextflow generation commands (process, subworkflow, workflow)
- Parallel execution commands (init-parallel, exec-parallel)
- taskwarrior-expert and timewarrior-expert agents
- nextflow Python script

Streamlines to only actively used git/jj commands and cursor agent, all with explicit model: sonnet directives.

Author: edmundmiller