v0.6.0 - Autonomous Workflow Tools

Major Update: Autonomous Workflow Tools for Bioinformatics

This release adds 20+ new tools enabling fully autonomous workflow execution through OpenCode or Claude Code.

New Features

Core I/O with Pane Targeting

• write_to_pane - Send text to any pane by name
• send_keys - Ctrl+C, arrows, function keys
• search_pane - Regex search in pane content

Output Monitoring

• wait_for_output - Block until pattern appears
• wait_for_idle - Wait for output to stabilize
• tail_pane - Incremental output reading

Compound Operations

• run_in_pane - Execute command with wait and capture
• create_named_pane - Idempotent pane creation with registry
• destroy_named_pane - Cleanup named panes

REPL Interaction

• repl_execute - Run code in IPython/R/Julia, capture output
• repl_interrupt - Send Ctrl+C with prompt detection

SSH/HPC Integration

• ssh_connect - Open SSH sessions in named panes
• ssh_run - Execute remote commands
• job_submit - Submit SLURM/PBS jobs with tracking
• job_status - Check job state

Infrastructure

• SessionState class for persistent pane/SSH/job registry
• with_pane_focus helper for transparent pane targeting
• strip_ansi utility for clean LLM output
• Enhanced layout parser with full metadata

Breaking Changes

• Removed write_bytes (use send_keys)
• Removed run_command (use run_in_pane)
• Removed dump_screen (use read_pane)

Tool Count

56 tools total (was 35 in v0.5.0)