feat: add direct command execution without templates

[proboscis]

Summary

Add the ability to run and log commands directly without requiring a template, making runbox more convenient for ad-hoc command execution.

New Commands

• runbox run -- <command> - Execute a command directly and log it as a Run
• runbox log -- <command> - Alias for runbox run --

Features

• Direct command execution: Run any command without creating a template first
• Git context capture: Automatically captures commit + uncommitted changes for reproducibility
• Options supported:
  • --runtime <bg|tmux> - Execution runtime (default: bg)
  • --timeout <seconds> - Command timeout (default: 0 = no timeout)
  • --env KEY=VALUE - Additional environment variables
  • --cwd <path> - Working directory (default: current)
  • --no-git - Skip git context capture
• Source field: Runs are marked with "source": "direct" to distinguish from template-based runs
• Full compatibility: Works with runbox ps, runbox show, runbox logs, runbox replay

Example Usage

# Simple command
runbox run -- echo hello

# With runtime option
runbox run --runtime tmux -- python train.py --epochs 10

# Using the log alias
runbox log -- make test

# With environment variables
runbox run --env CUDA_VISIBLE_DEVICES=0 -- python train.py

# Skip git context capture
runbox run --no-git -- echo "quick test"

Test plan

• All existing tests pass
• New integration tests for direct execution (20 tests)
• Tests cover: simple commands, timeout, env vars, cwd, no-git, runtimes, log alias, error cases

Related Issue

ISSUE-027

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