feat: wire repbox run to adapter execution path

[sheljustdoes]

Goal

Connect repbox run to execute a minimal end-to-end adapter flow (RepeatModeler -> RepeatMasker) using the new architecture.

Why

Milestone B needs a real execution path through the new CLI to prove migration feasibility and unblock validation.

Scope

In scope

• Update CLI run command to create runtime context
• Invoke RepeatModeler adapter, then RepeatMasker adapter
• Pass core parameters (input, output, threads, engine, optional library)
• Emit readable run summary + errors

Out of scope

• Full TE class orchestration
• Multi-branch workflow scheduling
• Backward compatibility for every legacy CLI arg

Acceptance Criteria

• repbox run executes adapter chain in expected order
• Fails fast with actionable errors when required tools are missing
• Writes outputs/logs into specified output directory
• Success/failure path returns consistent CLI exit codes
• Smoke test command and usage documented

Suggested files

• src/repbox/cli.py
• src/repbox/workflow/engine.py
• src/repbox/workflow/context.py
• tests/integration/test_run_smoke.py (or equivalent)

Project fields

• Area: CLI
• Priority: P0
• Size: L
• Target Release: v0.4.0