Create Amber MD workflow API

[aalexmmaldonado]

Description
Provide a high‑level Python API—AmberRunner—to configure, launch, monitor, and collect results from Amber molecular dynamics simulations. The runner should handle input file generation, job submission (local or via a scheduler), progress reporting, and seamless integration with AmberDigester.

Key tasks:

• Define methods: configure(structure, md_parameters), submit(executor), status(), and collect().
• Support execution backends: direct subprocess, SLURM, PBS.
• Stream logs in real time and expose callback hooks for custom progress monitoring.
• Automatically trigger digestion upon job completion if configured.

Acceptance Criteria

• AmberRunner API matches a documented interface and supports at least two execution modes.
• Example script in examples/workflows/amber_md.py runs through all steps and outputs a digested schema.
• Unit and integration tests verify job submission simulation (stubbed executor), status polling, and result collection.
• Clear error handling when input files are invalid or when the MD engine crashes.