Release v0.4.1

v0.4.1: rootless Docker support & dependency-free nodes fix (#67)

* fix: support rootless Docker by respecting DOCKER_HOST env var

* print docker socket path in headless mode for debugging

* fix: use connect_with_defaults to actually respect DOCKER_HOST env var

* fix: dependency-free nodes

dependency-free nodes

   Previously, input_files/ was only copied to the first job in execution
   order. Now it copies to ALL jobs that have no dependencies.

   - Modified copy_input_files_to_first_job() to accept workflow_metadata
   - Filter jobs by checking if dependencies list is empty
   - Copy input_files to each dependency-free job's inputs/ folder

   Fixes issue where workflows with multiple independent starting nodes
   (e.g., ligand-upload and protein-upload) only received input files
   in one node.

* refactor: extract copy_dir_recursive to shared utils module and rename misleading function

  Changes:
  - Extract duplicated copy_dir_recursive from headless.rs and docker/state.rs into silva/src/utils.rs
  - Rename copy_input_files_to_first_job → copy_input_files_to_dependency_free_jobs to reflect actual behavior

* cargo fmt