Fix get_wf_files to use git ls-files

[jonasscheid]

Description

get_wf_files() uses fnmatch to filter files based on .gitignore patterns, but fnmatch does not implement gitignore semantics correctly. For example, a .gitignore entry work/ should match scripts/work/ at any depth, but fnmatch.fnmatch("scripts/work/file", "work/*") returns False. This causes pipeline_if_empty_null (the only caller) to walk and open every file in untracked directories — freezing indefinitely on pipelines with large Nextflow work directories.

Replace the manual .gitignore parsing + fnmatch approach with git ls-files, which natively respects all .gitignore rules. This matches the existing Pipeline.list_files() method that already uses this approach.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 77.81%. Comparing base (a800f44) to head (ff84a0e).

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