IngestionPipeline.run cognitive complexity 18 (S3776) — flatten without a new call level #603

IngestionPipeline.run (src/cgis/pipeline/__init__.py) has Sonar cognitive complexity 18 (python:S3776, limit 15). Pre-existing: unchanged since before #602, which only moved the file (Sonar then saw it as new code). Quality gate passes.

Most of the weight is the walk loop (with Progress → for root, dirs, files → for file → if not extractor / try … except ValueError).

Constraint (memory of #458): extracting a helper out of run() that adds a call level once took pipeline self-drift 0.09 → 0.29 (orchestrator, tolerance 0.25) and was reverted. Reduce complexity by flattening (guard clauses, moving the relative-path check into _process_file), and measure pipeline drift before/after — currently 0.106 / unresolved 0.398 (lock 0.25 / 0.43).

Acceptance: S3776 clean on run, pipeline drift within lock, identity snapshot unchanged.