phipe: run-dir clean restructure — receipts, pkl path, remove run.jsonl

Clean up vestigial run-dir artifacts and align with PhiProvenance-as-source-of-truth design.

What?

• Remove run.jsonl writing/reading (duplicates LogTable)
• Scope subtask receipts per-run: {run_dir}/{run_id}/nodes/, {run_dir}/{run_id}/dynamic/
• Relocate provenance pkl outputs to {run_dir}/{run_id}/outputs/serialized/
• Delete dead code: graph.json check, log_sink_uri field, 4 duplicate receipt free functions
• Clean GCS bucket: delete phi_arr_bench_, phipe-test-, phipe-bench-*

Why?

Run directory structure was inconsistent with the design intent (PhiProvenance as source of truth). Accumulated debt from iterative development. Docs referenced aspirational layout, not actual layout.

Acceptance

• All toy pipelines (toy_pipeline.py, toy_pipeline_datatypes.py) run clean end-to-end
• phipe test suite passes
• pkl outputs stored at predictable {run_dir}/{run_id}/outputs/serialized/{node_id}/output.pkl
• nodes_table.output_uri always set for pkl outputs
• No run.jsonl files written
• Docs synchronized with actual layout