Validated atom grouping pipeline and Makefile fixes

• Day: 2026-05-25
• Time: 11:20 to 11:35
• Project: Dev
• Workspace: WP 2: Operational
• Status: In Progress
• Priority: HIGH
• Assignee: Matías Nehuen Iglesias
• Tags: Atom-Extraction, Makefile, Grouping, Validation, Pipeline-Debugging, Eda

Description

Session Goal

Validate the atom extraction outputs, consolidate candidate grouping, and harden the downstream automation so the pipeline can proceed without rerunning expensive PromptFlow extraction.

Key Activities

• Reviewed the post-extraction workflow for atom candidate validation and consolidation.
• Diagnosed a grouping failure caused by a missing PYTHONPATH=src and identified a separate pipeline ordering bug where materialize must run before group.
• Audited enum leakage / normalization issues in atom metadata and proposed a small cleanup rule rather than a full extraction rerun.
• Planned downstream-only processing on already validated outputs: report generation, grouping, inventory materialization, and EDA exports.
• Drafted Makefile and CLI improvements, including composite targets for atom-downstream-all, robust LIMIT handling, corrected script references, and cleanup of malformed all-run arguments.
• Considered artifact export strategy changes, including deterministic CSV EDA outputs and inventory/report slices for singleton and high-value groups.

Achievements

• Confirmed the extraction artifacts are structurally strong enough to avoid rerunning PromptFlow.
• Identified the correct fix for the grouping pipeline: materialize candidates before grouping.
• Clarified the next implementation target as downstream consolidation, inventory reporting, and EDA over grouped atom artifacts.
• Established a reusable Makefile-based workflow for report, grouping, and inventory generation.

Pending Tasks

• Patch the Makefile so downstream targets enforce materialize -> group -> inventory ordering.
• Run validation commands on the existing atom_outputs.all.valid.jsonl artifact and confirm group counts / singleton ratio.
• Generate the inventory report and inspect multi-candidate groups for consolidation opportunities.
• Implement deterministic CSV EDA exports and collection-specific slices if the grouping quality is acceptable.
• Add or verify enum normalization rules to prevent metadata leaks in grouped outputs.

Evidence

• source_file=2026-05-25.sessions.jsonl, line_number=2, event_count=0, session_id=c52ff91cb7994ff8e57f4c60c333166e3495270e55d36e62e20aeaef2ae83f2e
• event_ids: []