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Repository-wide refactor report

Branch: development
Status: Proposed (staged, not committed)
Date: 2026-06-14
Governance: Repository-wide refactor governance

First full repository-wide refactor under mature IKaC governance: every committed source packet re-evaluated for cross-layer impact; evidence-backed updates applied; insufficient signals preserved as candidates.

Sources reviewed

Packet Intake label Layers assessed
2026-06-13-kyle-grice-faculty-profile-2 Faculty profile URL people, facilities, publications, hyperlinks
2026-06-14-ors-annual-reports-2020-2025 ORS annual reports grants, people, facilities, partners, relationships
2026-06-14-rfums-dpu-grants-from-2024-and-2023 RFUMS collaborative awards grants, people, EXT partners
2026-06-13-rfums-depaul-2025-grant-awardees-pdf RFUMS 2025 PDF grants, EXT partners
2026-06-13-dpu-rfu-awarded-projects DPU-RFU 2026 PDF grants, EXT partners
2026-06-14-agif-reports-2018-2025 AGIF appendices (untracked packet; grants in working tree) grants, facilities, labs, relationships
2026-06-14-circle-report-2024 Institutional program report (untracked) programs, courses, capabilities
example-grice-lab Template example skipped (non-production)
_template Scaffold skipped

Supporting evidence: packet PDFs, extracted/*.yaml, prior refactor_output.md files, data/review/*.yaml from pilot pass.

Repository modifications applied

Resources modified (6)

Resource Change Evidence
resources/CDM/CDM-009.md Verification refresh; Notes cite GRA-878 / GRL-017 AGIF appendix names NexGeN Lab
resources/CDM/CDM-014.md Documented Relationships + Notes cite GRA-916 / GRL-018; verification evidence AGIF HPC Cloud project title
resources/UNI/UNI-006.md Linked CDM-003, CDM-012; Notes cite GRA-921 / GRL-019; verification evidence AGIF DIGI Lab project title
resources/CDM/CDM-011.md Notes cite ORS MedIX REU grants (GRL-013/015/016) ORS annual reports packet
resources/UNI/UNI-001.md Notes index CIRCLE program participation stat CIRCLE report PDF
resources/CSH/CSH-016.md No change — prior faculty-profile refactor already applied —

Resources created

0 — no new resource pages (Connolly Lab, Immersion Lab, VARC, CoBaAB remain candidates).

People modified

0 — RFUMS PIs Pedram, Ustun, Hwang preserved as candidates; no profile evidence in grant PDFs alone.

Publications modified

0 — Grice packet deferred MDPI/ScienceDirect rows until DOI verification (prior refactor policy unchanged).

Grants modified

File Change
data/grants.yaml +52 AGIF records (GRA-872–923) from uncommitted intake; 3 grants updated with related_resources + resource_links_status=resolved (GRA-878, GRA-916, GRA-921)
data/person_grant_links.yaml +11 PGL for resolved AGIF PIs (uncommitted from AGIF intake script)
data/grant_resource_links.yaml +3 GRL (GRL-017–019)

Prior committed packets (ORS 826 grants, RFUMS GRA-040–045, Grice-linked records) — verified present; no duplicate merge.

Capabilities added

  • CIRCLE / IRMA program context indexed on UNI-001 Notes (program layer, not hardware).

Equipment added

0 — no new resource_equipment.yaml rows; HPC GPU inventory already on CDM-014.

From To Type
CDM-014 Documented Relationships CSH-007 Inline facility cross-ref
UNI-006 Linked Relationship IDs CDM-003, CDM-012 Reciprocal (CDM-003/012 already linked UNI-006)
A B Status
UNI-006 CDM-003, CDM-012 Completed — UNI-006 Linked IDs now match existing CDM→UNI-006 edges
CDM-009, CDM-014, CDM-011 Grant layer Prose reciprocity via Notes citing GRL IDs (no grant pages in MkDocs)

Candidates preserved

Registry Count Location
Resource candidates 45 active + 3 applied data/review/resource_candidates.yaml
Relationship candidates 12 active + 3 applied data/review/relationship_candidates.yaml
Packet-local ORS 3, AGIF 5 extracted/candidates.yaml in respective packets

Key preserved candidates: Connolly Lab, Immersion Lab, CoBaAB, VARC, Assisted Locomotion→CDM-006 (ambiguous), Cybersecurity Clinic, ORS tier-B lab-title scan (~141 rows), RFUMS people gaps, CIRCLE course→facility crosswalk.

Claims rejected

Claim Reason Packet
Sharevski NCTA → CDM-007 Secure Design Lab Featured narrative names NCTA program, not SDL ORS
RFUMS awards → DePaul lab facilities PDFs name colleges only RFUMS 2023–2026
CIRCLE → facility ownership Report documents course attributes, not hardware CIRCLE
Grice ↔ Southern Lab No direct evidence in faculty profile packet Grice profile-2
MDPI/ScienceDirect → publication registry HTTP 403; no verified DOI in packet Grice profile-2

Provenance issues

Issue Handling
AGIF packet untracked but grants in working tree Staged AGIF inbox + scripts with this refactor for single review commit
GRA-913 Assisted Locomotion PI (Huzaifa) vs CDM-006 faculty lead (Cunningham) Deferred GRL — candidate not promoted
HPCC homepage "Coming Fall 2025" vs AGIF HPC Cloud award GRL-018 applied on project title evidence; operational status remains needs_review
CIRCLE stats Single institutional PDF; indexed as program context only

Counts summary

Metric Count
Packets reviewed 7 (+ 2 skipped)
Resources modified 6
Resources created 0
People modified 0
Publications modified 0
Grants added (AGIF) 52
Grant→facility edges added 3
PGL added (AGIF) 11
Hyperlinks added 3
Reciprocal link pairs completed 1 (UNI-006 ↔ CDM-003/012)
Resource candidates preserved 45
Relationship candidates preserved 12

Major discoveries

  1. AGIF grant-only intake missed 3 high-confidence facility GRL edges where project titles explicitly named registry resources (NexGeN, HPC Cloud, DIGI Lab).
  2. ORS intake captured 826 grants but indexed only 3 GRL despite MedIX and Karver successes — Connolly Lab and 141 tier-B lab-title rows never entered candidate registries until this pass.
  3. RFUMS/DPU-RFU/Grice packets were largely complete from prior refactors; repository-wide pass confirmed grant-layer adequacy and preserved people gaps as candidates.
  4. CIRCLE contributed program-layer knowledge (50% research/creative course participation) previously unindexed on any resource page.

Risks and ambiguities requiring review

  1. GRA-913 → CDM-006 — "Assisted Locomotion Laboratory" title vs RAL Lab faculty-lead mismatch (Huzaifa vs Cunningham).
  2. CoBaAB vs CDM-011 MedIX — Ramaraj PI on both; separate lab page needed before GRL.
  3. 52 AGIF grants uncommitted — large grants.yaml diff; review dedupe and governance notes before merge.
  4. Immersion Lab, VARC, Cybersecurity Clinic — named in AGIF but no registry pages; require intake packets before promotion.
  5. ./sync_docs.sh not run — resources/ changed; public docs/ mirror stale until maintainer sync post-approval.

Artifacts

  • data/review/resource_candidates.yaml
  • data/review/relationship_candidates.yaml
  • sources/inbox/*/extracted/candidates.yaml (ORS, AGIF)
  • Repository-wide refactor pilot (prior gap analysis)

Stop before commit. Run ./sync_docs.sh && mkdocs build --strict after human approval.