Add CA-TTI research manuscript package

.gitignore

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 *.njsproj
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+.gstack/

Aidaily_ca_tti_cover_letter.md

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+# Cover Letter
+
+June 26, 2026
+
+Dear Editor,
+
+Please consider the manuscript entitled "Transparency Drift in Human-AI Software Teams: A Confidence-Aware Team Transparency Index" as a conceptual framework paper with synthetic stress-test evidence.
+
+The manuscript addresses a growing software engineering problem: AI agents can improve the visible artifact layer of software work while human review depth, shared understanding, and accountability decline. It proposes CA-TTI as an early-warning measurement framework that separates artifact score, confidence, trend state, and Human-Agent Alignment Gap rather than compressing transparency into a single score.
+
+The paper contributes a bounded framework, a construct definition for transparency drift, and a synthetic stress test showing how multi-signal interpretation can expose failure modes missed by a raw artifact score. It does not claim field validation; the manuscript explicitly identifies event-level data collection and field feasibility testing as future work.
+
+This manuscript has not been published elsewhere and is not under consideration by another journal. All content, arguments, and conclusions remain the responsibility of the author.
+
+AI Disclosure: This manuscript was prepared with the assistance of AI-powered academic writing tools for research framing, structure planning, draft writing, reviewer simulation, revision planning, citation verification, integrity checking, and formatting support. The author directed and reviewed the work and takes full responsibility for its accuracy and integrity.
+
+Sincerely,
+
+[Author Name]
+

Aidaily_ca_tti_stage2_5_integrity_report.md

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+# Stage 2.5 Integrity Verification Report
+
+Manuscript: `Aidaily_ca_tti_manuscript_draft.md`
+
+Date: 2026-06-26
+
+Pipeline stage: Stage 2.5, pre-review integrity gate
+
+Verdict: PASS WITH CORRECTIONS APPLIED
+
+## Scope
+
+This audit checked reference existence, bibliographic metadata, citation presence, claim-reference fit, and synthetic-result consistency for the current CA-TTI draft.
+
+The audit does not establish real-world construct validity for CA-TTI. It only verifies that the current draft's cited sources, local experiment figures, and stated limitations are consistent enough to proceed to peer-review simulation.
+
+## Reference Audit
+
+| Reference | Status | Notes |
+| --- | --- | --- |
+| Ball (2021) | VERIFIED / CORRECTED | The report exists. The official JRC page and final PDF identify DOI `10.2760/5137`; the draft previously used another EU DOI variant, `10.2760/451453`. Updated to `10.2760/5137`. |
+| Cinkusz et al. (2025) | VERIFIED | DOI, title, journal, volume, issue, and article number verified via MDPI/Crossref metadata. |
+| Cleland-Huang et al. (2014) | VERIFIED / CORRECTED | DOI and proceedings metadata verified. Author name corrected from `Mader` to `Mäder`; proceedings venue clarified as ACM proceedings. |
+| Shneiderman (2020) | VERIFIED | DOI, title, journal, volume, issue, and pages verified. |
+| Stray et al. (2017) | VERIFIED | Springer page and Crossref metadata verify title, authors, pages, and DOI. |
+| Stray et al. (2020) | VERIFIED | IEEE/Crossref metadata verify title, authors, journal, volume, issue, pages, and DOI. |
+| Stray et al. (2016) | VERIFIED / CORRECTED | SINTEF and Crossref metadata verify title, authors, journal, volume, pages, and DOI. Author names corrected to `Sjøberg` and `Dybå`. |
+| Umar et al. (2025) | VERIFIED / CORRECTED | Frontiers and Crossref metadata verify title, authors, volume, article id, and DOI. First author shortened to APA-style `Umar, M. A.`. |
+
+## Claim-Reference Fit
+
+| Draft claim area | Status | Notes |
+| --- | --- | --- |
+| Daily stand-up meetings support awareness/coordination but depend on context and quality | SUPPORTED | Stray et al. (2016, 2017, 2020) support the contextual and mixed-value framing. |
+| Traceability is valuable but often ad hoc or after the fact | SUPPORTED | Cleland-Huang et al. (2014) directly supports this framing. |
+| AI/ML can support Agile project-management roles and requirements extraction | SUPPORTED AFTER TIGHTENING | The draft sentence was narrowed so Cinkusz et al. supports agent simulation/project-management roles and Umar et al. supports automated requirements extraction. |
+| Human-centered AI requires human control, safety, and trust | SUPPORTED | Shneiderman (2020) supports the human-control and reliable/safe/trustworthy framing. |
+| Monitoring systems can create workplace surveillance risk | SUPPORTED | Ball (2021) supports psychosocial and policy risks of workplace surveillance/monitoring. |
+
+## Data and Result Audit
+
+Local source checked: `/Users/trovo/conductor/workspaces/1/san-diego/experiments/ca_tti/sample_output`
+
+Files checked:
+
+- `manifest.json`
+- `summary.json`
+- `result_summary.md`
+- `observations.csv`
+- `scored_observations.csv`
+
+Verified values:
+
+| Scenario | Failure trials | Raw warning trials | CA-TTI warning trials | Mean CA-TTI lead | Mean HAG |
+| --- | ---: | ---: | ---: | ---: | ---: |
+| artifact_drift | 8/8 | 0/8 | 8/8 | 3.0 | 0.21 |
+| fluent_hallucination | 8/8 | 0/8 | 8/8 | 1.5 | 0.369 |
+| clean_baseline | 0/8 | 0/8 | 0/8 | n/a | 0.065 |
+| low_confidence_good_artifacts | 0/8 | 1/8 | 0/8 | n/a | 0.059 |
+| noisy_interaction_stable_artifacts | 0/8 | 7/8 | 0/8 | n/a | 0.094 |
+
+The draft table matches `summary.json` and `result_summary.md`. The sample output contains 400 observations plus one header row in each CSV.
+
+## Corrections Applied
+
+- Updated Material Passport verification status and version label.
+- Replaced Ball DOI with the official JRC final-PDF DOI `10.2760/5137`.
+- Corrected `Mader` to `Mäder`.
+- Corrected `Sjoberg` and `Dyba` to `Sjøberg` and `Dybå` in the 2016 reference.
+- Normalized the Umar first-author initials.
+- Narrowed the AI/ML support claim so it matches the cited papers more closely.
+- Added the 400-observation count to the synthetic result description.
+
+## Residual Risks
+
+- The manuscript remains a framework paper with synthetic stress testing, not a validated empirical study.
+- HAG is conceptually broader than the current prototype implementation, which only captures a hallucination/evidence mismatch subtype.
+- The literature base is still lean. Before journal submission, add more direct human-AI teaming, AI code agent, and team cognition literature.
+- No full APA formatting pass has been performed yet.
+
+## Gate Decision
+
+The Stage 2.5 integrity gate is clear enough to proceed to Stage 3 peer-review simulation.

Aidaily_ca_tti_stage3_prime_rereview_package.md

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+# Stage 3' Verification Review Report
+
+Manuscript reviewed: `Aidaily_ca_tti_manuscript_revised_stage4.md`
+
+Revision package reviewed: `Aidaily_ca_tti_stage4_revision_package.md`
+
+Original review package: `Aidaily_ca_tti_stage3_review_package.md`
+
+Date: 2026-06-26
+
+## Decision
+
+Minor Revision / proceed to Stage 4.5 final integrity.
+
+The Stage 4 revision substantively addresses the Stage 3 major-revision roadmap. No second major revision loop is required. The remaining issues are integrity and polish issues: new references added during revision require full verification, and the final manuscript should receive a formatting/citation pass.
+
+## Revision Response Checklist
+
+### Priority 1 — Required Revisions
+
+| # | Original Review Comment | Author's Claim | Response Status | Revision Location | Verified? | Quality Assessment |
+| --- | --- | --- | --- | --- | --- | --- |
+| SC-1 | Reframe the manuscript consistently as a conceptual measurement framework plus synthetic stress test. | The manuscript now states that CA-TTI is a conceptual measurement framework with synthetic stress-test evidence, not a validated field index. | FULLY_ADDRESSED | Material Passport; Abstract; Sections 1, 7, 12 | Yes | Verified. The revised draft explicitly names the contribution type and repeatedly limits claims to synthetic measurement behavior. |
+| SC-2 | Define HAG as a construct with subdimensions; distinguish conceptual HAG from the current `hag_proxy`. | A HAG subdimension table was added and the implemented synthetic measure is renamed/explained as `hag_proxy`. | FULLY_ADDRESSED | Section 5; Sections 6 and 10 | Yes | Verified. HAG now has subdimensions, observable indicators, and prototype coverage status. The construct/proxy distinction is clear. |
+| SC-3 | Add reproducible synthetic-method details, including generator assumptions, thresholds, baseline warning logic, and sensitivity/ablation discussion. | The methods now include row schema, scenario purposes, formulae, warning thresholds, baseline rule, and ablation leads. | FULLY_ADDRESSED | Sections 6 and 7 | Yes | Verified. The revised methods are reproducible enough for a reader to understand the stress-test logic without external code. The ablation is properly caveated as preliminary. |
+| SC-4 | Expand related work enough to position CA-TTI against existing software engineering and human-AI teaming literature. | Related work now covers Agile coordination, traceability, socio-technical congruence, code review quality, human-AI teaming, shared mental models, AI pair programming, and agentic code review. | FULLY_ADDRESSED | Section 2; References | Yes | Verified. The added literature materially improves positioning. Final source verification is deferred to Stage 4.5. |
+
+### Priority 2 — Suggested Revisions
+
+| # | Original Review Comment | Response Status | Notes |
+| --- | --- | --- | --- |
+| P2-1 | Add an operational "Use and Misuse" subsection. | FULLY_ADDRESSED | Section 8 directly addresses use, misuse, safeguards, and warnings as inquiry triggers. |
+| P2-2 | Add a deployment vignette showing how a team should respond to a CA-TTI warning. | FULLY_ADDRESSED | Section 8 includes a sprint-review vignette with rising HAG and safe team response. |
+| P2-3 | Add a table mapping CA-TTI signals to observable data sources and missingness/confidence rules. | PARTIALLY_ADDRESSED | The transparency taxonomy and HAG table map constructs to indicators. Confidence/missingness rules are discussed but not yet formalized as a separate table. This is minor and can be polished later. |
+| P2-4 | Add a concise statement of target use: dashboard, audit protocol, research instrument, or governance framework. | FULLY_ADDRESSED | Section 3 states that the intended use is a team-level diagnostic and audit protocol. |
+
+### Priority 3 — Nice to Fix
+
+| # | Original Review Comment | Response Status |
+| --- | --- | --- |
+| P3-1 | Add a figure showing CA-TTI signal flow. | FULLY_ADDRESSED |
+| P3-2 | Tighten terminology around transparency, traceability, shared understanding, and alignment. | FULLY_ADDRESSED |
+| P3-3 | Polish APA formatting and decide whether to preserve diacritics consistently. | PARTIALLY_ADDRESSED |
+
+## Commitment Ledger Verification
+
+| Concern ID | Commitment | Fulfillment Status | Verified? | Notes |
+| --- | --- | --- | --- | --- |
+| SC-1 | Reframe as conceptual framework plus synthetic stress test. | fulfilled | Yes | Present in Material Passport, Abstract, Introduction, Results interpretation, and Conclusion. |
+| SC-2a | Define HAG with subdimensions. | fulfilled | Yes | Section 5 includes six subdimensions. |
+| SC-2b | Distinguish HAG from `hag_proxy`. | fulfilled | Yes | Sections 5 and 6 explicitly distinguish full HAG from the implemented proxy. |
+| SC-3 | Add generator assumptions, thresholds, baseline warning logic, and ablation discussion. | fulfilled | Yes | Sections 6 and 7 include formulae, warning rules, raw baseline, and ablation table. |
+| SC-4 | Expand related work. | fulfilled | Yes | Section 2 and References add relevant software engineering and human-AI teaming sources. |
+| SC-5 | Add Use/Misuse plus safe deployment vignette. | fulfilled | Yes | Section 8 added. |
+
+No `COMMITMENT_GAP` findings were identified.
+
+## New Issues Discovered During Revision
+
+| # | Type | Location | Description | Severity |
+| --- | --- | --- | --- | --- |
+| NEW-1 | Citation integrity | References | Seven new references were added during Stage 4. They have plausible metadata, but the final integrity gate must verify existence, metadata, and claim-reference fit. | Minor / Stage 4.5 required |
+| NEW-2 | Methods polish | Section 3 / Section 6 | The revision maps constructs to indicators, but confidence and missingness could be expressed in a compact table before submission. | Minor |
+| NEW-3 | Formatting | References | Diacritics and APA proceedings formatting should be normalized across the full reference list. | Minor |
+
+## Decision Rationale
+
+The major concerns from Stage 3 have been addressed. The revised manuscript now has a clearer contribution category, a stronger HAG construct definition, a more reproducible synthetic method section, broader literature positioning, and a practical governance section. These changes materially improve the manuscript and resolve the main reasons for the prior Major Revision decision.
+
+The remaining gaps do not require another substantive rewrite. They are appropriate for the next pipeline stage: final integrity verification and final formatting.
+
+## Residual Issues
+
+1. Complete Stage 4.5 final integrity verification for all references, especially new Stage 4 additions and arXiv preprints.
+2. Optionally add a compact confidence/missingness table during final polish.
+3. Normalize APA style and diacritics in the final formatted manuscript.
+
+## Stage 3' Checkpoint
+
+Stage 3' is complete.
+
+Next pipeline stage: Stage 4.5 FINAL INTEGRITY.
+
+Recommended mode: full reference, citation, claim-reference, and data verification on `Aidaily_ca_tti_manuscript_revised_stage4.md`.