Align repository structure and epistemic claims with the framework’s stated standards

[raelovejoy]

Current status — 2026-09-16

This remains the canonical UCF cleanup and evidence-audit tracker. The original request is preserved below as a historical record, not an up-to-date statement that every original problem still exists.

Already present on main before the reconciliation

• The contribution guide is correctly named CONTRIBUTING.md.
• The README identifies UCF as an optional, exploratory framework within Root Sequence, distinguishes analogy from proof, and does not require other projects to adopt it.

Implemented in public drafts, not merged

UCF draft PR #2, latest verified head 9a459640f4d0683ddbbe0c6f6a335b9def48fc0e, contains the proposed v1.1 model, scoped glossary, revised time essay, evidence convention, ten-claim register, corrected indices/contribution rules, project citation metadata, and a reproducible booking example. Model v1 remains unchanged; six earlier documents are preserved as exact Git-blob snapshots.

The companion Root Sequence draft PR #6, head 20740c794a5a01b2d616abc6f74bad9dcf83054d, now explicitly integrates UCF's definitions, four layers versus optional states, internal provenance, and the shared worked example. No separate implementation is duplicated into the paper.

Recovery reran eight unittest tests and the 24-fixture report from saved, hash-verified source. Six additional sanity checks passed. Nine companion-paper changed file hashes and 40 relative links in those files were checked. These are arithmetic, implementation, and scoped document checks, not empirical or cross-domain validation. See the verification record.

A 700-case / 561-match statement in interrupted progress text has no recovered protocol or output and is excluded from the evidence record. CFF was checked as YAML, not against the full official schema or GitHub citation rendering.

Still open

• Author review and adoption decisions for both draft PRs; neither draft is a reviewed release.
• Full claim-level audit of foundations, with exact sources, scope, objections, and evidence labels.
• Recover the intended predictive-processing/distributed-cognition content: both files have the same blob in the audited base. Do not invent missing prose.
• Complete glossary term-level bibliographies and review domains, publications, and related-framework comparisons.
• Validate CFF against its official schema and check citation rendering; do not fabricate an approved byline or release identifier.
• Test added value against a competent existing review, not an artificially weak baseline. The current example does not demonstrate comparative superiority.
• Specify an independent-review protocol before claiming reviewer agreement or enrolling participants.
• Complete the remaining repository-wide navigation and claim-status checks before closing this issue.

No main-branch merge, website deployment, private-source publication, story-canon adoption, or automatic rewriting process is part of this update.

Original request and checklist, August 28, 2026 (preserved)

Why this needs a focused pass

The README already emphasizes testability, transparency, and distinctions among evidence, speculation, and interpretation. Several repository and wording details currently weaken those standards.

Verified structure problems

• CONTRUBUTING.md is misspelled; standard tooling and readers expect CONTRIBUTING.md.
• CITATION.cff is tracked but zero bytes, so GitHub cannot provide meaningful citation metadata.
• The README's structure block lists site/ and assets/, but those paths currently return 404.
• The repository contains related-frameworks/, which is not included in the documented structure.
• The Contributing section says “Submit via Issues, Pull Requests, or whitepapers” but does not link the actual contribution file.

Epistemic wording to review

The project can remain ambitious without presenting hypotheses as established cross-domain facts.

Current phrases worth revising include:

• “adaptive systems exhibit consistent patterns” across neuroscience, ecology, AI, organizations, and lived experience;
• “There is no unified framework describing coherence across humans, AI, collectives, and ecosystems”;
• “domain-agnostic standard”;
• examples under “Unity” that may blend operational descriptions, normative desirability, metaphor, and interpretation.

Possible safer framing:

• UCF proposes that selected systems may share useful structural analogies;
• cross-domain mappings are hypotheses to test, not evidence that the domains are governed by one mechanism;
• the four states are a working vocabulary, not yet a validated universal taxonomy;
• “coherence” must be operationalized separately in each domain before comparisons are treated as empirical;
• higher coherence is not automatically more ethical, free, healthy, or desirable;
• unity must not imply consensus, conformity, suppression of dissent, or loss of boundaries.

Proposed work

Structure

• Rename CONTRUBUTING.md to CONTRIBUTING.md through a history-preserving Git move.
• Populate CITATION.cff with creator, title, repository URL, license, version/status, and preferred citation—or remove it until accurate metadata exists.
• Reconcile the README tree against the actual repository.
• Add related-frameworks/ to the documented map if it remains part of the project.
• Link the contribution guide from the README.
• Add a link to the Root Sequence ECOSYSTEM.md while stating that UCF is one framework within the ecosystem, not its governing theory.

Epistemic clarity

• Label the four-state model explicitly as a proposed framework.
• Define what would count as evidence for or against each cross-domain mapping.
• Require citations for “Established Foundations” claims.
• Separate structural analogy from shared causal mechanism.
• Add known failure cases and domains where the vocabulary does not map cleanly.
• Explain how normative judgments enter terms such as “higher,” “stable,” “harmonic,” and “unity.”
• Add a clear warning that system coherence can support oppressive or pathological systems; coherence is not synonymous with justice.
• Create a claim/status register or front matter convention for foundation, hypothesis, interpretation, and metaphor.

Acceptance criteria

• README structure matches the repository.
• Citation and contribution metadata work through normal GitHub conventions.
• Empirical, analogical, speculative, and normative claims are visibly distinct.
• Every “established” claim has a credible source or is relabeled.
• UCF remains ambitious and generative without presenting itself as already scientifically universal.
• The framework is clearly related to—but does not silently govern—the rest of Root Sequence.

[raelovejoy]

2026-09-24 evidence-audit continuation

Draft PR #6 (dynamic-coherence evidence reconciliation) advances the still-open claim-level audit without closing it.

It adds a targeted source pass across adaptivity/viability, allostasis, resilience/adaptability/transformability, metastability, personality dynamics, capability theory, viability/reachability, and information-theoretic empowerment. It also marks several older pages whose universal/state-sequence claims exceed the current evidence convention.

The pass does not establish a universal mechanism, novelty, comparative superiority, or systematic literature coverage. It proposes the next actual validation step: a pre-specified bounded case compared against a competent existing method using the same evidence packet, including null-result criteria.

Issue #1 should remain open after PR #6; foundation-by-foundation audit, publication review, baseline comparison, and independent review remain unfinished.

[raelovejoy]

2026-09-24 evidence-audit update: draft PR #6 now addresses part of this tracker by adding a targeted dynamic-coherence/adaptive-continuity evidence reconciliation and a repo-wide migration audit.

Key result so far: the current v1.1 framing largely survives and is extended rather than replaced, while several older foundation/speculation pages require re-audit or explicit supersession of cross-domain claims. The new migration queue uses: PRESERVE / EXTEND / RE-AUDIT / SUPERSEDE ACTIVE CLAIM / RETIRE IF NO ADDED VALUE.

PR #6 also proposes an added-value comparison against competent baseline methods instead of treating successful description as validation. This remains AI-assisted draft work, not a completed literature review or validation, so issue #1 should remain open.