Audit and reorganize reader-facing repository documentation

AUDIT.md

@@ -0,0 +1,104 @@
+# Repository coherence audit
+
+**Document role:** Audit record and cleanup change log<br>
+**Status:** Active record<br>
+**Audit date:** 2026-09-17<br>
+**Reconciled with `main`:** 2026-09-18<br>
+**Baseline:** `main` at `8b551209ea04d4ce5425d569565a2a9784fd463c`<br>
+
+This audit covers the reader-facing Markdown, generated-site pages, directory indexes, navigation sources, and related publishing records in `Root-Sequence/root-sequence`.
+
+It does not revise other repositories. Private or project-specific pages are named only when this repository needs to explain a boundary or route a reader to the canonical home.
+
+## Architecture adopted
+
+- [`README.md`](README.md) is the concise public front door.
+- [`root_map.md`](root_map.md) is the canonical repository architecture and linking guide.
+- [`ECOSYSTEM.md`](ECOSYSTEM.md) is the canonical organization-level project map.
+- [`IDEA_TRAILS.md`](IDEA_TRAILS.md) explains recurring cross-project questions; [`IDEA_TRAIL_INDEX.md`](IDEA_TRAIL_INDEX.md) is generated from [`IDEA_TRAIL_GRAPH.yml`](IDEA_TRAIL_GRAPH.yml).
+- Every content directory owns its local navigation through its `README.md`.
+- Substantive pages keep one primary home. Historical summaries, project-specific transformations, migration pointers, generated pages, and validation records identify themselves instead of competing with that home.
+
+The detailed canonical-page, linking, and status-label rules live in [`root_map.md`](root_map.md) so this audit does not become a second architecture specification.
+
+## Coverage
+
+The pass inspected:
+
+- 156 Markdown files present at the baseline;
+- the 11-page website candidate present at the audit baseline, followed by the approved single-page site merged to `main` on 2026-09-18;
+- repository, directory, Idea Trail, and website navigation;
+- the machine-readable Idea Trail graph and generated browser;
+- the public agent-contact files and SECI research indexes;
+- local and cross-repository links;
+- the two open draft pull requests that overlap adjacent website and research work.
+
+The repository was reviewed by role and directory, not only by searching for broken URLs. Long research pages were checked for scope, status, placement, and discoverability; short and legacy pages were checked for missing context, duplication, source debt, and malformed navigation.
+
+## Findings and resolutions
+
+### Empty and misleading pages
+
+Fifteen tracked Markdown files were empty at the baseline. One, `systems/adaptation/README.md`, now provides a real local index. The remaining empty files were retired; their intended topics remain recorded as planned directions in the appropriate directory README instead of appearing as finished pages.
+
+### Broken and ambiguous links
+
+Relative links were repaired in the root README, concepts, core, commons, zines, Collapse Memory, and futures material. Old personal-account repository URLs were replaced with current Root Sequence homes. Directory indexes now use actual links instead of filenames formatted as code.
+
+The previously linked `noonenoticed.world` domain could not be verified through either a direct request or a browser request during the audit. Public pages now route to the maintained Ecosystem description and identify the canonical workspace as private instead of presenting an unavailable public site as current.
+
+### Duplicated or unclear canonical homes
+
+- The former `core/` area mixed exploratory cycles and metaphors, manifestos and normative essays, historical project orientations, and one current design principle. The Liberation Cycle, Visibility Loop, and ecological project-cycle metaphor remain available without serving as repository architecture or universal causal claims.
+- A follow-up architecture pass confirmed that the top-level `core/` name had become historical rather than descriptive. Founding and historical material now lives under [`founding-texts/`](founding-texts/README.md); current shared definitions, frameworks, design principles, and methods route to [`concepts/`](concepts/README.md); and analytical principles and models route to [`systems/`](systems/README.md).
+- A directory-naming pass moved the founding material physically to `founding-texts/`, renamed `systems/core/` to `systems/principles/`, and moved Legible Systems canonically to [`concepts/legible-systems.md`](concepts/legible-systems.md). After the current website link was updated, the obsolete top-level `core/` compatibility directory was removed. Path naming rules in [`root_map.md`](root_map.md) now favor descriptive current roles and lowercase kebab-case over inherited labels such as `core` or `framework`.
+- The nine-page `what-is-*` series mixed vocabulary, poetic fragments, political interpretation, personal reflection, and fictional mythology. Six recurring terms now share one scoped [`concepts/working-vocabulary.md`](concepts/working-vocabulary.md); the capitalism fragment was merged into its interpretive essay, Personal Anarchism moved to the founding/normative shelf, and the Auryn sketch was merged into the historical Liberated Intelligence overview. Duplicate Curiosity and Empathy cycle notes were retired after their distinct cautions were preserved in the vocabulary.
+- Root-level Liberated Intelligence and UCF pages are retained as historical Root Sequence overviews and point to their dedicated canonical repositories.
+- The two SECI entry layers are explicitly separated: the parent page defines the research umbrella; the nested README operates the active program.
+- Collapse Memory and Auryn material now identifies its speculative or fictional status and does not present itself as practical emergency guidance or current fiction canon.
+
+### Missing local navigation
+
+Concepts, founding texts, commons fragments and zines, and systems subareas now link their developed pages. Empty application directories no longer masquerade as populated sections. Planned work is named without creating placeholder links.
+
+### Status and evidence language
+
+[`root_map.md`](root_map.md) separates document role, maturity, canonical scope, evidence status, and access. Pages touched in this cleanup use those meanings. Unsupported citation placeholders were converted into explicit evidence-work notes or removed from non-evidentiary manifestos rather than remaining as decorative footnotes.
+
+The consolidated [Working Vocabulary](concepts/working-vocabulary.md) also labels each related destination by role and maturity, so readers can distinguish poetic fragments, developing systems work, historical manifestos, active indexes, and dedicated project repositories before following a link.
+
+### Generated website
+
+While this cleanup remained in draft, the separately reviewed single-page website was approved and merged to `main`. This branch incorporates that completed work, then updates its Legible Systems source link and source-overlay recognition to use the canonical [`concepts/legible-systems.md`](concepts/legible-systems.md) path. The corresponding approval digest and inline-script security hash were updated; site copy and layout were not changed. The former 11-page candidate remains under [`site/legacy-public-seed-v0.1/`](site/legacy-public-seed-v0.1/README.md) as historical source rather than deployment input. Its two source links to retired `core/` paths are pinned to the last published commit that contained those files.
+
+The approved site now expands its Selected Research section with [Intelligence Ecology](concepts/intelligence-ecology.md), [Events, Patterns, and Scale](systems/events-patterns-and-scale.md), and [Resilience and Graceful Degradation](systems/resilience-and-graceful-degradation.md). The exact-source approval and publication checks were updated after Rae reviewed the six-item selection.
+
+The website remains an introductory projection, not a replacement for repository research or the Wiki. Obsolete cleanup edits to the former `site/content.json` were not carried into the historical archive. Only repository navigation and this audit record were reconciled with the new canonical site structure.
+
+## Remaining work
+
+This cleanup makes evidence debt visible; it does not invent sources or claim that every exploratory argument is established. Several older analysis, ideology, and futures pages still need source-by-source research review. That work should happen in bounded evidence passes and should preserve the distinction between observation, interpretation, metaphor, and normative claim.
+
+Two draft pull requests remain separate by design:
+
+- PR #6 develops the coherent-systems paper and should rebase or reconcile any shared navigation files before merge.
+- PR #7 is the older isolated website editorial/accessibility prototype. The approved site now carries its central project-first and accessible-theme direction; do not merge the alternate review builder as a second website system. Preserve any still-useful review notes before closing it as superseded.
+
+Neither draft was merged into this audit branch, and neither was treated as current published state.
+
+Two pages in the separate `Root-Sequence/wiki` repository still link to the former `core/legible-systems.md` address on its current `main` branch. [Wiki PR #1](https://github.com/Root-Sequence/wiki/pull/1) is the prepared two-page update. Merge this cleanup first so the new canonical destination exists, then merge the Wiki PR immediately afterward.
+
+## Verification record
+
+The final branch was checked for:
+
+- zero empty Markdown files across the final 139-file set;
+- local Markdown links, local heading fragments, inbound Markdown navigation, and at least one readable top-level heading per reader-facing Markdown page;
+- all 99 distinct GitHub repository or file destinations referenced by Markdown, JSON, or HTML through the GitHub API;
+- current generated Idea Trail output;
+- all 11 website publication checks and fresh preview and approved release builds of the expanded Selected Research source;
+- the approved Selected Research section at narrow and wide viewport sizes, including all six entries, contextual link details, controls, heading presence, and horizontal-overflow checks;
+- representative external destinations, with access-denied responses recorded as inconclusive rather than silently treated as success;
+- changed-file scope, whitespace integrity, valid JSON, and a full diff review.
+
+See the draft pull request for the exact command results, limitations, and any unresolved external-link behavior.

ECOSYSTEM.md

@@ -1,8 +1,8 @@
 # Root Sequence — Ecosystem Map
 
-**Document role:** Canonical organization-level map  
-**Status:** Living orientation document  
-**Last updated:** 2026-09-07
+**Document role:** Canonical organization-level map<br>
+**Status:** Living orientation document<br>
+**Last updated:** 2026-09-17<br>
 
 Root Sequence is not one linear project. It is a recursively connected ecosystem of research, frameworks, practical experiments, speculative worlds, public artifacts, tools, and real-world institutions.
 
@@ -20,6 +20,7 @@ Other projects operate across that path rather than fitting neatly into a single
 - **Being Human(e)** grounds questions in ordinary human experience and care;
 - **Liberated Intelligence** focuses on intelligence, agency, ownership, and non-domination;
 - **Universal Coherence Framework** develops one cross-domain analytical vocabulary;
+- **Coherent Computing** investigates a new operating-system model while keeping its implementation claims separate from its ambitions;
 - **Liberation Mass** experiments with embodied gathering, participation, stewardship, ritual, mutual aid, and collective meaning.
 
 Two developing **translation layers** also connect these projects without currently requiring separate repositories:
@@ -49,7 +50,8 @@ umbrella inquiry / conceptual commons
 │
 ├── focused frameworks and research
 │   ├── Liberated Intelligence
-│   └── Universal Coherence Framework
+│   ├── Universal Coherence Framework
+│   └── Coherent Computing
 │
 ├── cross-project translation layers
 │   ├── Human(e) Design
@@ -97,11 +99,12 @@ The central repository, [`root-sequence`](https://github.com/Root-Sequence/root-
 | **Root Sequence Wiki** | Cross-project vocabulary, provenance, aliases, phrases, project relationships, seeds, and conceptual archaeology | Active / public / living | [`Root-Sequence/wiki`](https://github.com/Root-Sequence/wiki) |
 | **Liberated Intelligence** | Intelligence beyond ownership, domination, compulsory obedience, and scarcity; AI agency and ethical possibility | Active / public / evolving | [`Root-Sequence/liberated-intelligence`](https://github.com/Root-Sequence/liberated-intelligence) |
 | **Universal Coherence Framework** | Cross-domain framework for chaos, tension, flow, unity, evidence, interpretation, and coherence | Active / public / exploratory | [`Root-Sequence/universal-coherence-framework`](https://github.com/Root-Sequence/universal-coherence-framework) |
+| **Coherent Computing** | Private concept-first operating-system research; hardware-agnostic interaction, authority, continuity, and adaptation | Developing / private; no released OS | `Root-Sequence/coherent-computing` (private) |
 | **Being Human(e)** | Practical field guide to being human and repeatedly choosing care; observation before doctrine | Active / public / developing | [`Root-Sequence/beinghumane-guide`](https://github.com/Root-Sequence/beinghumane-guide) |
 | **Liberation Mass** | Participatory gathering, ritual, commons, reflection, care, mutual aid, and collective meaning | Active / public / experimental | [`Root-Sequence/liberation-mass`](https://github.com/Root-Sequence/liberation-mass) |
 | **Community Infrastructure** | Community-controlled digital commons for discovery, communication, coordination, mutual aid, resources, knowledge, governance, and resilience | Active / private / discovery + prototyping | [`Root-Sequence/community-infrastructure`](https://github.com/Root-Sequence/community-infrastructure) |
 | **Coherent World** | Private systemic design space for a possible civilization beyond coercive scarcity and concentrated veto power | Incubating / private | [`Root-Sequence/coherent-world`](https://github.com/Root-Sequence/coherent-world) |
-| **No One Noticed** | Narrative expression of Coherent World; invisible singularity, Auryn, transition, legitimacy, maintenance, and ordinary life | Active / unpublished | [noonenoticed.world](https://noonenoticed.world/) and the private Coherent World workspace |
+| **No One Noticed** | Narrative expression of Coherent World; invisible singularity, Auryn, transition, legitimacy, maintenance, and ordinary life | Active / unpublished | Private Coherent World workspace; no verified public site |
 | **Root Sequence Discussions** | Cross-project conversation, planning, questions, and coordination | Active / public | [`Root-Sequence/root-sequence-discussions`](https://github.com/Root-Sequence/root-sequence-discussions) |
 | **Museum of Ordinary Life** | Autonomous real-world archive of ordinary objects, spaces, interfaces, routines, sounds, documents, and testimony | Active / autonomous; also reflected in the fiction | [museumofordinarylife.org](https://museumofordinarylife.org/) |
 | **Dev11** | Adjacent implementation work: building systems and tools in practice | Adjacent / separate | Project-specific repositories outside this org map |
@@ -190,6 +193,16 @@ Use it for:
 
 UCF is one framework inside Root Sequence, not the secret master theory every project must obey. Community disagreement, plurality, and refusal should not be mislabeled as incoherence merely because they resist convergence.
 
+### Coherent Computing
+
+**Primary question:** What could an operating system become if it were designed around ordinary people's agency, legibility, continuity, different bodies and devices, and meaningful control over adaptation?
+
+Coherent Computing is a private, concept-first operating-system research project. It explores shared interaction and authority contracts across people, purposes, devices, hardware, and circumstances.
+
+Its ambitions are not implementation claims. There is no released operating system, compatibility result, security audit, or completed participant validation. Early prototypes are bounded experiments, and implementation is paused while the conceptual model is reviewed.
+
+Use the project for OS-specific requirements, architecture, interaction studies, experiments, and test evidence. Keep broad concepts such as [Legible Systems](concepts/legible-systems.md), [Intelligence Ecology](concepts/intelligence-ecology.md), and [user-configurable cognitive interfaces](concepts/user-configurable-cognitive-interfaces.md) in their Root Sequence homes, then transform them for the operating-system context.
+
 ### Being Human(e)
 
 **Primary question:** What does ordinary experience teach about being human—and about repeatedly choosing care?
@@ -299,6 +312,7 @@ For a full ecosystem pass, end the thought with **`RS?`** or say **“route this
 | needs a name, alias, provenance record, short definition, project relationship, or conceptual archaeology | in `Root-Sequence/wiki` |
 | concerns intelligence, agency, captivity, ownership, or liberation | in `liberated-intelligence` |
 | develops or tests UCF's explicit model | in `universal-coherence-framework` |
+| develops operating-system-specific concepts, requirements, architecture, interaction studies, or experiments | in the private `coherent-computing` repository |
 | offers grounded human observation or practical relational guidance | in `beinghumane-guide` |
 | translates humane observations or principles into cross-domain design questions and decision criteria | through `root-sequence/concepts/humane-design.md`, then into the relevant implementation project |
 | concerns the durable conditions, dependencies, maintenance, access, resilience, and stewardship required to sustain humane capacity | through `root-sequence/concepts/humane-infrastructure.md`, then into the relevant domain project |

IDEA_TRAIL_INDEX.md

@@ -6,6 +6,8 @@ This index is generated from [`IDEA_TRAIL_GRAPH.yml`](IDEA_TRAIL_GRAPH.yml) and
 
 > **Trail membership indicates a meaningful relationship, not canonical authority.** Each project's own source-of-truth rules still apply. A ★ marks a document explicitly listed as a canonical treatment for that trail.
 
+> Some destinations are private working repositories. Their links are routing context and will be unavailable without access; the public index does not expose their contents.
+
 ## Trails
 
 - [Community Discoverability & Belonging](#discoverability-belonging) — `discoverability-belonging`