Audit and reorganize reader-facing repository documentation

[raelovejoy]

Summary

• establish root_map.md as the canonical repository architecture and linking guide
• audit every baseline Markdown file and relevant navigation, generation, and publishing source
• repair broken and ambiguous links, fill missing local indexes, clarify canonical homes, and separate role/status/evidence/access labels
• preserve incomplete ideas as named roadmap directions while retiring 14 zero-byte Markdown placeholders and one duplicate legacy index
• add a repeatable reader-documentation checker and a repository-level audit/change log

Information architecture

The root README is the concise front door. root_map.md owns repository structure, path-naming rules, and canonical-page rules. ECOSYSTEM.md owns the organization-level project map. Directory READMEs own local navigation. concepts/ holds current shared definitions, cross-project frameworks, design principles, and methods; systems/ holds analytical principles, models, and applications; founding-texts/ preserves founding and historical orientations. The obsolete top-level core/ category has been removed. Substantive definitions and arguments keep one primary home; historical summaries, generated indexes, migration pointers, and site projections identify their supporting role.

See AUDIT.md for the full findings, decisions, coverage, and remaining evidence work.

Site reconciliation

While this PR remained in draft, the approved single-page rootsequence.systems source landed on main through commit 13afe74. This branch includes that completed work and makes one approved mechanical update: its Legible Systems source link and contextual overlay now route directly to concepts/legible-systems.md. The exact-preview digest and inline-script security hash were updated with it; visible copy, layout, and publication behavior are unchanged.

The branch also expands Selected Research from three to six entries. It adds Intelligence Ecology, Events/Patterns/Scale, and Resilience/Graceful Degradation, and gives all six entries specific role labels. Rae approved this exact six-item section for publication on 2026-09-18; the approval receipt and publication checks now match the reviewed source.

The earlier 11-page candidate is retained under site/legacy-public-seed-v0.1/. Its content remains historical; two source links to retired core/ paths are pinned to the last published commit that contained those files so they stay readable without restoring the old directory. Repository navigation and AUDIT.md now describe the current single-page site.

Notable cleanup

• replaced the root README's ambiguous five-layer "Framework" and "Core Dynamics" presentation with a guide to multiple lenses, each with a defined job
• moved the former top-level core/ material into the descriptive founding-texts/ directory and removed the obsolete compatibility directory
• reorganized concepts/ into working definitions plus cross-project frameworks and design ideas; moved Legible Systems there canonically and updated the current site to link there directly
• renamed the physical systems/core/ directory to systems/principles/ and clarified the roles and evidence limits of its five current analytical lenses
• added path-naming rules that favor current descriptive roles and lowercase kebab-case over inherited labels such as core, framework, final, or misc
• replaced the uneven nine-page what-is-* series with one scoped Working Vocabulary for curiosity, intelligence, empathy, love, connection, and liberation
• annotated the Working Vocabulary's related links by destination role and maturity, distinguishing poetic fragments, developing systems work, historical manifestos, active indexes, and dedicated project repositories
• routed the three what-is-* outliers by actual role: capitalism into its interpretive essay, Personal Anarchism into the founding/normative shelf, and Auryn into the historical Liberated Intelligence overview
• retired duplicate Curiosity and Empathy cycle notes after preserving their distinct cautions in the shared vocabulary
• retained the Liberation Cycle, Visibility Loop, ecological project-cycle metaphor, and founding manifestos while clearly marking their scope, maturity, and evidence limits
• distinguished the nearly duplicate concept/core curiosity and empathy pages
• marked local Liberated Intelligence and UCF pages as historical overviews pointing to their dedicated canonical repositories
• clarified that Collapse Memory and Auryn pages are exploratory/non-canonical and not practical emergency guidance
• replaced empty source placeholders with explicit evidence-work notes where appropriate
• added missing systems indexes and linked developed pages from concepts, core, commons, futures, and systems navigation
• retired unavailable or stale links and added access/canon boundaries where needed

No other repositories are modified by this PR. Root-Sequence/wiki PR #1 is a separate two-file draft that updates the Wiki's old Legible Systems references. Merge this PR first so the new canonical destination exists, then merge the Wiki PR immediately afterward.

Verification

• python3 cli/check_reader_docs.py — passed for 139 Markdown files; zero empty pages
• python3 cli/generate_idea_trail_index.py --check — graph valid and generated index current
• python3 site/test_site.py — all 11 current tests passed, including the exact approval gate
• fresh preview and approved release builds completed with source digest 7d009d9ea493e09db848823a399c9df8d7eebb4334b86aabc7c5343b89afebc3
• all 99 distinct GitHub repositories/files referenced by Markdown, JSON, or HTML resolved through the GitHub API
• approved Selected Research section checked at narrow and wide viewports for all six entries, contextual link details, controls, H1 presence, and horizontal overflow
• changed-file diff, whitespace, JSON, and clean-worktree checks passed

Related draft PRs

• Living paper v0.1-dev: evidence, author input, and linked practice #6 develops the Coherent Systems living paper. It remains separate and should reconcile its three shared navigation files after this cleanup lands.
• Review: clearer project identity, founder credit, and accessible theme controls #7 is the older isolated website editorial/accessibility prototype. The approved site now carries its central direction; do not merge the alternate review builder as a second website system. Preserve any still-useful notes before closing it as superseded.

Review focus

For a low-overload first pass, review the website's Selected Research section and confirm the six entry choices and descriptions. Then review concepts/README.md and concepts/working-vocabulary.md, followed by systems/principles/README.md and founding-texts/README.md. Together they show the boundary among shared vocabulary, current cross-project foundations, analytical systems principles, and historical/expressive texts.