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chore: absorb quandledb into monorepo + align with KRL stack
Per monorepo rule (no .git dirs in subdirs), flatten the nested quandledb git repo into nextgen-databases. Absorbed history summary: 6889ffc feat: quandle semantic sidecar + ABI/FFI stack (Idris2/Zig/V/BEAM) ce4490a fix: replace Obj.magic with typed Fetch API bindings in Api.res 0a20355 chore: batch RSR compliance 816272f docs: add KQL safety model — two-tier architecture with TypeLL levels cb1caa5 feat: KQL query language design — SQL compat + dependent type variants Contents: - Quandle semantic sidecar server with SQLite index over Skein.jl - QuandleSemantic module (presentation extraction + canonical hashing) - Idris2 ABI additions, Zig FFI layer, V-lang API triples, Elixir BEAM NIFs - 21 tests passing (9 extraction + 12 semantic integration) Also updates nextgen-databases README.adoc with KRL architecture map link and aligns QuandleDB description with Lithoglyph/Glyphbase naming. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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‎README.adoc‎

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// SPDX-License-Identifier: PMPL-1.0-or-later
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// Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
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= Next-Gen Databases
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:author: Jonathan D.A. Jewell
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:email: j.d.a.jewell@open.ac.uk
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:revdate: 2026-02-13
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:toc:
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= Next-Generation Databases
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Jonathan Jewell (hyperpolymath)
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:toc: left
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:toc-title: Contents
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:doctype: article
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:icons: font
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*Parent repository for tracking and coordinating database application development*
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**IMPORTANT:** This is a **PARENT REPOSITORY ONLY** — it contains documentation and tracking but NO implementation code.
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link:../tangle/docs/krl_map.html[→ KRL architecture map (HTML)]
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== Overview
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This repository serves as the central tracking hub for the Next-Gen Databases initiative — a coordinated effort to build specialised database applications across different domains, each with its own query language, storage engine, and web interface.
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This category contains database systems built on mathematical foundations
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that go beyond the relational and document models.
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The common thread is _semantic identity_: each system represents objects in
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a way that captures structural and algebraic meaning, not just data fields.
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**All database implementations are in their respective canonical repositories.**
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== Projects
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== Database Portfolio
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=== QuandleDB
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Algebraic database using quandle structure as the semantic identity layer.
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Quandles provide a canonical fingerprint for equivalence classes under
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transformation, grounded in knot-theoretic coloring invariants.
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[cols="1,2,2,2,1"]
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|===
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| Database | Description | Technology | Query Language | Status
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| *VeriSimDB*
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| Cross-system entity consistency engine — 8 modalities (octad), drift detection, self-normalisation, formally verified queries. **Primary database project.** Operates as standalone database OR federation coordinator over existing databases (PostgreSQL, ArangoDB, Elasticsearch).
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| Rust (core) + ReScript (VQL parser) + Elixir (orchestration)
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| VQL (VeriSim Query Language) + VQL-DT (dependent types)
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| Active — beta
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| *QuandleDB*
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| Knot-theory database — stores knots as Gauss codes, computes invariants (Jones polynomial, genus, Seifert circles), queries by topological properties. **Exploratory/research project**: a thought experiment in applying knot theory to database design, not yet intended as a production tool.
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| Julia (Skein.jl engine) + ReScript frontend
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| KQL (Knot Query Language) — in development
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| Exploratory
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| *LithoGlyph*
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| Narrative-first, reversible, audit-grade database core for journalism, narrative arts, and media/comms. Working towards production but **secondary priority** to VeriSimDB. Long-term vision: intimate integration with portfolio tools (bofig, etc.) for journalism and PR applications.
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| Forth (storage) + Zig (bridge) + Factor (FQL) + Idris2 (proofs) + Lean 4 (normalizer)
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| GQL (Glyph Query Language) — planned
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| Active — on backburner
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| *Glyphbase*
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| Web interface for LithoGlyph — browser-based search, visualisation, and annotation of glyph specimens
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| ReScript frontend + LithoGlyph API
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| (via LithoGlyph)
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| Planned
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Primary role in the KRL stack: semantic equivalence search and fingerprinting.
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|===
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link:../quandle-db/README.adoc[→ QuandleDB documentation]
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[NOTE]
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====
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**Project priorities:** VeriSimDB is the primary database engineering project, receiving active development focus. LithoGlyph is working towards production for specialist use in journalism and narrative arts, but is secondary priority while VeriSimDB matures. QuandleDB is a research exploration into knot theory's applications in database design — valuable for the mathematical insights but not positioned as a production tool at this stage.
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=== Skein.jl
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Persistence, indexing, and query layer for topological objects (tangles, knots, links).
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Stores canonical `TangleIR` objects, caches invariants, indexes by algebraic fingerprint,
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and maintains a rewrite-step graph for provenance and simplification tracking.
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Lessons learned from VeriSimDB development (drift detection, formal verification, federation) will directly improve LithoGlyph when development focus returns to it.
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====
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Primary role in the KRL stack: the database engine.
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== Architecture
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link:../skein-jl/README.adoc[→ Skein.jl documentation]
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Each database in the portfolio follows a layered architecture:
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=== VeriSimDB / VanguardDB
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Self-normalising multimodal database with formal verification properties.
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Rust core, Elixir/OTP orchestration, Podman deployment.
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----
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Query Language (DSL)
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↓
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Database Engine (storage, indexing, computation)
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↓
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HTTP API Server (JSON endpoints)
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↓
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Web Frontend (ReScript SPA)
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----
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link:../verisimdb/README.adoc[→ VeriSimDB documentation]
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=== Common Patterns
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=== Lithoglyph / Glyphbase / GQL
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Narrative-first database for documentary journalism.
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Dependent types extension; GQL (Glyph Query Language) front-end.
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Glyphbase is the web interface layer over Lithoglyph.
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* *Engines* are domain-specific libraries (Julia, Rust, Elixir)
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* *APIs* expose JSON endpoints wrapping engine queries
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* *Frontends* are ReScript + React SPAs with TEA-style state management
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* *Query languages* are typed DSLs parsed with ReScript or domain-native parsers
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* *Databases* use SQLite or custom storage depending on domain needs
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link:../lithoglyph/README.adoc[→ Lithoglyph documentation]
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== Satellite Repositories
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== Common Principles
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|===
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| Project | Repository | Description | Status
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| QuandleDB
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| link:https://github.com/hyperpolymath/quandledb[quandledb]
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| Knot-theory database wrapping Skein.jl
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| Active
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| Skein.jl
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| link:https://github.com/hyperpolymath/Skein.jl[Skein.jl]
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| Knot database engine (Julia library)
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| Active
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| VeriSimDB
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| link:https://github.com/hyperpolymath/verisimdb[verisimdb]
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| Multimodal verification database
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| Active
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| VeriSimDB Data
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| link:https://github.com/hyperpolymath/verisimdb-data[verisimdb-data]
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| Scan data ingestion pipeline
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| Active
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| Lithoglyph
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| link:https://github.com/hyperpolymath/lithoglyph[lithoglyph]
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| Glyph and inscription database
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| Active
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| Glyphbase
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| link:https://github.com/hyperpolymath/glyphbase[glyphbase]
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| Web frontend for Lithoglyph
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| Active
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* Mathematical objects as primary storage units, not rows
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* Structural and semantic fingerprinting for identity and deduplication
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* Equivalence as a first-class database concept, not a post-query computation
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* Invariant caches as indexed columns, not application-layer lookups
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* Provenance and rewrite history stored alongside objects
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|===
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== Relationship to Next-Generation Languages
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== Query Language Ecosystem
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The databases in this category are designed to be driven by the languages
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in `nextgen-languages`. In particular:
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The database portfolio contributes three query languages to the link:https://github.com/hyperpolymath/nextgen-languages[nextgen-languages] portfolio:
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* *KRL* (Knot Resolution Language) is the surface language for QuandleDB and Skein.jl
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* *Eclexia* is the language for resource-constraint databases
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* *Phronesis* is the language for multi-agent ethical constraint systems
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== Status
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|===
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| Language | Database | Status
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| *KQL* (Knot Query Language)
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| QuandleDB
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| In development
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| *VQL* (Verification Query Language)
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| VeriSimDB
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| ~40% complete
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| *FBQL-DT* (FormDB Query Language)
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| FormDB
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| ~50% complete
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|Project |Status |Notes
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|QuandleDB |Active — early stage |Quandle extraction and fingerprinting in progress
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|Skein.jl |Active — refactoring |Migrating to TangleIR as primary stored type
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|VeriSimDB |Active — design phase |Rust core skeleton in place
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|Lithoglyph |Specified |GQL grammar defined; implementation pending
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|===
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== Documentation
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* `.machine_readable/STATE.scm` — Project state and progress
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* `.machine_readable/META.scm` — Architecture decisions
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* `.machine_readable/ECOSYSTEM.scm` — Ecosystem relationships
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== Contributing
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Each database welcomes contributions. See individual satellite repositories for project-specific contribution guidelines.
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== License
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PMPL-1.0-or-later (Palimpsest Licence)
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Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath)
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== Architecture
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See link:TOPOLOGY.md[TOPOLOGY.md] for a visual architecture map and completion dashboard.

‎quandledb‎

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‎quandledb/.bot_directives/README.scm‎

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;; SPDX-License-Identifier: PMPL-1.0-or-later
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;; .bot_directives — per-bot rules and constraints
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;; Media-Type: application/vnd.bot-directives+scm
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(bot-directives
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(version "1.0")
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(notes
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"Repo-specific bot constraints."
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"Bots must follow these directives in addition to global policies."))

‎quandledb/.bot_directives/echidnabot.scm‎

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;; SPDX-License-Identifier: PMPL-1.0-or-later
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(bot-directive
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(bot "echidnabot")
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(scope "formal verification and fuzzing")
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(allow ("analysis" "fuzzing" "proof checks"))
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(deny ("write to core modules" "write to bindings"))
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(notes "May open findings; code changes require explicit approval"))

‎quandledb/.bot_directives/finishbot.scm‎

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;; SPDX-License-Identifier: PMPL-1.0-or-later
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(bot-directive
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(bot "finishbot")
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(scope "release readiness")
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(allow ("release checklists" "docs updates" "metadata fixes"))
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(deny ("code changes without approval"))
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(notes "Focus on polish, licensing, and packaging"))

‎quandledb/.bot_directives/glambot.scm‎

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;; SPDX-License-Identifier: PMPL-1.0-or-later
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(bot-directive
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(bot "glambot")
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(scope "presentation + accessibility")
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(allow ("docs" "readme badges" "ui/accessibility suggestions"))
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(deny ("logic changes"))
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(notes "Edits limited to presentation layers"))

‎quandledb/.bot_directives/rhodibot.scm‎

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;; SPDX-License-Identifier: PMPL-1.0-or-later
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(bot-directive
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(bot "rhodibot")
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(scope "rsr-compliance")
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(allow ("metadata" "docs" "repo-structure checks"))
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(deny ("destructive edits without approval"))
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(notes "Auto-fix allowed only for formatting in docs and metadata"))

‎quandledb/.bot_directives/robot-repo-automaton.scm‎

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;; SPDX-License-Identifier: PMPL-1.0-or-later
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(bot-directive
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(bot "robot-repo-automaton")
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(scope "automated fixes")
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(allow ("low-risk automated edits"))
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(deny ("core logic changes without approval"))
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(notes "Only apply fixes backed by explicit rule approval"))

‎quandledb/.bot_directives/seambot.scm‎

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;; SPDX-License-Identifier: PMPL-1.0-or-later
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(bot-directive
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(bot "seambot")
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(scope "integration health")
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(allow ("analysis" "contract checks" "docs updates"))
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(deny ("code changes without approval"))
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(notes "May add integration test suggestions"))

‎quandledb/.bot_directives/sustainabot.scm‎

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;; SPDX-License-Identifier: PMPL-1.0-or-later
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(bot-directive
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(bot "sustainabot")
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(scope "eco/economic standards")
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(allow ("analysis" "reporting" "docs updates"))
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(deny ("code changes without approval"))
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(notes "Focus on measurement and recommendations"))

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