From 5d9f4e83e413df7cf47fd790e60cc466f43d9289 Mon Sep 17 00:00:00 2001
From: Allaun Silverfox <28494262+allaunthefox@users.noreply.github.com>
Date: Thu, 2 Jul 2026 03:36:22 +0200
Subject: [PATCH] Remove HACHIMOJI_DNA_ENCODING.md

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-# Hachimoji DNA Encoding Specification
-
-**Version:** 0.1
-**Status:** Draft
-**Purpose:** Computational substrate, not compression format.
-
-## 1. Alphabet
-
-Eight bases, ASCII-ordered for monotone lexicographic sorting:
-
-| Index | Base | Phase | Bits |
-|-------|------|-------|------|
-| 0 | A | 0° | 000 |
-| 1 | B | 45° | 001 |
-| 2 | C | 90° | 010 |
-| 3 | G | 135° | 011 |
-| 4 | P | 180° | 100 |
-| 5 | S | 225° | 101 |
-| 6 | T | 270° | 110 |
-| 7 | Z | 315° | 111 |
-
-**Key property:** ASCII sort order = index order = lexicographic rank.
-This means `sorted(sequences)` produces the same order as `sorted(sequences, key=dna_to_int)`.
-
-## 2. Symbol Encoding
-
-Each symbol (byte, word, or chunk) maps to a fixed-length DNA sequence.
-
-- **1-byte chunks:** 256 symbols → 3 bases/symbol (8³ = 512 ≥ 256)
-- **2-byte chunks:** 65,536 symbols → 6 bases/symbol (8⁶ = 262,144 ≥ 65,536)
-- **n unique symbols:** `ceil(log₈(n))` bases/symbol
-
-The LUT assigns sequences by rank:
-- Rank 0 → "AAA...A" (lowest)
-- Rank 1 → "AAA...B"
-- Rank n → highest sequence
-
-## 3. Monotone Property
-
-If symbols are ranked by frequency (most frequent = rank 0), then:
-- Most frequent symbol → shortest/lowest DNA sequence
-- Lexicographic sort of DNA = frequency sort of symbols
-- This is NOT compression — it's structured representation
-
-## 4. LUT Format
-
-```json
-{
-  "format": "hachimoji_lut_v1",
-  "bases": "ABCGPSTZ",
-  "chunk_size": 1,
-  "bases_per_symbol": 3,
-  "entries": {
-    "AAA": "20",
-    "AAB": "65",
-    "AAC": "74"
-  }
-}
-```
-
-- Keys: DNA sequences (base-8 encoded ranks)
-- Values: hex-encoded byte chunks
-- Portable: JSON, human-readable, self-describing
-
-## 5. File Format
-
-```
-.dna file:  raw DNA sequence (text, A-Z only)
-.lut file:  JSON LUT (see above)
-.meta file: encoding metadata (optional JSON)
-```
-
-## 6. Roundtrip Guarantee
-
-```
-decode(encode(data)) == data
-```
-
-Verified at encode time. No lossy steps. No approximation.
-
-## 7. Computational Properties
-
-The DNA sequence is not just encoded data — it's a computational address:
-
-- **Sequence index** (base-8 integer) = symbolic rank
-- **Lexicographic order** = rank order (monotone)
-- **LUT lookup** = O(1) per symbol
-- **Sortable** by standard string sort (= rank sort)
-- **Portable** across systems (plain text + JSON)
-
-## 8. Integration with SilverSight
-
-- `HachimojiCodec.lean` — formal encode/decode specification
-- `HachimojiLUT.lean` — LUT hierarchy (k=2, k=6, k=50)
-- `PhaseCircle` — ℤ/360ℤ address space
-- `dna_lut.py` — Python LUT implementation
-- `dna_encode_file.py` — file encoder/decoder
-
-## 9. Not This
-
-- ❌ Not a compression format (bits/byte not the goal)
-- ❌ Not a DNA storage format (no synthesis/sequencing constraints)
-- ❌ Not a cryptographic scheme (no security claims)
-- ✅ A computational substrate for manifold/QUBO/eigenvalue work