symbiote-cli 0.1.0

package/dist/src/dna/embeddings.js

@@ -0,0 +1,46 @@
+import { pipeline } from '@huggingface/transformers';
+const MODEL_NAME = 'Xenova/all-MiniLM-L6-v2';
+const EMBEDDING_DIM = 384;
+export function cosineSimilarity(a, b) {
+    let dotProduct = 0;
+    let normA = 0;
+    let normB = 0;
+    for (let i = 0; i < a.length; i++) {
+        dotProduct += a[i] * b[i];
+        normA += a[i] * a[i];
+        normB += b[i] * b[i];
+    }
+    const denominator = Math.sqrt(normA) * Math.sqrt(normB);
+    if (denominator === 0)
+        return 0;
+    return dotProduct / denominator;
+}
+export class EmbeddingModel {
+    extractor = null;
+    async embed(text) {
+        const extractor = await this.getExtractor();
+        const output = await extractor(text, { pooling: 'mean', normalize: true });
+        return Array.from(output.data).slice(0, EMBEDDING_DIM);
+    }
+    async embedBatch(texts) {
+        if (texts.length === 0)
+            return [];
+        const extractor = await this.getExtractor();
+        const output = await extractor(texts, { pooling: 'mean', normalize: true });
+        const flat = Array.from(output.data);
+        const results = [];
+        for (let i = 0; i < texts.length; i++) {
+            results.push(flat.slice(i * EMBEDDING_DIM, (i + 1) * EMBEDDING_DIM));
+        }
+        return results;
+    }
+    async getExtractor() {
+        if (!this.extractor) {
+            const raw = await pipeline('feature-extraction', MODEL_NAME, { dtype: 'fp32' });
+            this.extractor = (input, opts) => raw(input, opts);
+        }
+        return this.extractor;
+    }
+}
+export { EMBEDDING_DIM };
+//# sourceMappingURL=embeddings.js.map

package/dist/src/dna/embeddings.js.map

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package/dist/src/dna/engine.d.ts

@@ -0,0 +1,30 @@
+import { DnaStorage } from './storage.js';
+import { type EmbeddingModel } from './embeddings.js';
+import type { DnaCategory, DnaEntry, DnaSource } from './types.js';
+export interface SimilarMatch {
+    entry: DnaEntry;
+    similarity: number;
+}
+export declare class DnaEngine {
+    private storage;
+    private embeddings?;
+    private embeddingCache;
+    constructor(storage: DnaStorage, embeddings?: EmbeddingModel | undefined);
+    captureInstruction(instruction: string, sessionId: string, source: DnaSource): DnaEntry;
+    private cachedEmbed;
+    captureInstructionWithPatternMatch(instruction: string, sessionId: string, source: DnaSource): Promise<DnaEntry>;
+    findSimilar(instruction: string): Promise<SimilarMatch[]>;
+    approveEntry(id: string): DnaEntry | null;
+    rejectEntry(id: string): DnaEntry | null;
+    editEntry(id: string, newContent: string): DnaEntry | null;
+    getActiveEntries(): DnaEntry[];
+    batchPassiveReinforce(): void;
+    decayUnseenEntries(currentSessionId: string): void;
+    autoPromote(): void;
+    reinforceObservedEntries(patterns: string[]): void;
+    private updateExistingEntry;
+    private computeConfidence;
+    static classifyCategory(instruction: string): DnaCategory;
+    static generateId(category: DnaCategory, content: string): string;
+}
+//# sourceMappingURL=engine.d.ts.map

package/dist/src/dna/engine.d.ts.map

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package/dist/src/dna/engine.js

@@ -0,0 +1,254 @@
+import crypto from 'node:crypto';
+import { cosineSimilarity } from './embeddings.js';
+import { slugify } from '#utils/strings.js';
+const SIMILARITY_THRESHOLD = 0.85;
+const AUTO_PROMOTE_SESSIONS = 3;
+const BASE_CONFIDENCE = 0.3;
+const EXPLICIT_CONFIDENCE = 1.0;
+function contentHash(text) {
+    return crypto.createHash('sha256').update(text).digest('hex');
+}
+export class DnaEngine {
+    storage;
+    embeddings;
+    embeddingCache = new Map();
+    constructor(storage, embeddings) {
+        this.storage = storage;
+        this.embeddings = embeddings;
+    }
+    captureInstruction(instruction, sessionId, source) {
+        const category = DnaEngine.classifyCategory(instruction);
+        const id = DnaEngine.generateId(category, instruction);
+        const existing = this.storage.readEntry(id);
+        if (existing) {
+            return this.updateExistingEntry(existing, sessionId, source);
+        }
+        const isExplicit = source === 'explicit';
+        const today = new Date().toISOString().split('T')[0];
+        const entry = {
+            frontmatter: {
+                id,
+                confidence: isExplicit ? EXPLICIT_CONFIDENCE : BASE_CONFIDENCE,
+                source,
+                status: isExplicit ? 'approved' : 'suggested',
+                category,
+                firstSeen: today,
+                lastSeen: today,
+                occurrences: 1,
+                sessionIds: [sessionId],
+            },
+            content: instruction,
+        };
+        this.storage.writeEntry(entry);
+        return entry;
+    }
+    async cachedEmbed(text) {
+        const hash = contentHash(text);
+        const cached = this.embeddingCache.get(hash);
+        if (cached)
+            return cached;
+        const embedding = await this.embeddings.embed(text);
+        this.embeddingCache.set(hash, embedding);
+        return embedding;
+    }
+    async captureInstructionWithPatternMatch(instruction, sessionId, source) {
+        if (!this.embeddings) {
+            return this.captureInstruction(instruction, sessionId, source);
+        }
+        const category = DnaEngine.classifyCategory(instruction);
+        const sameCategoryEntries = this.storage.listEntries({ category });
+        if (sameCategoryEntries.length > 0) {
+            const queryEmbedding = await this.cachedEmbed(instruction);
+            let bestMatch = null;
+            let bestSimilarity = 0;
+            for (const entry of sameCategoryEntries) {
+                const entryEmbedding = await this.cachedEmbed(entry.content);
+                const similarity = cosineSimilarity(queryEmbedding, entryEmbedding);
+                if (similarity > SIMILARITY_THRESHOLD && similarity > bestSimilarity) {
+                    bestMatch = entry;
+                    bestSimilarity = similarity;
+                }
+            }
+            if (bestMatch) {
+                return this.updateExistingEntry(bestMatch, sessionId, source);
+            }
+        }
+        return this.captureInstruction(instruction, sessionId, source);
+    }
+    async findSimilar(instruction) {
+        if (!this.embeddings)
+            return [];
+        const allEntries = this.storage.listEntries();
+        if (allEntries.length === 0)
+            return [];
+        const queryEmbedding = await this.cachedEmbed(instruction);
+        const matches = [];
+        for (const entry of allEntries) {
+            const entryEmbedding = await this.cachedEmbed(entry.content);
+            const similarity = cosineSimilarity(queryEmbedding, entryEmbedding);
+            if (similarity > 0.3) {
+                matches.push({ entry, similarity });
+            }
+        }
+        return matches.sort((a, b) => b.similarity - a.similarity);
+    }
+    approveEntry(id) {
+        const entry = this.storage.readEntry(id);
+        if (!entry)
+            return null;
+        entry.frontmatter.status = 'approved';
+        entry.frontmatter.confidence = EXPLICIT_CONFIDENCE;
+        this.storage.writeEntry(entry);
+        return entry;
+    }
+    rejectEntry(id) {
+        const entry = this.storage.readEntry(id);
+        if (!entry)
+            return null;
+        entry.frontmatter.status = 'rejected';
+        this.storage.writeEntry(entry);
+        return entry;
+    }
+    editEntry(id, newContent) {
+        const entry = this.storage.readEntry(id);
+        if (!entry)
+            return null;
+        entry.content = newContent;
+        this.storage.writeEntry(entry);
+        return entry;
+    }
+    getActiveEntries() {
+        return this.storage.listEntries().filter((e) => e.frontmatter.status !== 'rejected');
+    }
+    batchPassiveReinforce() {
+        const entries = this.storage
+            .listEntries()
+            .filter((e) => e.frontmatter.status === 'suggested');
+        for (const entry of entries) {
+            entry.frontmatter.confidence = Math.min(entry.frontmatter.confidence + 0.05, 0.99);
+            this.storage.writeEntry(entry);
+        }
+    }
+    decayUnseenEntries(currentSessionId) {
+        const entries = this.storage
+            .listEntries()
+            .filter((e) => e.frontmatter.status !== 'rejected');
+        for (const entry of entries) {
+            if (entry.frontmatter.sessionIds.includes(currentSessionId))
+                continue;
+            const lastSeen = new Date(entry.frontmatter.lastSeen).getTime();
+            const daysSinceSeen = (Date.now() - lastSeen) / (1000 * 60 * 60 * 24);
+            if (daysSinceSeen >= 30) {
+                entry.frontmatter.confidence = Math.max(entry.frontmatter.confidence - 0.05, 0.05);
+                this.storage.writeEntry(entry);
+            }
+        }
+    }
+    autoPromote() {
+        const entries = this.storage
+            .listEntries()
+            .filter((e) => e.frontmatter.status === 'suggested');
+        for (const entry of entries) {
+            if (entry.frontmatter.confidence >= 0.7 &&
+                entry.frontmatter.sessionIds.length >= AUTO_PROMOTE_SESSIONS) {
+                entry.frontmatter.status = 'approved';
+                this.storage.writeEntry(entry);
+            }
+        }
+    }
+    reinforceObservedEntries(patterns) {
+        if (patterns.length === 0)
+            return;
+        const entries = this.storage
+            .listEntries()
+            .filter((e) => e.frontmatter.status !== 'rejected');
+        const lowerPatterns = patterns.map((p) => p.toLowerCase());
+        for (const entry of entries) {
+            const lowerContent = entry.content.toLowerCase();
+            const matches = lowerPatterns.some((p) => lowerContent.includes(p));
+            if (matches) {
+                entry.frontmatter.confidence = Math.min(entry.frontmatter.confidence + 0.1, 0.99);
+                this.storage.writeEntry(entry);
+            }
+        }
+    }
+    updateExistingEntry(entry, sessionId, source) {
+        const fm = entry.frontmatter;
+        const today = new Date().toISOString().split('T')[0];
+        fm.lastSeen = today;
+        fm.occurrences++;
+        if (!fm.sessionIds.includes(sessionId)) {
+            fm.sessionIds.push(sessionId);
+            if (fm.sessionIds.length > 50) {
+                fm.sessionIds = fm.sessionIds.slice(-50);
+            }
+        }
+        if (source === 'explicit') {
+            fm.confidence = EXPLICIT_CONFIDENCE;
+            fm.status = 'approved';
+            fm.source = 'explicit';
+        }
+        else {
+            fm.confidence = this.computeConfidence(fm);
+            if (fm.status === 'suggested' && fm.sessionIds.length >= AUTO_PROMOTE_SESSIONS) {
+                fm.status = 'approved';
+            }
+        }
+        this.storage.writeEntry(entry);
+        return entry;
+    }
+    computeConfidence(fm) {
+        const uniqueSessions = fm.sessionIds.length;
+        if (uniqueSessions >= AUTO_PROMOTE_SESSIONS) {
+            return Math.min(0.8 + (uniqueSessions - AUTO_PROMOTE_SESSIONS) * 0.05, 0.99);
+        }
+        return BASE_CONFIDENCE + (uniqueSessions - 1) * 0.2;
+    }
+    static classifyCategory(instruction) {
+        const lower = instruction.toLowerCase();
+        const antiPatternRegexes = [
+            /\bnever\b/,
+            /\bdon'?t\b/,
+            /\bdo not\b/,
+            /\bavoid\b/,
+            /\bno\s/,
+            /\bstop\s/,
+            /\bforbid/,
+        ];
+        if (antiPatternRegexes.some((r) => r.test(lower))) {
+            return 'anti-patterns';
+        }
+        const decisionRegexes = [
+            /\bchose\b/,
+            /\bdecided\b/,
+            /\breason\b/,
+            /\bbecause\b/,
+            /\brationale\b/,
+            /\bwhy we\b/,
+            /\bthe reason\b/,
+        ];
+        if (decisionRegexes.some((r) => r.test(lower))) {
+            return 'decisions';
+        }
+        const preferenceRegexes = [
+            /\bprefer\b/,
+            /\binstead of\b/,
+            /\bover\s/,
+            /\brather than\b/,
+            /\bswitch to\b/,
+            /\bmigrate to\b/,
+        ];
+        if (preferenceRegexes.some((r) => r.test(lower))) {
+            return 'preferences';
+        }
+        if (lower.startsWith('use ') && !lower.includes(' in ')) {
+            return 'preferences';
+        }
+        return 'style';
+    }
+    static generateId(category, content) {
+        const maxSlugLength = 60 - category.length - 1;
+        return `${category}-${slugify(content, maxSlugLength)}`;
+    }
+}
+//# sourceMappingURL=engine.js.map

package/dist/src/dna/engine.js.map

@@ -0,0 +1 @@
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package/dist/src/dna/index.d.ts

@@ -0,0 +1,5 @@
+export { DNA_CATEGORIES, DNA_STATUSES, parseFrontmatter, serializeEntry, type DnaCategory, type DnaStatus, type DnaSource, type DnaFrontmatter, type DnaEntry, type DnaIndex, type DnaIndexEntry, } from './types.js';
+export { DnaStorage, type ListOptions } from './storage.js';
+export { EmbeddingModel, cosineSimilarity, EMBEDDING_DIM } from './embeddings.js';
+export { DnaEngine, type SimilarMatch } from './engine.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/src/dna/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/dna/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACH,cAAc,EACd,YAAY,EACZ,gBAAgB,EAChB,cAAc,EACd,KAAK,WAAW,EAChB,KAAK,SAAS,EACd,KAAK,SAAS,EACd,KAAK,cAAc,EACnB,KAAK,QAAQ,EACb,KAAK,QAAQ,EACb,KAAK,aAAa,GACrB,MAAM,YAAY,CAAC;AACpB,OAAO,EAAE,UAAU,EAAE,KAAK,WAAW,EAAE,MAAM,cAAc,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAClF,OAAO,EAAE,SAAS,EAAE,KAAK,YAAY,EAAE,MAAM,aAAa,CAAC"}

package/dist/src/dna/index.js

@@ -0,0 +1,5 @@
+export { DNA_CATEGORIES, DNA_STATUSES, parseFrontmatter, serializeEntry, } from './types.js';
+export { DnaStorage } from './storage.js';
+export { EmbeddingModel, cosineSimilarity, EMBEDDING_DIM } from './embeddings.js';
+export { DnaEngine } from './engine.js';
+//# sourceMappingURL=index.js.map

package/dist/src/dna/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/dna/index.ts"],"names":[],"mappings":"AAAA,OAAO,EACH,cAAc,EACd,YAAY,EACZ,gBAAgB,EAChB,cAAc,GAQjB,MAAM,YAAY,CAAC;AACpB,OAAO,EAAE,UAAU,EAAoB,MAAM,cAAc,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAClF,OAAO,EAAE,SAAS,EAAqB,MAAM,aAAa,CAAC"}

package/dist/src/dna/storage.d.ts

@@ -0,0 +1,19 @@
+import { type DnaCategory, type DnaEntry, type DnaIndex, type DnaStatus } from './types.js';
+export interface ListOptions {
+    status?: DnaStatus;
+    category?: DnaCategory;
+}
+export declare class DnaStorage {
+    private dnaDir;
+    private cachedIndex;
+    constructor(dnaDir: string);
+    ensureDirectories(): void;
+    readIndex(): DnaIndex;
+    readEntry(id: string): DnaEntry | null;
+    writeEntry(entry: DnaEntry): void;
+    deleteEntry(id: string): void;
+    listEntries(options?: ListOptions): DnaEntry[];
+    private writeIndex;
+    private idToFileName;
+}
+//# sourceMappingURL=storage.d.ts.map

package/dist/src/dna/storage.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"storage.d.ts","sourceRoot":"","sources":["../../../src/dna/storage.ts"],"names":[],"mappings":"AAEA,OAAO,EAIH,KAAK,WAAW,EAChB,KAAK,QAAQ,EACb,KAAK,QAAQ,EAEb,KAAK,SAAS,EACjB,MAAM,YAAY,CAAC;AAEpB,MAAM,WAAW,WAAW;IACxB,MAAM,CAAC,EAAE,SAAS,CAAC;IACnB,QAAQ,CAAC,EAAE,WAAW,CAAC;CAC1B;AAED,qBAAa,UAAU;IAGP,OAAO,CAAC,MAAM;IAF1B,OAAO,CAAC,WAAW,CAAyB;gBAExB,MAAM,EAAE,MAAM;IAElC,iBAAiB,IAAI,IAAI;IAazB,SAAS,IAAI,QAAQ;IAQrB,SAAS,CAAC,EAAE,EAAE,MAAM,GAAG,QAAQ,GAAG,IAAI;IAgBtC,UAAU,CAAC,KAAK,EAAE,QAAQ,GAAG,IAAI;IA4BjC,WAAW,CAAC,EAAE,EAAE,MAAM,GAAG,IAAI;IAe7B,WAAW,CAAC,OAAO,CAAC,EAAE,WAAW,GAAG,QAAQ,EAAE;IAwB9C,OAAO,CAAC,UAAU;IAQlB,OAAO,CAAC,YAAY;CAKvB"}

package/dist/src/dna/storage.js

@@ -0,0 +1,112 @@
+import fs from 'node:fs';
+import path from 'node:path';
+import { DNA_CATEGORIES, parseFrontmatter, serializeEntry, } from './types.js';
+export class DnaStorage {
+    dnaDir;
+    cachedIndex = null;
+    constructor(dnaDir) {
+        this.dnaDir = dnaDir;
+    }
+    ensureDirectories() {
+        for (const category of DNA_CATEGORIES) {
+            fs.mkdirSync(path.join(this.dnaDir, category), {
+                recursive: true,
+            });
+        }
+        const indexPath = path.join(this.dnaDir, 'index.json');
+        if (!fs.existsSync(indexPath)) {
+            this.writeIndex({ version: 1, entries: [] });
+        }
+    }
+    readIndex() {
+        if (this.cachedIndex)
+            return this.cachedIndex;
+        const indexPath = path.join(this.dnaDir, 'index.json');
+        const raw = fs.readFileSync(indexPath, 'utf-8');
+        this.cachedIndex = JSON.parse(raw);
+        return this.cachedIndex;
+    }
+    readEntry(id) {
+        const index = this.readIndex();
+        const indexEntry = index.entries.find((e) => e.id === id);
+        if (!indexEntry)
+            return null;
+        const filePath = path.join(this.dnaDir, indexEntry.category, indexEntry.fileName);
+        if (!fs.existsSync(filePath))
+            return null;
+        const raw = fs.readFileSync(filePath, 'utf-8');
+        const parsed = parseFrontmatter(raw);
+        if (!parsed)
+            return null;
+        return { frontmatter: parsed.frontmatter, content: parsed.content };
+    }
+    writeEntry(entry) {
+        const fm = entry.frontmatter;
+        const fileName = this.idToFileName(fm.id, fm.category);
+        const filePath = path.join(this.dnaDir, fm.category, fileName);
+        fs.mkdirSync(path.dirname(filePath), { recursive: true });
+        fs.writeFileSync(filePath, serializeEntry(entry));
+        const index = this.readIndex();
+        const existingIdx = index.entries.findIndex((e) => e.id === fm.id);
+        const indexEntry = {
+            id: fm.id,
+            category: fm.category,
+            status: fm.status,
+            confidence: fm.confidence,
+            fileName,
+        };
+        if (existingIdx >= 0) {
+            index.entries[existingIdx] = indexEntry;
+        }
+        else {
+            index.entries.push(indexEntry);
+        }
+        this.writeIndex(index);
+    }
+    deleteEntry(id) {
+        const index = this.readIndex();
+        const indexEntry = index.entries.find((e) => e.id === id);
+        if (!indexEntry)
+            return;
+        const filePath = path.join(this.dnaDir, indexEntry.category, indexEntry.fileName);
+        if (fs.existsSync(filePath)) {
+            fs.unlinkSync(filePath);
+        }
+        index.entries = index.entries.filter((e) => e.id !== id);
+        this.writeIndex(index);
+    }
+    listEntries(options) {
+        const index = this.readIndex();
+        let filtered = index.entries;
+        if (options?.status) {
+            filtered = filtered.filter((e) => e.status === options.status);
+        }
+        if (options?.category) {
+            filtered = filtered.filter((e) => e.category === options.category);
+        }
+        const entries = [];
+        for (const indexEntry of filtered) {
+            const filePath = path.join(this.dnaDir, indexEntry.category, indexEntry.fileName);
+            if (!fs.existsSync(filePath))
+                continue;
+            const raw = fs.readFileSync(filePath, 'utf-8');
+            const parsed = parseFrontmatter(raw);
+            if (parsed)
+                entries.push({ frontmatter: parsed.frontmatter, content: parsed.content });
+        }
+        return entries;
+    }
+    writeIndex(index) {
+        const indexPath = path.join(this.dnaDir, 'index.json');
+        const tmpPath = indexPath + '.tmp';
+        fs.writeFileSync(tmpPath, JSON.stringify(index, null, 4) + '\n');
+        fs.renameSync(tmpPath, indexPath);
+        this.cachedIndex = index;
+    }
+    idToFileName(id, category) {
+        const prefix = `${category}-`;
+        const name = id.startsWith(prefix) ? id.slice(prefix.length) : id;
+        return `${name}.md`;
+    }
+}
+//# sourceMappingURL=storage.js.map

package/dist/src/dna/storage.js.map

@@ -0,0 +1 @@
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package/dist/src/dna/types.d.ts

@@ -0,0 +1,38 @@
+export declare const DNA_CATEGORIES: readonly ["style", "preferences", "anti-patterns", "decisions"];
+export type DnaCategory = (typeof DNA_CATEGORIES)[number];
+export declare const DNA_STATUSES: readonly ["suggested", "approved", "rejected"];
+export type DnaStatus = (typeof DNA_STATUSES)[number];
+export type DnaSource = 'correction' | 'explicit' | 'pattern';
+export interface DnaFrontmatter {
+    id: string;
+    confidence: number;
+    source: DnaSource;
+    status: DnaStatus;
+    category: DnaCategory;
+    firstSeen: string;
+    lastSeen: string;
+    occurrences: number;
+    sessionIds: string[];
+}
+export interface DnaEntry {
+    frontmatter: DnaFrontmatter;
+    content: string;
+}
+export interface DnaIndexEntry {
+    id: string;
+    category: DnaCategory;
+    status: DnaStatus;
+    confidence: number;
+    fileName: string;
+}
+export interface DnaIndex {
+    version: number;
+    entries: DnaIndexEntry[];
+}
+export declare function parseFrontmatter(raw: string): {
+    frontmatter: DnaFrontmatter;
+    content: string;
+} | null;
+export declare function serializeEntry(entry: DnaEntry): string;
+export declare function parseYamlBlock(block: string): Record<string, unknown> | null;
+//# sourceMappingURL=types.d.ts.map

package/dist/src/dna/types.d.ts.map

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