symbiote-cli 0.1.0

package/dist/src/core/parser.js.map

@@ -0,0 +1 @@
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package/dist/src/core/scanner.d.ts

@@ -0,0 +1,26 @@
+import type { Repository } from '#storage/repository.js';
+import type { SymbioteDB } from '#storage/db.js';
+export interface ScanOptions {
+    force?: boolean;
+    embeddings?: boolean;
+    skipAlgorithms?: boolean;
+}
+export interface ScanResult {
+    filesScanned: number;
+    filesSkipped: number;
+    nodesCreated: number;
+    edgesCreated: number;
+    embeddingsGenerated: number;
+    errors: Array<{
+        file: string;
+        error: string;
+    }>;
+}
+export declare class Scanner {
+    private repo;
+    private db?;
+    private embeddingService;
+    constructor(repo: Repository, db?: SymbioteDB | undefined);
+    scan(rootDir: string, options?: ScanOptions): Promise<ScanResult>;
+}
+//# sourceMappingURL=scanner.d.ts.map

package/dist/src/core/scanner.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"scanner.d.ts","sourceRoot":"","sources":["../../../src/core/scanner.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,wBAAwB,CAAC;AACzD,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,gBAAgB,CAAC;AAEjD,MAAM,WAAW,WAAW;IACxB,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,UAAU,CAAC,EAAE,OAAO,CAAC;IACrB,cAAc,CAAC,EAAE,OAAO,CAAC;CAC5B;AAED,MAAM,WAAW,UAAU;IACvB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,mBAAmB,EAAE,MAAM,CAAC;IAC5B,MAAM,EAAE,KAAK,CAAC;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CAClD;AAED,qBAAa,OAAO;IAIZ,OAAO,CAAC,IAAI;IACZ,OAAO,CAAC,EAAE,CAAC;IAJf,OAAO,CAAC,gBAAgB,CAAiC;gBAG7C,IAAI,EAAE,UAAU,EAChB,EAAE,CAAC,EAAE,UAAU,YAAA;IAGrB,IAAI,CAAC,OAAO,EAAE,MAAM,EAAE,OAAO,GAAE,WAAgB,GAAG,OAAO,CAAC,UAAU,CAAC;CAkF9E"}

package/dist/src/core/scanner.js

@@ -0,0 +1,87 @@
+import fs from 'node:fs/promises';
+import { walkFiles, hashFileContent } from '#utils/files.js';
+import { parseFile } from './parser.js';
+import { EmbeddingService } from './embeddings.js';
+import { GraphAlgorithms } from './algorithms.js';
+import { CortexEngine } from '#cortex/engine.js';
+import { CortexRepository } from '#cortex/repository.js';
+export class Scanner {
+    repo;
+    db;
+    embeddingService = null;
+    constructor(repo, db) {
+        this.repo = repo;
+        this.db = db;
+    }
+    async scan(rootDir, options = {}) {
+        const files = await walkFiles(rootDir);
+        const result = {
+            filesScanned: 0,
+            filesSkipped: 0,
+            nodesCreated: 0,
+            edgesCreated: 0,
+            embeddingsGenerated: 0,
+            errors: [],
+        };
+        if (options.embeddings && this.db) {
+            this.embeddingService = new EmbeddingService();
+            await this.embeddingService.initialize();
+        }
+        for (const filePath of files) {
+            try {
+                const source = await fs.readFile(filePath, 'utf-8');
+                const hash = hashFileContent(filePath, source);
+                if (!options.force && !(await this.repo.isFileChanged(filePath, hash))) {
+                    result.filesSkipped++;
+                    continue;
+                }
+                const parsed = parseFile(filePath, source);
+                if (!parsed) {
+                    result.filesSkipped++;
+                    continue;
+                }
+                await this.repo.updateFileNodes(filePath, hash, parsed.nodes, parsed.edges);
+                if (this.embeddingService && this.db) {
+                    await this.embeddingService.clearForFile(this.db, filePath);
+                    result.embeddingsGenerated += await this.embeddingService.generateForNodes(this.db, parsed.nodes, new Map([[filePath, source]]));
+                }
+                result.filesScanned++;
+                result.nodesCreated += parsed.nodes.length;
+                result.edgesCreated += parsed.edges.length;
+            }
+            catch (error) {
+                result.errors.push({
+                    file: filePath,
+                    error: error instanceof Error ? error.message : String(error),
+                });
+            }
+        }
+        this.embeddingService?.dispose();
+        this.embeddingService = null;
+        if (!options.skipAlgorithms && result.filesScanned > 0) {
+            try {
+                const algorithms = new GraphAlgorithms(this.repo);
+                await algorithms.runAll();
+            }
+            catch {
+                // Algorithm failures are non-fatal
+            }
+        }
+        if (this.db) {
+            try {
+                const cortexRepo = new CortexRepository(this.db);
+                const engine = new CortexEngine(cortexRepo);
+                await engine.run({
+                    rootDir,
+                    force: options.force,
+                    maxStage: 3,
+                });
+            }
+            catch {
+                // Cortex pipeline failures are non-fatal
+            }
+        }
+        return result;
+    }
+}
+//# sourceMappingURL=scanner.js.map

package/dist/src/core/scanner.js.map

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package/dist/src/core/search.d.ts

@@ -0,0 +1,34 @@
+import type { SymbioteDB } from '#storage/db.js';
+import type { Repository, NodeRecord } from '#storage/repository.js';
+export interface SearchResult {
+    node: NodeRecord;
+    score: number;
+    source: 'text' | 'vector' | 'hybrid';
+}
+interface RankedItem {
+    nodeId: string;
+    score: number;
+}
+export interface SearchOptions {
+    limit?: number;
+    useVector?: boolean;
+}
+export declare class HybridSearch {
+    private db;
+    private repo;
+    private ftsReady;
+    private ftsLock;
+    private embeddingService;
+    constructor(db: SymbioteDB, repo: Repository);
+    private getEmbeddingService;
+    textSearch(query: string, limit?: number): Promise<SearchResult[]>;
+    vectorSearch(query: string, limit?: number): Promise<SearchResult[]>;
+    search(query: string, options?: SearchOptions): Promise<SearchResult[]>;
+    static rrfFuse(listA: RankedItem[], listB: RankedItem[], k?: number): RankedItem[];
+    private ensureFts;
+    private buildFtsIndex;
+    private fallback;
+    private hasEmbeddings;
+}
+export {};
+//# sourceMappingURL=search.d.ts.map

package/dist/src/core/search.d.ts.map

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package/dist/src/core/search.js

@@ -0,0 +1,146 @@
+import { EmbeddingService } from './embeddings.js';
+export class HybridSearch {
+    db;
+    repo;
+    ftsReady = false;
+    ftsLock = null;
+    embeddingService = null;
+    constructor(db, repo) {
+        this.db = db;
+        this.repo = repo;
+    }
+    async getEmbeddingService() {
+        if (!this.embeddingService) {
+            console.warn('[symbiote] First vector search — downloading embedding model, this may take a moment.');
+            this.embeddingService = new EmbeddingService();
+            await this.embeddingService.initialize();
+        }
+        return this.embeddingService;
+    }
+    async textSearch(query, limit = 20) {
+        await this.ensureFts();
+        const rows = await this.db.all(`SELECT node_id, MAX(score) as score FROM (
+                SELECT *, fts_main_nodes_fts.match_bm25(node_id, $1, fields := 'name') as score
+                FROM nodes_fts WHERE score IS NOT NULL
+                UNION ALL
+                SELECT *, fts_main_nodes_fts.match_bm25(node_id, $1, fields := 'file_path') as score
+                FROM nodes_fts WHERE score IS NOT NULL
+            ) GROUP BY node_id ORDER BY score DESC LIMIT $2`, query, limit);
+        if (rows.length === 0)
+            return this.fallback(query, limit);
+        const ids = rows.map((r) => r.node_id);
+        const nodeMap = await this.repo.getNodesByIds(ids);
+        const results = [];
+        for (const row of rows) {
+            const node = nodeMap.get(row.node_id);
+            if (node)
+                results.push({ node, score: row.score, source: 'text' });
+        }
+        return results;
+    }
+    async vectorSearch(query, limit = 20) {
+        const svc = await this.getEmbeddingService();
+        const qv = await svc.embed(query);
+        const rows = await this.db.all(`SELECT e.node_id, array_cosine_similarity(e.vector, $1::FLOAT[384]) as score
+                 FROM embeddings e WHERE e.vector IS NOT NULL ORDER BY score DESC LIMIT $2`, JSON.stringify(qv), limit);
+        const ids = rows.map((r) => r.node_id);
+        const nodeMap = await this.repo.getNodesByIds(ids);
+        const results = [];
+        for (const row of rows) {
+            const node = nodeMap.get(row.node_id);
+            if (node)
+                results.push({ node, score: row.score, source: 'vector' });
+        }
+        return results;
+    }
+    async search(query, options = {}) {
+        const limit = options.limit ?? 20;
+        const textResults = await this.textSearch(query, limit * 2);
+        const textRanked = textResults.map((r) => ({
+            nodeId: r.node.id,
+            score: r.score,
+        }));
+        let vectorRanked = [];
+        if (options.useVector !== false) {
+            const hasEmb = await this.hasEmbeddings();
+            if (hasEmb) {
+                const vr = await this.vectorSearch(query, limit * 2);
+                vectorRanked = vr.map((r) => ({ nodeId: r.node.id, score: r.score }));
+            }
+        }
+        if (vectorRanked.length === 0)
+            return textResults.slice(0, limit);
+        const fused = HybridSearch.rrfFuse(textRanked, vectorRanked);
+        const topItems = fused.slice(0, limit);
+        const ids = topItems.map((item) => item.nodeId);
+        const nodeMap = await this.repo.getNodesByIds(ids);
+        const results = [];
+        for (const item of topItems) {
+            const node = nodeMap.get(item.nodeId);
+            if (node)
+                results.push({ node, score: item.score, source: 'hybrid' });
+        }
+        return results;
+    }
+    static rrfFuse(listA, listB, k = 60) {
+        const scores = new Map();
+        listA.forEach((item, rank) => scores.set(item.nodeId, (scores.get(item.nodeId) ?? 0) + 1 / (k + rank + 1)));
+        listB.forEach((item, rank) => scores.set(item.nodeId, (scores.get(item.nodeId) ?? 0) + 1 / (k + rank + 1)));
+        return Array.from(scores.entries())
+            .map(([nodeId, score]) => ({ nodeId, score }))
+            .sort((a, b) => b.score - a.score);
+    }
+    async ensureFts() {
+        if (this.ftsReady)
+            return;
+        if (this.ftsLock) {
+            await this.ftsLock;
+            return;
+        }
+        this.ftsLock = this.buildFtsIndex();
+        try {
+            await this.ftsLock;
+        }
+        finally {
+            this.ftsLock = null;
+        }
+    }
+    async buildFtsIndex() {
+        try {
+            await this.db.exec('BEGIN TRANSACTION');
+            try {
+                await this.db.exec('DROP TABLE IF EXISTS nodes_fts;');
+                await this.db.exec('CREATE TABLE nodes_fts AS SELECT id as node_id, name, file_path FROM nodes;');
+                await this.db.exec("PRAGMA create_fts_index('nodes_fts', 'node_id', 'name', 'file_path');");
+                await this.db.exec('COMMIT');
+            }
+            catch (err) {
+                await this.db.exec('ROLLBACK');
+                throw err;
+            }
+            this.ftsReady = true;
+        }
+        catch (err) {
+            this.ftsReady = false;
+            throw new Error(`Failed to build FTS index: ${err instanceof Error ? err.message : String(err)}`);
+        }
+    }
+    async fallback(query, limit) {
+        const nodes = await this.repo.searchNodesByName(query);
+        return nodes.slice(0, limit).map((node, i) => ({
+            node,
+            score: 1 / (i + 1),
+            source: 'text',
+        }));
+    }
+    async hasEmbeddings() {
+        try {
+            const rows = await this.db.all('SELECT 1 as count FROM embeddings LIMIT 1');
+            return rows.length > 0;
+        }
+        catch {
+            return false;
+        }
+    }
+}
+//# sourceMappingURL=search.js.map

package/dist/src/core/search.js.map

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

@@ -0,0 +1,29 @@
+declare const GraphConstructor: new (opts?: {
+    multi?: boolean;
+    type?: "directed" | "undirected" | "mixed";
+}) => GraphInstance;
+export interface GraphInstance {
+    order: number;
+    size: number;
+    addNode(id: string, attrs?: Record<string, unknown>): void;
+    hasNode(id: string): boolean;
+    addEdge(source: string, target: string, attrs?: Record<string, unknown>): void;
+    hasEdge(source: string, target: string): boolean;
+    getNodeAttribute(id: string, attr: string): unknown;
+    setNodeAttribute(id: string, attr: string, value: unknown): void;
+    getNodeAttributes(id: string): Record<string, unknown>;
+    forEachNode(cb: (id: string, attrs: Record<string, unknown>) => void): void;
+    forEachEdge(cb: (edge: string, attrs: Record<string, unknown>, source: string, target: string) => void): void;
+    forEachOutEdge(node: string, cb: (edge: string, attrs: Record<string, unknown>, source: string, target: string) => void): void;
+    forEachInEdge(node: string, cb: (edge: string, attrs: Record<string, unknown>, source: string) => void): void;
+    inEdges(node: string): string[];
+    outEdges(node: string): string[];
+    source(edge: string): string;
+    target(edge: string): string;
+    getEdgeAttribute(edge: string, attr: string): unknown;
+    filterNodes(predicate: (id: string, attrs: Record<string, unknown>) => boolean): string[];
+}
+export { GraphConstructor as Graph };
+export type RiskLevel = 'HIGH' | 'MEDIUM' | 'LOW';
+export declare function computeRiskLevel(maxConfidence: number): RiskLevel;
+//# sourceMappingURL=types.d.ts.map

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

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package/dist/src/core/types.js

@@ -0,0 +1,12 @@
+import { createRequire } from 'node:module';
+const cjsRequire = createRequire(import.meta.url);
+const GraphConstructor = cjsRequire('graphology');
+export { GraphConstructor as Graph };
+export function computeRiskLevel(maxConfidence) {
+    if (maxConfidence > 0.7)
+        return 'HIGH';
+    if (maxConfidence > 0.4)
+        return 'MEDIUM';
+    return 'LOW';
+}
+//# sourceMappingURL=types.js.map

package/dist/src/core/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/core/types.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAE5C,MAAM,UAAU,GAAG,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AAClD,MAAM,gBAAgB,GAAG,UAAU,CAAC,YAAY,CAG7B,CAAC;AAgCpB,OAAO,EAAE,gBAAgB,IAAI,KAAK,EAAE,CAAC;AAIrC,MAAM,UAAU,gBAAgB,CAAC,aAAqB;IAClD,IAAI,aAAa,GAAG,GAAG;QAAE,OAAO,MAAM,CAAC;IACvC,IAAI,aAAa,GAAG,GAAG;QAAE,OAAO,QAAQ,CAAC;IACzC,OAAO,KAAK,CAAC;AACjB,CAAC"}

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

@@ -0,0 +1,10 @@
+import { CortexRepository } from './repository.js';
+import type { PipelineOptions, PipelineResult } from './types.js';
+export declare class CortexEngine {
+    private repo;
+    constructor(repo: CortexRepository);
+    run(options: PipelineOptions): Promise<PipelineResult>;
+    private cascadeInvalidation;
+    private getChangedFileIds;
+}
+//# sourceMappingURL=engine.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"engine.d.ts","sourceRoot":"","sources":["../../../src/cortex/engine.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AASnD,OAAO,KAAK,EAAE,eAAe,EAAE,cAAc,EAAe,MAAM,YAAY,CAAC;AAmB/E,qBAAa,YAAY;IACT,OAAO,CAAC,IAAI;gBAAJ,IAAI,EAAE,gBAAgB;IAEpC,GAAG,CAAC,OAAO,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC;YA+B9C,mBAAmB;YAsCnB,iBAAiB;CAKlC"}

package/dist/src/cortex/engine.js

@@ -0,0 +1,93 @@
+import { runStage0 } from './stage-0-structure.js';
+import { runStage1 } from './stage-1-symbols.js';
+import { runStage2 } from './stage-2-resolution.js';
+import { runStage3 } from './stage-3-callgraph.js';
+import { runStage4 } from './stage-4-types.js';
+import { runStage5 } from './stage-5-flow.js';
+import { runStage6 } from './stage-6-topology.js';
+import { runStage7 } from './stage-7-intelligence.js';
+const STAGES = [
+    runStage0,
+    runStage1,
+    runStage2,
+    runStage3,
+    runStage4,
+    runStage5,
+    runStage6,
+    runStage7,
+];
+export class CortexEngine {
+    repo;
+    constructor(repo) {
+        this.repo = repo;
+    }
+    async run(options) {
+        const start = Date.now();
+        const maxStage = options.maxStage ?? STAGES.length - 1;
+        const stages = [];
+        let totalNodes = 0;
+        let totalEdges = 0;
+        for (let i = 0; i <= maxStage && i < STAGES.length; i++) {
+            const result = await STAGES[i](this.repo, options.rootDir, {
+                force: options.force,
+                targetFiles: options.targetFiles,
+            });
+            stages.push(result);
+            totalNodes += result.nodesCreated;
+            totalEdges += result.edgesCreated;
+            if (i === 0 && result.filesProcessed > 0) {
+                await this.cascadeInvalidation(result);
+            }
+        }
+        return {
+            stages,
+            totalFiles: Math.max(...stages.map((s) => s.filesProcessed), 0),
+            totalNodes,
+            totalEdges,
+            totalDurationMs: Date.now() - start,
+            maxDepth: maxStage,
+        };
+    }
+    async cascadeInvalidation(stage0Result) {
+        const changedFileIds = await this.getChangedFileIds(stage0Result);
+        if (changedFileIds.length === 0)
+            return;
+        const visited = new Set(changedFileIds);
+        let frontier = [...changedFileIds];
+        let depth = 0;
+        const maxCascadeDepth = 10;
+        while (frontier.length > 0 && depth < maxCascadeDepth) {
+            const nextFrontier = [];
+            for (const fileId of frontier) {
+                const importers = await this.repo.getImportersOf(fileId);
+                for (const imp of importers) {
+                    if (!visited.has(imp.sourceId)) {
+                        visited.add(imp.sourceId);
+                        nextFrontier.push(imp.sourceId);
+                    }
+                }
+            }
+            frontier = nextFrontier;
+            depth++;
+        }
+        for (const id of changedFileIds) {
+            visited.delete(id);
+        }
+        for (const fileId of visited) {
+            const file = await this.repo.getFileNode(fileId);
+            if (file && file.depthLevel > 1) {
+                await this.repo.upsertFileNode({
+                    ...file,
+                    depthLevel: 1,
+                });
+            }
+        }
+    }
+    async getChangedFileIds(stage0Result) {
+        if (stage0Result.filesProcessed === 0)
+            return [];
+        const allFiles = await this.repo.getAllFileNodes();
+        return allFiles.filter((f) => f.depthLevel === 0).map((f) => f.id);
+    }
+}
+//# sourceMappingURL=engine.js.map

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

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

@@ -0,0 +1,13 @@
+export { CortexEngine } from './engine.js';
+export { CortexRepository } from './repository.js';
+export { createCortexSchema, CORTEX_TABLES, refreshSymbolsTable } from './schema.js';
+export { installPgq, createPropertyGraph, isPgqAvailable } from './pgq.js';
+export { executePgqQuery, validatePgqQuery } from './pgq-queries.js';
+export { runStage0 } from './stage-0-structure.js';
+export { runStage1 } from './stage-1-symbols.js';
+export { runStage2 } from './stage-2-resolution.js';
+export { runStage3 } from './stage-3-callgraph.js';
+export { runStage4 } from './stage-4-types.js';
+export { runStage5 } from './stage-5-flow.js';
+export type * from './types.js';
+//# sourceMappingURL=index.d.ts.map

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

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package/dist/src/cortex/index.js

@@ -0,0 +1,12 @@
+export { CortexEngine } from './engine.js';
+export { CortexRepository } from './repository.js';
+export { createCortexSchema, CORTEX_TABLES, refreshSymbolsTable } from './schema.js';
+export { installPgq, createPropertyGraph, isPgqAvailable } from './pgq.js';
+export { executePgqQuery, validatePgqQuery } from './pgq-queries.js';
+export { runStage0 } from './stage-0-structure.js';
+export { runStage1 } from './stage-1-symbols.js';
+export { runStage2 } from './stage-2-resolution.js';
+export { runStage3 } from './stage-3-callgraph.js';
+export { runStage4 } from './stage-4-types.js';
+export { runStage5 } from './stage-5-flow.js';
+//# sourceMappingURL=index.js.map

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

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