symbiote-cli 0.1.0

package/dist/src/cortex/stage-7-intelligence.js

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+import { execSync } from 'node:child_process';
+import { detectGodClasses, detectCircularDependencies, detectLayerViolations, detectComplexityHotspots, } from './patterns.js';
+export async function collectFindings(repo) {
+    const findings = [];
+    const classes = await repo.getAllClasses();
+    const methods = await repo.getAllMethods();
+    const classMetrics = classes.map((cls) => {
+        const classMethods = methods.filter((m) => m.className === cls.name);
+        return {
+            nodeId: cls.id,
+            name: cls.name,
+            filePath: cls.filePath,
+            methodCount: classMethods.length,
+            betweenness: cls.betweenness ?? 0,
+        };
+    });
+    findings.push(...detectGodClasses(classMetrics, {
+        methodThreshold: 10,
+        betweennessThreshold: 0.3,
+    }));
+    const fileNodes = await repo.getAllFileNodes();
+    const importEdges = [];
+    for (const file of fileNodes) {
+        const imports = await repo.getImportsFrom(file.id);
+        for (const imp of imports) {
+            importEdges.push({ sourceId: imp.sourceId, targetId: imp.targetId });
+        }
+    }
+    findings.push(...detectCircularDependencies(importEdges));
+    const layersRaw = await repo.getMeta('layers');
+    if (layersRaw) {
+        const layerData = JSON.parse(layersRaw);
+        const layerNodes = layerData.flatMap((entry) => entry.nodeIds.map((nodeId) => ({
+            nodeId,
+            layer: entry.layer,
+            confidence: 1.0,
+        })));
+        const fileImportEdges = importEdges.map((e) => ({
+            sourceId: e.sourceId,
+            targetId: e.targetId,
+        }));
+        findings.push(...detectLayerViolations(layerNodes, fileImportEdges));
+    }
+    const functions = await repo.getAllFunctions();
+    const nodeMetrics = functions.map((fn) => ({
+        nodeId: fn.id,
+        name: fn.name,
+        filePath: fn.filePath,
+        pageRank: fn.pageRank ?? 0,
+        betweenness: fn.betweenness ?? 0,
+        lineCount: fn.lineEnd - fn.lineStart + 1,
+    }));
+    findings.push(...detectComplexityHotspots(nodeMetrics, {
+        topN: 10,
+        minScore: 0.3,
+    }));
+    return findings;
+}
+export async function saveTemporalSnapshot(repo, commitHash) {
+    const stats = await repo.getStats();
+    const nodeCounts = {
+        files: stats.files,
+        functions: stats.functions,
+        classes: stats.classes,
+        methods: stats.methods,
+        interfaces: stats.interfaces,
+        types: stats.types,
+        variables: stats.variables,
+        modules: stats.modules,
+    };
+    const edgeCounts = {
+        calls: stats.calls,
+        imports: stats.imports,
+        extends: stats.extends,
+        implements: stats.implements,
+        contains: stats.contains,
+        flowsTo: stats.flowsTo,
+        reads: stats.reads,
+        writes: stats.writes,
+        returns: stats.returns,
+    };
+    const functions = await repo.getAllFunctions();
+    const topPagerank = functions
+        .filter((fn) => fn.pageRank !== null && fn.pageRank > 0)
+        .sort((a, b) => (b.pageRank ?? 0) - (a.pageRank ?? 0))
+        .slice(0, 10)
+        .map((fn) => ({ nodeId: fn.id, score: fn.pageRank ?? 0 }));
+    const nodeMetrics = functions.map((fn) => ({
+        nodeId: fn.id,
+        name: fn.name,
+        filePath: fn.filePath,
+        pageRank: fn.pageRank ?? 0,
+        betweenness: fn.betweenness ?? 0,
+        lineCount: fn.lineEnd - fn.lineStart + 1,
+    }));
+    const hotspotFindings = detectComplexityHotspots(nodeMetrics, {
+        topN: 10,
+        minScore: 0.1,
+    });
+    const hotspotRankings = hotspotFindings.map((f) => ({
+        nodeId: f.nodeIds[0],
+        score: f.metadata.score ?? 0,
+    }));
+    const communityHash = computeCommunityHash(functions.map((fn) => ({
+        id: fn.id,
+        community: fn.community ?? 0,
+    })));
+    const snapshot = {
+        commitHash,
+        timestamp: new Date(),
+        nodeCounts,
+        edgeCounts,
+        communityHash,
+        topPagerank,
+        hotspotRankings,
+    };
+    await repo.insertTemporalSnapshot(snapshot);
+}
+function computeCommunityHash(nodes) {
+    const sorted = [...nodes].sort((a, b) => a.id.localeCompare(b.id));
+    const input = sorted.map((n) => `${n.id}:${n.community}`).join('|');
+    let hash = 0;
+    for (let i = 0; i < input.length; i++) {
+        const char = input.charCodeAt(i);
+        hash = ((hash << 5) - hash + char) | 0;
+    }
+    return Math.abs(hash).toString(36);
+}
+function getCommitHash(rootDir) {
+    try {
+        return execSync('git rev-parse HEAD', { cwd: rootDir }).toString().trim();
+    }
+    catch {
+        return 'unknown';
+    }
+}
+export async function runStage7(repo, rootDir, options) {
+    const start = Date.now();
+    const errors = [];
+    const maxDepth = await repo.getMaxDepthLevel();
+    if (maxDepth < 6 && !options?.force) {
+        return {
+            stage: 7,
+            filesProcessed: 0,
+            nodesCreated: 0,
+            edgesCreated: 0,
+            durationMs: Date.now() - start,
+            errors: [],
+        };
+    }
+    const findings = await collectFindings(repo);
+    await repo.setMeta('findings', JSON.stringify(findings));
+    const commitHash = getCommitHash(rootDir);
+    await saveTemporalSnapshot(repo, commitHash);
+    const allFiles = await repo.getAllFileNodes();
+    const filesToUpdate = allFiles.filter((f) => f.depthLevel >= 6 || options?.force);
+    for (const file of filesToUpdate) {
+        await repo.upsertFileNode({ ...file, depthLevel: 7 });
+    }
+    return {
+        stage: 7,
+        filesProcessed: filesToUpdate.length,
+        nodesCreated: 0,
+        edgesCreated: 0,
+        durationMs: Date.now() - start,
+        errors,
+    };
+}
+export function detectStyleDeviations(dnaEntries, nodePatterns) {
+    const activeStyleEntries = dnaEntries.filter((e) => e.frontmatter.status !== 'rejected' && e.frontmatter.category === 'style');
+    if (activeStyleEntries.length === 0)
+        return [];
+    const findings = [];
+    const hasAsyncAwaitRule = activeStyleEntries.some((e) => e.content.toLowerCase().includes('async/await') ||
+        e.content.toLowerCase().includes('async await'));
+    if (hasAsyncAwaitRule) {
+        for (const node of nodePatterns) {
+            if (node.usesPromiseChains && !node.usesAsyncAwait) {
+                findings.push({
+                    kind: 'style_deviation',
+                    severity: 'info',
+                    message: `${node.nodeId} uses promise chains instead of async/await`,
+                    nodeIds: [node.nodeId],
+                    filePaths: [node.filePath],
+                    metadata: {
+                        dnaRule: 'async/await preference',
+                        usesPromiseChains: true,
+                        usesAsyncAwait: false,
+                    },
+                });
+            }
+        }
+    }
+    return findings;
+}
+export function detectDecisionContradictions(dnaEntries, observedPatterns) {
+    const activeDecisions = dnaEntries.filter((e) => e.frontmatter.status === 'approved' && e.frontmatter.category === 'decisions');
+    if (activeDecisions.length === 0)
+        return [];
+    const findings = [];
+    for (const pattern of observedPatterns) {
+        for (const decision of activeDecisions) {
+            const content = decision.content.toLowerCase();
+            const patternDesc = pattern.description.toLowerCase();
+            const patternName = pattern.pattern.toLowerCase().replace(/_/g, ' ');
+            const isContradiction = (content.includes('repository pattern') && patternName.includes('direct db')) ||
+                (content.includes('repository') && patternDesc.includes('directly calls database'));
+            if (isContradiction) {
+                findings.push({
+                    kind: 'decision_contradiction',
+                    severity: 'warning',
+                    message: `${pattern.nodeId} contradicts decision: ${decision.content}`,
+                    nodeIds: [pattern.nodeId],
+                    filePaths: [pattern.filePath],
+                    metadata: {
+                        decisionId: decision.frontmatter.id,
+                        decisionContent: decision.content,
+                        observedPattern: pattern.pattern,
+                    },
+                });
+            }
+        }
+    }
+    return findings;
+}
+export function predictImpact(changeHistory, currentFile, options) {
+    const coOccurrences = new Map();
+    for (const record of changeHistory) {
+        if (record.file !== currentFile)
+            continue;
+        for (const coFile of record.changedWith) {
+            coOccurrences.set(coFile, (coOccurrences.get(coFile) ?? 0) + 1);
+        }
+    }
+    const predictedFiles = [];
+    for (const [file, count] of coOccurrences) {
+        if (count >= options.minCoOccurrence) {
+            predictedFiles.push(file);
+        }
+    }
+    if (predictedFiles.length === 0)
+        return [];
+    return [
+        {
+            kind: 'predictive_impact',
+            severity: 'info',
+            message: `Changes to ${currentFile} historically co-occur with: ${predictedFiles.join(', ')}`,
+            nodeIds: [],
+            filePaths: [currentFile, ...predictedFiles],
+            metadata: {
+                sourceFile: currentFile,
+                coChangeFiles: predictedFiles,
+                frequencies: Object.fromEntries(predictedFiles.map((f) => [f, coOccurrences.get(f)])),
+            },
+        },
+    ];
+}
+//# sourceMappingURL=stage-7-intelligence.js.map

package/dist/src/cortex/stage-7-intelligence.js.map

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

@@ -0,0 +1,78 @@
+export type LayerKind = 'controller' | 'service' | 'repository' | 'database' | 'utility' | 'unknown';
+export interface TopologyResults {
+    communities: Record<string, number>;
+    pageRank: Record<string, number>;
+    betweenness: Record<string, number>;
+    flows: ExecutionFlow[];
+    layers: LayerAssignment[];
+}
+export interface ExecutionFlow {
+    id: string;
+    name: string;
+    entryPointId: string;
+    nodeIds: string[];
+    hasAsync: boolean;
+    hasErrorPath: boolean;
+}
+export interface LayerAssignment {
+    nodeId: string;
+    layer: LayerKind;
+    confidence: number;
+}
+export type FindingKind = 'god_class' | 'circular_dependency' | 'feature_envy' | 'shotgun_surgery' | 'layer_violation' | 'dependency_direction' | 'barrel_abuse' | 'complexity_hotspot' | 'style_deviation' | 'decision_contradiction' | 'predictive_impact';
+export type FindingSeverity = 'info' | 'warning' | 'error';
+export interface Finding {
+    kind: FindingKind;
+    severity: FindingSeverity;
+    message: string;
+    nodeIds: string[];
+    filePaths: string[];
+    metadata: Record<string, unknown>;
+}
+export interface TemporalSnapshot {
+    commitHash: string;
+    timestamp: Date;
+    nodeCounts: Record<string, number>;
+    edgeCounts: Record<string, number>;
+    communityHash: string;
+    topPagerank: Array<{
+        nodeId: string;
+        score: number;
+    }>;
+    hotspotRankings: Array<{
+        nodeId: string;
+        score: number;
+    }>;
+}
+export interface AttentionWeight {
+    nodeId: string;
+    weight: number;
+    lastAccessed: number;
+    decayRate: number;
+}
+export interface InvestigationContext {
+    recentFiles: string[];
+    inferredScope: string[];
+    communityIds: number[];
+}
+export interface ArchitectureOverview {
+    layers: Array<{
+        layer: LayerKind;
+        nodeCount: number;
+        nodeIds: string[];
+    }>;
+    boundaries: Array<{
+        fromLayer: LayerKind;
+        toLayer: LayerKind;
+        edgeCount: number;
+    }>;
+    violations: Finding[];
+    communityCount: number;
+    topHubs: Array<{
+        nodeId: string;
+        name: string;
+        pageRank: number;
+        betweenness: number;
+    }>;
+}
+//# sourceMappingURL=topology-types.d.ts.map

package/dist/src/cortex/topology-types.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/cortex/topology-types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=topology-types.js.map

package/dist/src/cortex/topology-types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"topology-types.js","sourceRoot":"","sources":["../../../src/cortex/topology-types.ts"],"names":[],"mappings":""}

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

@@ -0,0 +1,250 @@
+export type NodeKind = 'function' | 'class' | 'method' | 'interface' | 'type' | 'variable' | 'file' | 'module';
+export type EdgeKind = 'calls' | 'imports' | 'extends' | 'implements' | 'contains' | 'flows_to' | 'reads' | 'writes' | 'returns';
+export type ImportKind = 'named' | 'default' | 'namespace' | 're_export' | 'dynamic';
+export interface FileNode {
+    id: string;
+    path: string;
+    hash: string | null;
+    language: string | null;
+    depthLevel: number;
+    lastIndexed: Date | null;
+}
+export interface FunctionNode {
+    id: string;
+    name: string;
+    qualifiedName: string;
+    filePath: string;
+    lineStart: number;
+    lineEnd: number;
+    isAsync: boolean;
+    isExported: boolean;
+    isEntryPoint: boolean;
+    entryPointScore: number;
+    signature: string | null;
+    community: number | null;
+    pageRank: number | null;
+    betweenness: number | null;
+}
+export interface ClassNode {
+    id: string;
+    name: string;
+    filePath: string;
+    lineStart: number;
+    lineEnd: number;
+    isAbstract: boolean;
+    isExported: boolean;
+    community: number | null;
+    pageRank: number | null;
+    betweenness: number | null;
+}
+export interface MethodNode {
+    id: string;
+    name: string;
+    className: string;
+    qualifiedName: string;
+    filePath: string;
+    lineStart: number;
+    lineEnd: number;
+    visibility: string;
+    isStatic: boolean;
+    isAsync: boolean;
+    community: number | null;
+    pageRank: number | null;
+    betweenness: number | null;
+}
+export interface InterfaceNode {
+    id: string;
+    name: string;
+    filePath: string;
+    lineStart: number;
+    lineEnd: number;
+    isExported: boolean;
+}
+export interface TypeNode {
+    id: string;
+    name: string;
+    kind: string;
+    filePath: string;
+    lineStart: number;
+    lineEnd: number;
+    isExported: boolean;
+}
+export interface VariableNode {
+    id: string;
+    name: string;
+    scope: string;
+    filePath: string;
+    lineStart: number;
+    lineEnd: number;
+    isExported: boolean;
+    inferredType: string | null;
+}
+export interface ToolResponse<T> {
+    data: T;
+    depth: number;
+    deepening: boolean;
+    stale_since?: string;
+}
+export interface ModuleNode {
+    id: string;
+    path: string;
+    isBarrel: boolean;
+}
+export type SymbolNode = FunctionNode | ClassNode | MethodNode | InterfaceNode | TypeNode | VariableNode;
+export interface CallsEdge {
+    sourceId: string;
+    targetId: string;
+    line: number | null;
+    confidence: number;
+    isDynamic: boolean;
+    isAsync: boolean;
+    isIndirect: boolean;
+    stage: number;
+    reason: string | null;
+}
+export interface ImportsEdge {
+    sourceId: string;
+    targetId: string;
+    line: number | null;
+    kind: ImportKind;
+    originalName: string | null;
+    alias: string | null;
+    confidence: number;
+    stage: number;
+    reason: string | null;
+}
+export interface ExtendsEdge {
+    sourceId: string;
+    targetId: string;
+    line: number | null;
+    confidence: number;
+    stage: number;
+    reason: string | null;
+}
+export interface ImplementsEdge {
+    sourceId: string;
+    targetId: string;
+    line: number | null;
+    confidence: number;
+    stage: number;
+    reason: string | null;
+}
+export interface ContainsEdge {
+    sourceId: string;
+    targetId: string;
+    confidence: number;
+    stage: number;
+    reason: string | null;
+}
+export type ConstraintSource = 'annotation' | 'constructor' | 'return_type' | 'assignment' | 'parameter' | 'typeof' | 'implements' | 'extends' | 'duck_type';
+export interface TypeConstraint {
+    symbolId: string;
+    typeName: string;
+    source: ConstraintSource;
+    confidence: number;
+    filePath: string;
+    line: number;
+}
+export interface GenericInstantiation {
+    symbolId: string;
+    genericName: string;
+    typeArguments: string[];
+    filePath: string;
+    line: number;
+}
+export type FlowPointKind = 'parameter' | 'return' | 'field_read' | 'field_write' | 'assignment' | 'call_arg';
+export interface FlowPoint {
+    symbolId: string;
+    kind: FlowPointKind;
+    name: string;
+    parameterIndex: number | null;
+    filePath: string;
+    line: number;
+}
+export type TaintLabel = string;
+export interface TaintConfig {
+    sources: string[];
+    sinks: string[];
+}
+export interface FlowsToEdge {
+    sourceId: string;
+    targetId: string;
+    parameterIndex: number | null;
+    transform: 'passthrough' | 'destructure' | 'wrap' | 'map';
+    taintLabel: string | null;
+    confidence: number;
+    stage: number;
+    reason: string | null;
+}
+export interface ReadsEdge {
+    sourceId: string;
+    targetId: string;
+    line: number | null;
+    field: string | null;
+    confidence: number;
+    stage: number;
+    reason: string | null;
+}
+export interface WritesEdge {
+    sourceId: string;
+    targetId: string;
+    line: number | null;
+    field: string | null;
+    confidence: number;
+    stage: number;
+    reason: string | null;
+}
+export interface ReturnsEdge {
+    sourceId: string;
+    targetId: string;
+    line: number | null;
+    returnType: string | null;
+    confidence: number;
+    stage: number;
+    reason: string | null;
+}
+export interface FlowPath {
+    nodes: string[];
+    hasAsync: boolean;
+    hasErrorPath: boolean;
+    taintLabels: string[];
+}
+export type CortexEdge = CallsEdge | ImportsEdge | ExtendsEdge | ImplementsEdge | ContainsEdge | FlowsToEdge | ReadsEdge | WritesEdge | ReturnsEdge;
+export interface StageResult {
+    stage: number;
+    filesProcessed: number;
+    nodesCreated: number;
+    edgesCreated: number;
+    durationMs: number;
+    errors: StageError[];
+}
+export interface StageError {
+    filePath: string;
+    stage: number;
+    message: string;
+}
+export interface PipelineResult {
+    stages: StageResult[];
+    totalFiles: number;
+    totalNodes: number;
+    totalEdges: number;
+    totalDurationMs: number;
+    maxDepth: number;
+}
+export interface PipelineOptions {
+    rootDir: string;
+    force?: boolean;
+    maxStage?: number;
+    targetFiles?: string[];
+}
+export interface SymbolTableEntry {
+    localName: string;
+    originalName: string;
+    sourcePath: string;
+    resolvedSourcePath: string;
+    kind: ImportKind;
+}
+export type SymbolTable = Map<string, SymbolTableEntry>;
+export type { TopologyResults, ExecutionFlow, LayerAssignment } from './topology-types.js';
+export type { FindingKind, FindingSeverity, Finding, TemporalSnapshot, AttentionWeight, InvestigationContext, ArchitectureOverview, LayerKind, } from './topology-types.js';
+//# sourceMappingURL=types.d.ts.map

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

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package/dist/src/cortex/types.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/cortex/types.ts"],"names":[],"mappings":""}

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

@@ -0,0 +1,10 @@
+declare const EMBEDDING_DIM = 384;
+export declare function cosineSimilarity(a: number[], b: number[]): number;
+export declare class EmbeddingModel {
+    private extractor;
+    embed(text: string): Promise<number[]>;
+    embedBatch(texts: string[]): Promise<number[][]>;
+    private getExtractor;
+}
+export { EMBEDDING_DIM };
+//# sourceMappingURL=embeddings.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"embeddings.d.ts","sourceRoot":"","sources":["../../../src/dna/embeddings.ts"],"names":[],"mappings":"AAGA,QAAA,MAAM,aAAa,MAAM,CAAC;AAW1B,wBAAgB,gBAAgB,CAAC,CAAC,EAAE,MAAM,EAAE,EAAE,CAAC,EAAE,MAAM,EAAE,GAAG,MAAM,CAcjE;AAED,qBAAa,cAAc;IACvB,OAAO,CAAC,SAAS,CAA0B;IAErC,KAAK,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAMtC,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC;YAexC,YAAY;CAO7B;AAED,OAAO,EAAE,aAAa,EAAE,CAAC"}