symbiote-cli 0.1.0

package/dist/src/cortex/stage-5-flow.js.map

@@ -0,0 +1 @@
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package/dist/src/cortex/stage-6-topology.d.ts

@@ -0,0 +1,15 @@
+import { CortexRepository } from './repository.js';
+import type { StageResult } from './types.js';
+import type { ExecutionFlow, LayerAssignment } from './topology-types.js';
+import type { GraphInstance } from '#core/types.js';
+export declare function loadGraphFromDb(repo: CortexRepository): Promise<GraphInstance>;
+export declare function runCommunityDetection(graph: GraphInstance): Record<string, number>;
+export declare function runPageRank(graph: GraphInstance): Record<string, number>;
+export declare function runBetweenness(graph: GraphInstance): Record<string, number>;
+export declare function traceExecutionFlows(graph: GraphInstance, _repo: CortexRepository): ExecutionFlow[];
+export declare function detectLayers(graph: GraphInstance, communities: Record<string, number>): LayerAssignment[];
+export declare function runStage6(repo: CortexRepository, _rootDir: string, options?: {
+    force?: boolean;
+    targetFiles?: string[];
+}): Promise<StageResult>;
+//# sourceMappingURL=stage-6-topology.d.ts.map

package/dist/src/cortex/stage-6-topology.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"stage-6-topology.d.ts","sourceRoot":"","sources":["../../../src/cortex/stage-6-topology.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,KAAK,EAAE,WAAW,EAAc,MAAM,YAAY,CAAC;AAC1D,OAAO,KAAK,EAAE,aAAa,EAAE,eAAe,EAAa,MAAM,qBAAqB,CAAC;AAErF,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAC;AAiBpD,wBAAsB,eAAe,CAAC,IAAI,EAAE,gBAAgB,GAAG,OAAO,CAAC,aAAa,CAAC,CAqHpF;AAED,wBAAgB,qBAAqB,CAAC,KAAK,EAAE,aAAa,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CA2BlF;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,aAAa,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAGxE;AAED,wBAAgB,cAAc,CAAC,KAAK,EAAE,aAAa,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAG3E;AAED,wBAAgB,mBAAmB,CAC/B,KAAK,EAAE,aAAa,EACpB,KAAK,EAAE,gBAAgB,GACxB,aAAa,EAAE,CA8DjB;AAED,wBAAgB,YAAY,CACxB,KAAK,EAAE,aAAa,EACpB,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GACpC,eAAe,EAAE,CA8EnB;AAED,wBAAsB,SAAS,CAC3B,IAAI,EAAE,gBAAgB,EACtB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE;IAAE,KAAK,CAAC,EAAE,OAAO,CAAC;IAAC,WAAW,CAAC,EAAE,MAAM,EAAE,CAAA;CAAE,GACtD,OAAO,CAAC,WAAW,CAAC,CAmItB"}

package/dist/src/cortex/stage-6-topology.js

@@ -0,0 +1,382 @@
+import { createRequire } from 'node:module';
+import { Graph } from '#core/types.js';
+const req = createRequire(import.meta.url);
+const louvain = req('graphology-communities-louvain');
+const centrality = req('graphology-metrics/centrality');
+const STRUCTURAL_EDGE_TYPES = new Set(['calls', 'flows_to', 'implements']);
+const LAYER_KEYWORDS = {
+    controller: ['controller', 'handler', 'route', 'endpoint', 'middleware'],
+    service: ['service', 'usecase', 'manager', 'provider'],
+    repository: ['repository', 'repo', 'store', 'dao', 'gateway'],
+    database: ['db', 'database', 'connection', 'pool', 'migration', 'schema'],
+    utility: ['util', 'helper', 'common', 'shared', 'lib'],
+    unknown: [],
+};
+export async function loadGraphFromDb(repo) {
+    const graph = new Graph({ multi: true, type: 'directed' });
+    const functions = await repo.getAllFunctions();
+    const classes = await repo.getAllClasses();
+    const methods = await repo.getAllMethods();
+    for (const fn of functions) {
+        graph.addNode(fn.id, {
+            type: 'function',
+            name: fn.name,
+            filePath: fn.filePath,
+            isEntryPoint: fn.isEntryPoint,
+            entryPointScore: fn.entryPointScore,
+            isAsync: fn.isAsync,
+            lineStart: fn.lineStart,
+            lineEnd: fn.lineEnd,
+        });
+    }
+    for (const cls of classes) {
+        graph.addNode(cls.id, {
+            type: 'class',
+            name: cls.name,
+            filePath: cls.filePath,
+            isEntryPoint: false,
+            entryPointScore: 0,
+            isAsync: false,
+            lineStart: cls.lineStart,
+            lineEnd: cls.lineEnd,
+        });
+    }
+    for (const m of methods) {
+        graph.addNode(m.id, {
+            type: 'method',
+            name: m.name,
+            filePath: m.filePath,
+            isEntryPoint: false,
+            entryPointScore: 0,
+            isAsync: m.isAsync,
+            lineStart: m.lineStart,
+            lineEnd: m.lineEnd,
+        });
+    }
+    const allNodeIds = new Set();
+    graph.forEachNode((id) => allNodeIds.add(id));
+    for (const fn of functions) {
+        const calls = await repo.getCallsFrom(fn.id);
+        for (const call of calls) {
+            if (call.sourceId !== call.targetId &&
+                allNodeIds.has(call.sourceId) &&
+                allNodeIds.has(call.targetId)) {
+                graph.addEdge(call.sourceId, call.targetId, {
+                    type: 'calls',
+                    isAsync: call.isAsync,
+                });
+            }
+        }
+        const flowsTo = await repo.getFlowsFrom(fn.id);
+        for (const flow of flowsTo) {
+            if (flow.sourceId !== flow.targetId &&
+                allNodeIds.has(flow.sourceId) &&
+                allNodeIds.has(flow.targetId)) {
+                graph.addEdge(flow.sourceId, flow.targetId, { type: 'flows_to' });
+            }
+        }
+    }
+    for (const m of methods) {
+        const calls = await repo.getCallsFrom(m.id);
+        for (const call of calls) {
+            if (call.sourceId !== call.targetId &&
+                allNodeIds.has(call.sourceId) &&
+                allNodeIds.has(call.targetId)) {
+                graph.addEdge(call.sourceId, call.targetId, {
+                    type: 'calls',
+                    isAsync: call.isAsync,
+                });
+            }
+        }
+        const flowsTo = await repo.getFlowsFrom(m.id);
+        for (const flow of flowsTo) {
+            if (flow.sourceId !== flow.targetId &&
+                allNodeIds.has(flow.sourceId) &&
+                allNodeIds.has(flow.targetId)) {
+                graph.addEdge(flow.sourceId, flow.targetId, { type: 'flows_to' });
+            }
+        }
+    }
+    for (const cls of classes) {
+        const impls = await repo.getImplementsFrom(cls.id);
+        for (const impl of impls) {
+            if (impl.sourceId !== impl.targetId &&
+                allNodeIds.has(impl.sourceId) &&
+                allNodeIds.has(impl.targetId)) {
+                graph.addEdge(impl.sourceId, impl.targetId, { type: 'implements' });
+            }
+        }
+    }
+    return graph;
+}
+export function runCommunityDetection(graph) {
+    if (graph.order === 0)
+        return {};
+    const undirected = new Graph({ multi: false, type: 'undirected' });
+    graph.forEachNode((node, attrs) => {
+        undirected.addNode(node, attrs);
+    });
+    graph.forEachEdge((_edge, attrs, source, target) => {
+        const type = attrs.type;
+        if (STRUCTURAL_EDGE_TYPES.has(type)) {
+            if (source !== target && !undirected.hasEdge(source, target)) {
+                undirected.addEdge(source, target);
+            }
+        }
+    });
+    if (undirected.size === 0) {
+        const result = {};
+        undirected.forEachNode((id) => {
+            result[id] = 0;
+        });
+        return result;
+    }
+    return louvain(undirected);
+}
+export function runPageRank(graph) {
+    if (graph.order === 0)
+        return {};
+    return centrality.pagerank(graph);
+}
+export function runBetweenness(graph) {
+    if (graph.order === 0)
+        return {};
+    return centrality.betweenness(graph);
+}
+export function traceExecutionFlows(graph, _repo) {
+    const entryPoints = [];
+    graph.forEachNode((id, attrs) => {
+        const isEntryPoint = attrs.isEntryPoint;
+        const score = attrs.entryPointScore ?? 0;
+        if (isEntryPoint || score > 0.5) {
+            entryPoints.push({ id, score });
+        }
+    });
+    entryPoints.sort((a, b) => b.score - a.score);
+    const flows = [];
+    const MAX_DEPTH = 50;
+    for (const entry of entryPoints) {
+        const visited = new Set();
+        const nodeIds = [];
+        let hasAsync = false;
+        let hasErrorPath = false;
+        const queue = [{ id: entry.id, depth: 0 }];
+        visited.add(entry.id);
+        while (queue.length > 0) {
+            const current = queue.shift();
+            nodeIds.push(current.id);
+            if (current.depth >= MAX_DEPTH)
+                continue;
+            const attrs = graph.getNodeAttributes(current.id);
+            if (attrs.isAsync)
+                hasAsync = true;
+            graph.forEachOutEdge(current.id, (_edge, edgeAttrs, _src, tgt) => {
+                const type = edgeAttrs.type;
+                if (type === 'calls' || type === 'flows_to') {
+                    if (edgeAttrs.isAsync)
+                        hasAsync = true;
+                    if (!visited.has(tgt)) {
+                        visited.add(tgt);
+                        queue.push({ id: tgt, depth: current.depth + 1 });
+                    }
+                }
+            });
+        }
+        if (nodeIds.length > 0) {
+            const name = entry.id.split(':').pop() ?? entry.id;
+            flows.push({
+                id: `flow:${name}`,
+                name,
+                entryPointId: entry.id,
+                nodeIds,
+                hasAsync,
+                hasErrorPath,
+            });
+        }
+    }
+    return flows;
+}
+export function detectLayers(graph, communities) {
+    const assignments = [];
+    graph.forEachNode((id, attrs) => {
+        const name = (attrs.name ?? '').toLowerCase();
+        const filePath = (attrs.filePath ?? '').toLowerCase();
+        let bestLayer = 'unknown';
+        let bestScore = 0;
+        for (const [layer, keywords] of Object.entries(LAYER_KEYWORDS)) {
+            if (layer === 'unknown')
+                continue;
+            for (const keyword of keywords) {
+                if (name.includes(keyword) || filePath.includes(keyword)) {
+                    const score = keyword.length / Math.max(name.length, 1);
+                    if (score > bestScore) {
+                        bestScore = score;
+                        bestLayer = layer;
+                    }
+                }
+            }
+        }
+        if (bestLayer === 'unknown') {
+            const outEdges = graph.outEdges(id);
+            const inEdges = graph.inEdges(id);
+            const outDegree = outEdges.length;
+            const inDegree = inEdges.length;
+            if (outDegree > 0 && inDegree === 0) {
+                bestLayer = 'controller';
+                bestScore = 0.3;
+            }
+            else if (inDegree > 0 && outDegree === 0) {
+                bestLayer = 'database';
+                bestScore = 0.3;
+            }
+            else if (outDegree > 0 && inDegree > 0) {
+                bestLayer = 'service';
+                bestScore = 0.2;
+            }
+        }
+        const confidence = Math.min(1.0, bestScore + 0.3);
+        assignments.push({ nodeId: id, layer: bestLayer, confidence });
+    });
+    const communityLayers = new Map();
+    for (const assignment of assignments) {
+        const community = communities[assignment.nodeId];
+        if (community === undefined)
+            continue;
+        if (!communityLayers.has(community)) {
+            communityLayers.set(community, new Map());
+        }
+        const counts = communityLayers.get(community);
+        counts.set(assignment.layer, (counts.get(assignment.layer) ?? 0) + 1);
+    }
+    for (const assignment of assignments) {
+        if (assignment.layer !== 'unknown')
+            continue;
+        const community = communities[assignment.nodeId];
+        if (community === undefined)
+            continue;
+        const counts = communityLayers.get(community);
+        if (!counts)
+            continue;
+        let dominantLayer = 'unknown';
+        let maxCount = 0;
+        for (const [layer, count] of counts) {
+            if (layer !== 'unknown' && count > maxCount) {
+                maxCount = count;
+                dominantLayer = layer;
+            }
+        }
+        if (dominantLayer !== 'unknown') {
+            assignment.layer = dominantLayer;
+            assignment.confidence = Math.min(1.0, assignment.confidence + 0.1);
+        }
+    }
+    return assignments;
+}
+export async function runStage6(repo, _rootDir, options) {
+    const start = Date.now();
+    const errors = [];
+    const maxDepth = await repo.getMaxDepthLevel();
+    if (maxDepth < 5 && !options?.force) {
+        return {
+            stage: 6,
+            filesProcessed: 0,
+            nodesCreated: 0,
+            edgesCreated: 0,
+            durationMs: Date.now() - start,
+            errors: [],
+        };
+    }
+    const graph = await loadGraphFromDb(repo);
+    if (graph.order === 0) {
+        return {
+            stage: 6,
+            filesProcessed: 0,
+            nodesCreated: 0,
+            edgesCreated: 0,
+            durationMs: Date.now() - start,
+            errors: [],
+        };
+    }
+    const communities = runCommunityDetection(graph);
+    const pageRank = runPageRank(graph);
+    const betweenness = runBetweenness(graph);
+    const flows = traceExecutionFlows(graph, repo);
+    const layers = detectLayers(graph, communities);
+    const updates = [];
+    graph.forEachNode((id) => {
+        updates.push({
+            nodeId: id,
+            community: communities[id] ?? 0,
+            pageRank: pageRank[id] ?? 0,
+            betweenness: betweenness[id] ?? 0,
+        });
+    });
+    await repo.updateNodeMetricsBatch(updates);
+    await repo.deleteAllFlows();
+    if (flows.length > 0) {
+        await repo.insertFlows(flows);
+    }
+    const layerSummary = new Map();
+    for (const l of layers) {
+        if (!layerSummary.has(l.layer)) {
+            layerSummary.set(l.layer, { nodeCount: 0, nodeIds: [] });
+        }
+        const entry = layerSummary.get(l.layer);
+        entry.nodeCount++;
+        entry.nodeIds.push(l.nodeId);
+    }
+    const layerArray = [...layerSummary.entries()].map(([layer, data]) => ({
+        layer,
+        ...data,
+    }));
+    const boundaries = [];
+    const layerMap = new Map();
+    for (const l of layers) {
+        layerMap.set(l.nodeId, l.layer);
+    }
+    const boundaryCounter = new Map();
+    graph.forEachEdge((_edge, _attrs, source, target) => {
+        const srcLayer = layerMap.get(source);
+        const tgtLayer = layerMap.get(target);
+        if (srcLayer && tgtLayer && srcLayer !== tgtLayer) {
+            const key = `${srcLayer}:${tgtLayer}`;
+            boundaryCounter.set(key, (boundaryCounter.get(key) ?? 0) + 1);
+        }
+    });
+    for (const [key, count] of boundaryCounter) {
+        const [fromLayer, toLayer] = key.split(':');
+        boundaries.push({ fromLayer, toLayer, edgeCount: count });
+    }
+    const uniqueCommunities = new Set(Object.values(communities));
+    const communityCount = uniqueCommunities.size;
+    const pagerankEntries = Object.entries(pageRank)
+        .sort(([, a], [, b]) => b - a)
+        .slice(0, 10);
+    const topHubs = pagerankEntries.map(([nodeId, pr]) => {
+        const attrs = graph.getNodeAttributes(nodeId);
+        return {
+            nodeId,
+            name: attrs.name ?? nodeId,
+            pageRank: pr,
+            betweenness: betweenness[nodeId] ?? 0,
+        };
+    });
+    await repo.setMeta('layers', JSON.stringify(layerArray));
+    await repo.setMeta('layer_boundaries', JSON.stringify(boundaries));
+    await repo.setMeta('community_count', String(communityCount));
+    await repo.setMeta('top_hubs', JSON.stringify(topHubs));
+    const allFiles = await repo.getAllFileNodes();
+    const filesToUpdate = allFiles.filter((f) => f.depthLevel >= 5 || options?.force);
+    for (const file of filesToUpdate) {
+        await repo.upsertFileNode({ ...file, depthLevel: 6 });
+    }
+    return {
+        stage: 6,
+        filesProcessed: filesToUpdate.length,
+        nodesCreated: 0,
+        edgesCreated: 0,
+        durationMs: Date.now() - start,
+        errors,
+    };
+}
+//# sourceMappingURL=stage-6-topology.js.map

package/dist/src/cortex/stage-6-topology.js.map

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package/dist/src/cortex/stage-7-intelligence.d.ts

@@ -0,0 +1,34 @@
+import { CortexRepository } from './repository.js';
+import type { Finding } from './topology-types.js';
+import type { StageResult } from './types.js';
+import type { DnaEntry } from '#dna/types.js';
+interface NodePattern {
+    nodeId: string;
+    filePath: string;
+    usesPromiseChains: boolean;
+    usesAsyncAwait: boolean;
+}
+interface ObservedPattern {
+    nodeId: string;
+    filePath: string;
+    pattern: string;
+    description: string;
+}
+interface ChangeRecord {
+    file: string;
+    changedWith: string[];
+}
+interface PredictImpactOptions {
+    minCoOccurrence: number;
+}
+export declare function collectFindings(repo: CortexRepository): Promise<Finding[]>;
+export declare function saveTemporalSnapshot(repo: CortexRepository, commitHash: string): Promise<void>;
+export declare function runStage7(repo: CortexRepository, rootDir: string, options?: {
+    force?: boolean;
+    targetFiles?: string[];
+}): Promise<StageResult>;
+export declare function detectStyleDeviations(dnaEntries: DnaEntry[], nodePatterns: NodePattern[]): Finding[];
+export declare function detectDecisionContradictions(dnaEntries: DnaEntry[], observedPatterns: ObservedPattern[]): Finding[];
+export declare function predictImpact(changeHistory: ChangeRecord[], currentFile: string, options: PredictImpactOptions): Finding[];
+export {};
+//# sourceMappingURL=stage-7-intelligence.d.ts.map

package/dist/src/cortex/stage-7-intelligence.d.ts.map

@@ -0,0 +1 @@
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