symbiote-cli 0.1.0

package/dist/src/mcp/tools/trace-tools.js

@@ -0,0 +1,268 @@
+import { z } from 'zod';
+async function resolveSymbol(repo, nameOrId) {
+    const byId = await repo.getSymbolById(nameOrId);
+    if (byId)
+        return byId;
+    const byName = await repo.getSymbolByName(nameOrId);
+    if (byName.length > 0)
+        return byName[0];
+    return null;
+}
+async function traceExecutionFlow(repo, entryPoint, maxDepth, includeAsync, includeErrors) {
+    const resolved = await resolveSymbol(repo, entryPoint);
+    if (!resolved)
+        return [];
+    const precomputed = await repo.getFlowsByEntryPoint(resolved.id);
+    if (precomputed.length > 0) {
+        const flow = precomputed[0];
+        const steps = [];
+        for (let i = 0; i < flow.nodeIds.length; i++) {
+            const nodeId = flow.nodeIds[i];
+            if (nodeId === resolved.id)
+                continue;
+            const sym = await repo.getSymbolById(nodeId);
+            steps.push({
+                symbolId: nodeId,
+                symbol: sym,
+                depth: i,
+                edgeType: 'precomputed_flow',
+                isAsync: flow.hasAsync,
+                confidence: 1.0,
+            });
+        }
+        return steps;
+    }
+    const steps = [];
+    const visited = new Set();
+    const queue = [{ id: resolved.id, depth: 0 }];
+    while (queue.length > 0) {
+        const { id, depth } = queue.shift();
+        if (visited.has(id) || depth > maxDepth)
+            continue;
+        visited.add(id);
+        const calls = await repo.getCallsFrom(id);
+        for (const call of calls) {
+            if (!includeAsync && call.isAsync)
+                continue;
+            const sym = await repo.getSymbolById(call.targetId);
+            steps.push({
+                symbolId: call.targetId,
+                symbol: sym,
+                depth: depth + 1,
+                edgeType: 'calls',
+                isAsync: call.isAsync,
+                confidence: call.confidence,
+            });
+            if (!visited.has(call.targetId) && depth + 1 < maxDepth) {
+                queue.push({ id: call.targetId, depth: depth + 1 });
+            }
+        }
+        const flows = await repo.getFlowsFrom(id);
+        for (const flow of flows) {
+            const sym = await repo.getSymbolById(flow.targetId);
+            steps.push({
+                symbolId: flow.targetId,
+                symbol: sym,
+                depth: depth + 1,
+                edgeType: 'flows_to',
+                isAsync: false,
+                confidence: flow.confidence,
+            });
+            if (!visited.has(flow.targetId) && depth + 1 < maxDepth) {
+                queue.push({ id: flow.targetId, depth: depth + 1 });
+            }
+        }
+        const reads = await repo.getReadsFrom(id);
+        for (const r of reads) {
+            const sym = await repo.getSymbolById(r.targetId);
+            steps.push({
+                symbolId: r.targetId,
+                symbol: sym,
+                depth: depth + 1,
+                edgeType: 'reads',
+                isAsync: false,
+                confidence: r.confidence,
+            });
+        }
+        const writes = await repo.getWritesFrom(id);
+        for (const w of writes) {
+            const sym = await repo.getSymbolById(w.targetId);
+            steps.push({
+                symbolId: w.targetId,
+                symbol: sym,
+                depth: depth + 1,
+                edgeType: 'writes',
+                isAsync: false,
+                confidence: w.confidence,
+            });
+        }
+        if (includeErrors) {
+            const returns = await repo.getReturnsFrom(id);
+            for (const ret of returns) {
+                const sym = await repo.getSymbolById(ret.targetId);
+                steps.push({
+                    symbolId: ret.targetId,
+                    symbol: sym,
+                    depth: depth + 1,
+                    edgeType: 'returns',
+                    isAsync: false,
+                    confidence: ret.confidence,
+                });
+            }
+        }
+    }
+    return steps;
+}
+async function traceDataFlow(repo, symbol, direction, maxDepth) {
+    const resolved = await resolveSymbol(repo, symbol);
+    if (!resolved)
+        return [];
+    const steps = [];
+    const visited = new Set();
+    const queue = [{ id: resolved.id, depth: 0 }];
+    while (queue.length > 0) {
+        const { id, depth } = queue.shift();
+        if (visited.has(id) || depth > maxDepth)
+            continue;
+        visited.add(id);
+        const edges = direction === 'forward' ? await repo.getFlowsFrom(id) : await repo.getFlowsTo(id);
+        for (const edge of edges) {
+            const nextId = direction === 'forward' ? edge.targetId : edge.sourceId;
+            const sym = await repo.getSymbolById(nextId);
+            steps.push({
+                symbolId: nextId,
+                symbol: sym,
+                depth: depth + 1,
+                direction,
+                transform: edge.transform,
+                confidence: edge.confidence,
+            });
+            if (!visited.has(nextId) && depth + 1 < maxDepth) {
+                queue.push({ id: nextId, depth: depth + 1 });
+            }
+        }
+        if (direction === 'forward') {
+            const reads = await repo.getReadsFrom(id);
+            for (const r of reads) {
+                const sym = await repo.getSymbolById(r.targetId);
+                steps.push({
+                    symbolId: r.targetId,
+                    symbol: sym,
+                    depth: depth + 1,
+                    direction,
+                    transform: null,
+                    confidence: r.confidence,
+                });
+            }
+        }
+        else {
+            const writes = await repo.getWritesTo(id);
+            for (const w of writes) {
+                const sym = await repo.getSymbolById(w.sourceId);
+                steps.push({
+                    symbolId: w.sourceId,
+                    symbol: sym,
+                    depth: depth + 1,
+                    direction,
+                    transform: null,
+                    confidence: w.confidence,
+                });
+            }
+        }
+    }
+    return steps;
+}
+async function findImplementors(repo, interfaceName, includeIndirect) {
+    const resolved = await resolveSymbol(repo, interfaceName);
+    if (!resolved)
+        return [];
+    const directImpls = await repo.getImplementorsOf(resolved.id);
+    const results = [];
+    for (const impl of directImpls) {
+        const sym = await repo.getSymbolById(impl.sourceId);
+        results.push({
+            symbolId: impl.sourceId,
+            symbol: sym,
+            confidence: impl.confidence,
+            isIndirect: false,
+        });
+    }
+    if (includeIndirect) {
+        const visited = new Set(results.map((r) => r.symbolId));
+        const queue = [...results.map((r) => r.symbolId)];
+        while (queue.length > 0) {
+            const id = queue.shift();
+            const subImpls = await repo.getImplementorsOf(id);
+            for (const sub of subImpls) {
+                if (!visited.has(sub.sourceId)) {
+                    visited.add(sub.sourceId);
+                    const sym = await repo.getSymbolById(sub.sourceId);
+                    results.push({
+                        symbolId: sub.sourceId,
+                        symbol: sym,
+                        confidence: sub.confidence * 0.8,
+                        isIndirect: true,
+                    });
+                    queue.push(sub.sourceId);
+                }
+            }
+        }
+    }
+    return results;
+}
+function textResult(data) {
+    return { type: 'text', text: JSON.stringify(data, null, 2) };
+}
+export function registerTraceTools(server, repo) {
+    server.tool('trace_flow', 'Trace execution flow from an entry point through calls and data flows.', {
+        entryPoint: z.string().describe('Symbol ID or name to start tracing from'),
+        maxDepth: z
+            .number()
+            .optional()
+            .default(5)
+            .describe('Maximum traversal depth (default: 5)'),
+        includeAsync: z
+            .boolean()
+            .optional()
+            .default(true)
+            .describe('Include async call edges (default: true)'),
+        includeErrors: z
+            .boolean()
+            .optional()
+            .default(false)
+            .describe('Include error/return paths (default: false)'),
+    }, async (input) => ({
+        content: [
+            textResult(await traceExecutionFlow(repo, input.entryPoint, input.maxDepth, input.includeAsync, input.includeErrors)),
+        ],
+    }));
+    server.tool('trace_data', 'Trace data flow forward or backward from a symbol.', {
+        symbol: z.string().describe('Symbol ID or name to trace data flow from'),
+        direction: z
+            .enum(['forward', 'backward'])
+            .default('forward')
+            .describe('Trace direction: forward or backward'),
+        maxDepth: z
+            .number()
+            .optional()
+            .default(5)
+            .describe('Maximum traversal depth (default: 5)'),
+    }, async (input) => ({
+        content: [
+            textResult(await traceDataFlow(repo, input.symbol, input.direction, input.maxDepth)),
+        ],
+    }));
+    server.tool('find_implementations', 'Find all classes that implement an interface or extend a base class.', {
+        interfaceName: z.string().describe('Interface or base class name/ID'),
+        includeIndirect: z
+            .boolean()
+            .optional()
+            .default(false)
+            .describe('Include indirect implementations (default: false)'),
+    }, async (input) => ({
+        content: [
+            textResult(await findImplementors(repo, input.interfaceName, input.includeIndirect)),
+        ],
+    }));
+}
+//# sourceMappingURL=trace-tools.js.map

package/dist/src/mcp/tools/trace-tools.js.map

@@ -0,0 +1 @@
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package/dist/src/storage/db.d.ts

@@ -0,0 +1,13 @@
+export declare class SymbioteDB {
+    private instance;
+    private conn;
+    private constructor();
+    static create(path: string): Promise<SymbioteDB>;
+    exec(sql: string): Promise<void>;
+    run(sql: string, ...params: unknown[]): Promise<void>;
+    all<T extends Record<string, unknown> = Record<string, unknown>>(sql: string, ...params: unknown[]): Promise<T[]>;
+    close(): Promise<void>;
+    private bindParam;
+}
+export declare function createDatabase(path: string): Promise<SymbioteDB>;
+//# sourceMappingURL=db.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"db.d.ts","sourceRoot":"","sources":["../../../src/storage/db.ts"],"names":[],"mappings":"AAKA,qBAAa,UAAU;IAEf,OAAO,CAAC,QAAQ;IAChB,OAAO,CAAC,IAAI;IAFhB,OAAO;WAKM,MAAM,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,UAAU,CAAC;IAMhD,IAAI,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC;IAIhC,GAAG,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,MAAM,EAAE,OAAO,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC;IAgBrD,GAAG,CAAC,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACjE,GAAG,EAAE,MAAM,EACX,GAAG,MAAM,EAAE,OAAO,EAAE,GACrB,OAAO,CAAC,CAAC,EAAE,CAAC;IAiBT,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC;IAK5B,OAAO,CAAC,SAAS;CAuBpB;AAED,wBAAsB,cAAc,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,UAAU,CAAC,CA2HtE"}

package/dist/src/storage/db.js

@@ -0,0 +1,230 @@
+import { DuckDBInstance } from '@duckdb/node-api';
+import { createCortexSchema } from '#cortex/schema.js';
+const SCHEMA_VERSION = 2;
+export class SymbioteDB {
+    instance;
+    conn;
+    constructor(instance, conn) {
+        this.instance = instance;
+        this.conn = conn;
+    }
+    static async create(path) {
+        const instance = await DuckDBInstance.create(path);
+        const conn = await instance.connect();
+        return new SymbioteDB(instance, conn);
+    }
+    async exec(sql) {
+        await this.conn.run(sql);
+    }
+    async run(sql, ...params) {
+        if (params.length === 0) {
+            await this.conn.run(sql);
+            return;
+        }
+        const prepared = await this.conn.prepare(sql);
+        try {
+            for (let i = 0; i < params.length; i++) {
+                this.bindParam(prepared, i + 1, params[i]);
+            }
+            await prepared.run();
+        }
+        finally {
+            prepared.destroySync();
+        }
+    }
+    async all(sql, ...params) {
+        if (params.length === 0) {
+            const reader = await this.conn.runAndReadAll(sql);
+            return reader.getRowObjects();
+        }
+        const prepared = await this.conn.prepare(sql);
+        try {
+            for (let i = 0; i < params.length; i++) {
+                this.bindParam(prepared, i + 1, params[i]);
+            }
+            const result = await prepared.run();
+            return (await result.getRowObjects());
+        }
+        finally {
+            prepared.destroySync();
+        }
+    }
+    async close() {
+        this.conn.closeSync();
+        this.instance.closeSync();
+    }
+    bindParam(prepared, index, value) {
+        if (value === null || value === undefined) {
+            prepared.bindNull(index);
+        }
+        else if (typeof value === 'string') {
+            prepared.bindVarchar(index, value);
+        }
+        else if (typeof value === 'number') {
+            if (Number.isInteger(value)) {
+                prepared.bindInteger(index, value);
+            }
+            else {
+                prepared.bindDouble(index, value);
+            }
+        }
+        else if (typeof value === 'bigint') {
+            prepared.bindBigInt(index, value);
+        }
+        else if (typeof value === 'boolean') {
+            prepared.bindBoolean(index, value);
+        }
+        else {
+            prepared.bindVarchar(index, String(value));
+        }
+    }
+}
+export async function createDatabase(path) {
+    const db = await SymbioteDB.create(path);
+    await db.exec(`
+        CREATE SEQUENCE IF NOT EXISTS health_snapshot_seq START 1;
+
+        CREATE TABLE IF NOT EXISTS nodes (
+            id VARCHAR PRIMARY KEY,
+            type VARCHAR NOT NULL,
+            name VARCHAR NOT NULL,
+            file_path VARCHAR NOT NULL,
+            line_start INTEGER NOT NULL,
+            line_end INTEGER NOT NULL,
+            metadata VARCHAR DEFAULT '{}'
+        );
+
+        CREATE TABLE IF NOT EXISTS edges (
+            source_id VARCHAR NOT NULL,
+            target_id VARCHAR NOT NULL,
+            type VARCHAR NOT NULL,
+            PRIMARY KEY (source_id, target_id, type)
+        );
+
+        CREATE TABLE IF NOT EXISTS files (
+            path VARCHAR PRIMARY KEY,
+            hash VARCHAR NOT NULL,
+            last_scanned VARCHAR NOT NULL
+        );
+
+        CREATE TABLE IF NOT EXISTS meta (
+            key VARCHAR PRIMARY KEY,
+            value VARCHAR NOT NULL
+        );
+
+        CREATE TABLE IF NOT EXISTS embeddings (
+            node_id VARCHAR PRIMARY KEY,
+            vector FLOAT[384]
+        );
+
+        CREATE TABLE IF NOT EXISTS health_snapshots (
+            id INTEGER PRIMARY KEY DEFAULT nextval('health_snapshot_seq'),
+            score INTEGER NOT NULL,
+            constraint_score INTEGER NOT NULL,
+            circular_dep_score INTEGER NOT NULL,
+            dead_code_score INTEGER NOT NULL,
+            coupling_score INTEGER NOT NULL,
+            constraint_violation_count INTEGER NOT NULL,
+            circular_dep_count INTEGER NOT NULL,
+            dead_code_count INTEGER NOT NULL,
+            coupling_hotspot_count INTEGER NOT NULL,
+            created_at VARCHAR NOT NULL DEFAULT current_timestamp
+        );
+
+        CREATE INDEX IF NOT EXISTS idx_nodes_file ON nodes(file_path);
+        CREATE INDEX IF NOT EXISTS idx_nodes_type ON nodes(type);
+        CREATE INDEX IF NOT EXISTS idx_nodes_name ON nodes(name);
+        CREATE INDEX IF NOT EXISTS idx_edges_source ON edges(source_id);
+        CREATE INDEX IF NOT EXISTS idx_edges_target ON edges(target_id);
+        CREATE INDEX IF NOT EXISTS idx_edges_type ON edges(type);
+    `);
+    await db.exec(`
+        CREATE SEQUENCE IF NOT EXISTS session_obs_seq START 1;
+
+        CREATE TABLE IF NOT EXISTS sessions (
+            session_id TEXT PRIMARY KEY,
+            started_at BIGINT NOT NULL,
+            ended_at BIGINT,
+            reason TEXT,
+            files_touched TEXT,
+            symbols_modified TEXT,
+            tool_counts TEXT,
+            failure_count INTEGER DEFAULT 0,
+            interaction_count INTEGER DEFAULT 0
+        );
+
+        CREATE TABLE IF NOT EXISTS session_observations (
+            id INTEGER DEFAULT nextval('session_obs_seq'),
+            session_id TEXT NOT NULL,
+            timestamp BIGINT NOT NULL,
+            tool_name TEXT NOT NULL,
+            event TEXT NOT NULL,
+            file_path TEXT,
+            symbols_affected TEXT,
+            metadata TEXT
+        );
+
+        CREATE INDEX IF NOT EXISTS idx_obs_session ON session_observations(session_id);
+        CREATE INDEX IF NOT EXISTS idx_obs_tool ON session_observations(tool_name);
+        CREATE INDEX IF NOT EXISTS idx_obs_file ON session_observations(file_path);
+
+        CREATE TABLE IF NOT EXISTS session_snapshots (
+            session_id TEXT PRIMARY KEY,
+            snapshot TEXT NOT NULL
+        );
+    `);
+    await createCortexSchema(db);
+    await db.exec('INSTALL fts; LOAD fts;');
+    const existing = await db.all("SELECT value FROM meta WHERE key = 'schema_version'");
+    if (existing.length === 0) {
+        await db.run('INSERT INTO meta (key, value) VALUES ($1, $2)', 'schema_version', String(SCHEMA_VERSION));
+    }
+    else {
+        const storedVersion = parseInt(existing[0].value, 10);
+        if (storedVersion < SCHEMA_VERSION) {
+            await migrateSchema(db, storedVersion, SCHEMA_VERSION);
+            await db.run("UPDATE meta SET value = $1 WHERE key = 'schema_version'", String(SCHEMA_VERSION));
+        }
+    }
+    return db;
+}
+async function migrateSchema(db, from, _to) {
+    if (from < 2) {
+        await db.exec(`
+            CREATE SEQUENCE IF NOT EXISTS session_obs_seq START 1;
+
+            CREATE TABLE IF NOT EXISTS sessions (
+                session_id TEXT PRIMARY KEY,
+                started_at BIGINT NOT NULL,
+                ended_at BIGINT,
+                reason TEXT,
+                files_touched TEXT,
+                symbols_modified TEXT,
+                tool_counts TEXT,
+                failure_count INTEGER DEFAULT 0,
+                interaction_count INTEGER DEFAULT 0
+            );
+
+            CREATE TABLE IF NOT EXISTS session_observations (
+                id INTEGER DEFAULT nextval('session_obs_seq'),
+                session_id TEXT NOT NULL,
+                timestamp BIGINT NOT NULL,
+                tool_name TEXT NOT NULL,
+                event TEXT NOT NULL,
+                file_path TEXT,
+                symbols_affected TEXT,
+                metadata TEXT
+            );
+
+            CREATE INDEX IF NOT EXISTS idx_obs_session ON session_observations(session_id);
+            CREATE INDEX IF NOT EXISTS idx_obs_tool ON session_observations(tool_name);
+            CREATE INDEX IF NOT EXISTS idx_obs_file ON session_observations(file_path);
+
+            CREATE TABLE IF NOT EXISTS session_snapshots (
+                session_id TEXT PRIMARY KEY,
+                snapshot TEXT NOT NULL
+            );
+        `);
+    }
+}
+//# sourceMappingURL=db.js.map

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

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

@@ -0,0 +1,54 @@
+import type { SymbioteDB } from './db.js';
+export interface NodeRecord {
+    id: string;
+    type: string;
+    name: string;
+    filePath: string;
+    lineStart: number;
+    lineEnd: number;
+    metadata?: Record<string, unknown>;
+}
+export interface EdgeRecord {
+    sourceId: string;
+    targetId: string;
+    type: string;
+}
+export interface FileRecord {
+    path: string;
+    hash: string;
+    lastScanned: string;
+}
+export declare class Repository {
+    private db;
+    constructor(db: SymbioteDB);
+    upsertFile(path: string, hash: string): Promise<void>;
+    getFile(filePath: string): Promise<FileRecord | undefined>;
+    isFileChanged(path: string, currentHash: string): Promise<boolean>;
+    insertNodes(nodes: NodeRecord[]): Promise<void>;
+    clearNodesForFile(filePath: string): Promise<void>;
+    updateFileNodes(filePath: string, hash: string, nodes: NodeRecord[], edges: EdgeRecord[]): Promise<void>;
+    getNodesByFile(filePath: string): Promise<NodeRecord[]>;
+    getNodeById(id: string): Promise<NodeRecord | undefined>;
+    getNodesByIds(ids: string[]): Promise<Map<string, NodeRecord>>;
+    searchNodesByName(query: string): Promise<NodeRecord[]>;
+    insertEdges(edges: EdgeRecord[]): Promise<void>;
+    getDependencies(nodeId: string): Promise<EdgeRecord[]>;
+    getDependents(nodeId: string): Promise<EdgeRecord[]>;
+    getDependenciesBatch(nodeIds: string[]): Promise<EdgeRecord[]>;
+    getDependentsBatch(nodeIds: string[]): Promise<EdgeRecord[]>;
+    getStats(): Promise<{
+        nodes: number;
+        edges: number;
+        files: number;
+    }>;
+    getNodeCountByType(): Promise<Record<string, number>>;
+    getHubs(limit?: number): Promise<Array<{
+        node: NodeRecord;
+        edgeCount: number;
+    }>>;
+    getAllNodes(): Promise<NodeRecord[]>;
+    getAllEdges(): Promise<EdgeRecord[]>;
+    private mapNodeRow;
+    private mapEdgeRow;
+}
+//# sourceMappingURL=repository.d.ts.map

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

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