symbiote-cli 0.1.0

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

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

@@ -0,0 +1,9 @@
+import { SymbioteDB } from '#storage/db.js';
+export declare const CORTEX_TABLES: {
+    readonly nodes: readonly ["nodes_file", "nodes_function", "nodes_class", "nodes_method", "nodes_interface", "nodes_type", "nodes_variable", "nodes_module"];
+    readonly edges: readonly ["edges_calls", "edges_imports", "edges_extends", "edges_implements", "edges_contains", "edges_flows_to", "edges_reads", "edges_writes", "edges_returns"];
+    readonly auxiliary: readonly ["cortex_embeddings", "cortex_health_snapshots", "cortex_temporal_snapshots", "cortex_flows", "cortex_meta", "type_constraints", "generic_instantiations"];
+};
+export declare function createCortexSchema(db: SymbioteDB): Promise<void>;
+export declare function refreshSymbolsTable(db: SymbioteDB): Promise<void>;
+//# sourceMappingURL=schema.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"schema.d.ts","sourceRoot":"","sources":["../../../src/cortex/schema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,gBAAgB,CAAC;AAE5C,eAAO,MAAM,aAAa;;;;CA+BhB,CAAC;AAmSX,wBAAsB,kBAAkB,CAAC,EAAE,EAAE,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,CAiBtE;AAED,wBAAsB,mBAAmB,CAAC,EAAE,EAAE,UAAU,GAAG,OAAO,CAAC,IAAI,CAAC,CAyBvE"}

package/dist/src/cortex/schema.js

@@ -0,0 +1,364 @@
+export const CORTEX_TABLES = {
+    nodes: [
+        'nodes_file',
+        'nodes_function',
+        'nodes_class',
+        'nodes_method',
+        'nodes_interface',
+        'nodes_type',
+        'nodes_variable',
+        'nodes_module',
+    ],
+    edges: [
+        'edges_calls',
+        'edges_imports',
+        'edges_extends',
+        'edges_implements',
+        'edges_contains',
+        'edges_flows_to',
+        'edges_reads',
+        'edges_writes',
+        'edges_returns',
+    ],
+    auxiliary: [
+        'cortex_embeddings',
+        'cortex_health_snapshots',
+        'cortex_temporal_snapshots',
+        'cortex_flows',
+        'cortex_meta',
+        'type_constraints',
+        'generic_instantiations',
+    ],
+};
+const NODE_TABLES_DDL = `
+CREATE TABLE IF NOT EXISTS nodes_file (
+    id VARCHAR PRIMARY KEY,
+    path VARCHAR NOT NULL,
+    hash VARCHAR,
+    language VARCHAR,
+    depth_level TINYINT DEFAULT 0,
+    last_indexed TIMESTAMP
+);
+
+CREATE TABLE IF NOT EXISTS nodes_function (
+    id VARCHAR PRIMARY KEY,
+    name VARCHAR NOT NULL,
+    qualified_name VARCHAR NOT NULL,
+    file_path VARCHAR NOT NULL,
+    line_start INTEGER,
+    line_end INTEGER,
+    is_async BOOLEAN DEFAULT false,
+    is_exported BOOLEAN DEFAULT false,
+    is_entry_point BOOLEAN DEFAULT false,
+    entry_point_score FLOAT DEFAULT 0,
+    signature VARCHAR,
+    community INTEGER,
+    page_rank FLOAT,
+    betweenness FLOAT
+);
+
+CREATE TABLE IF NOT EXISTS nodes_class (
+    id VARCHAR PRIMARY KEY,
+    name VARCHAR NOT NULL,
+    file_path VARCHAR NOT NULL,
+    line_start INTEGER,
+    line_end INTEGER,
+    is_abstract BOOLEAN DEFAULT false,
+    is_exported BOOLEAN DEFAULT false,
+    community INTEGER,
+    page_rank FLOAT,
+    betweenness FLOAT
+);
+
+CREATE TABLE IF NOT EXISTS nodes_method (
+    id VARCHAR PRIMARY KEY,
+    name VARCHAR NOT NULL,
+    class_name VARCHAR NOT NULL,
+    qualified_name VARCHAR NOT NULL,
+    file_path VARCHAR NOT NULL,
+    line_start INTEGER,
+    line_end INTEGER,
+    visibility VARCHAR DEFAULT 'public',
+    is_static BOOLEAN DEFAULT false,
+    is_async BOOLEAN DEFAULT false,
+    community INTEGER,
+    page_rank FLOAT,
+    betweenness FLOAT
+);
+
+CREATE TABLE IF NOT EXISTS nodes_interface (
+    id VARCHAR PRIMARY KEY,
+    name VARCHAR NOT NULL,
+    file_path VARCHAR NOT NULL,
+    line_start INTEGER,
+    line_end INTEGER,
+    is_exported BOOLEAN DEFAULT false
+);
+
+CREATE TABLE IF NOT EXISTS nodes_type (
+    id VARCHAR PRIMARY KEY,
+    name VARCHAR NOT NULL,
+    kind VARCHAR NOT NULL,
+    file_path VARCHAR NOT NULL,
+    line_start INTEGER,
+    line_end INTEGER,
+    is_exported BOOLEAN DEFAULT false
+);
+
+CREATE TABLE IF NOT EXISTS nodes_variable (
+    id VARCHAR PRIMARY KEY,
+    name VARCHAR NOT NULL,
+    scope VARCHAR NOT NULL,
+    file_path VARCHAR NOT NULL,
+    line_start INTEGER,
+    line_end INTEGER,
+    is_exported BOOLEAN DEFAULT false,
+    inferred_type VARCHAR
+);
+
+CREATE TABLE IF NOT EXISTS nodes_module (
+    id VARCHAR PRIMARY KEY,
+    path VARCHAR NOT NULL,
+    is_barrel BOOLEAN DEFAULT false
+);
+`;
+const EDGE_TABLES_DDL = `
+CREATE TABLE IF NOT EXISTS edges_calls (
+    source_id VARCHAR NOT NULL,
+    target_id VARCHAR NOT NULL,
+    line INTEGER,
+    confidence FLOAT DEFAULT 0.9,
+    is_dynamic BOOLEAN DEFAULT false,
+    is_async BOOLEAN DEFAULT false,
+    is_indirect BOOLEAN DEFAULT false,
+    stage TINYINT NOT NULL,
+    reason VARCHAR
+);
+
+CREATE TABLE IF NOT EXISTS edges_imports (
+    source_id VARCHAR NOT NULL,
+    target_id VARCHAR NOT NULL,
+    line INTEGER,
+    kind VARCHAR NOT NULL,
+    original_name VARCHAR,
+    alias VARCHAR,
+    confidence FLOAT DEFAULT 1.0,
+    stage TINYINT NOT NULL,
+    reason VARCHAR
+);
+
+CREATE TABLE IF NOT EXISTS edges_extends (
+    source_id VARCHAR NOT NULL,
+    target_id VARCHAR NOT NULL,
+    line INTEGER,
+    confidence FLOAT DEFAULT 1.0,
+    stage TINYINT NOT NULL,
+    reason VARCHAR
+);
+
+CREATE TABLE IF NOT EXISTS edges_implements (
+    source_id VARCHAR NOT NULL,
+    target_id VARCHAR NOT NULL,
+    line INTEGER,
+    confidence FLOAT DEFAULT 1.0,
+    stage TINYINT NOT NULL,
+    reason VARCHAR
+);
+
+CREATE TABLE IF NOT EXISTS edges_contains (
+    source_id VARCHAR NOT NULL,
+    target_id VARCHAR NOT NULL,
+    confidence FLOAT DEFAULT 1.0,
+    stage TINYINT NOT NULL,
+    reason VARCHAR
+);
+
+CREATE TABLE IF NOT EXISTS edges_flows_to (
+    source_id VARCHAR NOT NULL,
+    target_id VARCHAR NOT NULL,
+    parameter_index INTEGER,
+    transform VARCHAR,
+    taint_label VARCHAR,
+    confidence FLOAT DEFAULT 0.8,
+    stage TINYINT NOT NULL,
+    reason VARCHAR
+);
+
+CREATE TABLE IF NOT EXISTS edges_reads (
+    source_id VARCHAR NOT NULL,
+    target_id VARCHAR NOT NULL,
+    line INTEGER,
+    field VARCHAR,
+    confidence FLOAT DEFAULT 0.9,
+    stage TINYINT NOT NULL,
+    reason VARCHAR
+);
+
+CREATE TABLE IF NOT EXISTS edges_writes (
+    source_id VARCHAR NOT NULL,
+    target_id VARCHAR NOT NULL,
+    line INTEGER,
+    field VARCHAR,
+    confidence FLOAT DEFAULT 0.9,
+    stage TINYINT NOT NULL,
+    reason VARCHAR
+);
+
+CREATE TABLE IF NOT EXISTS edges_returns (
+    source_id VARCHAR NOT NULL,
+    target_id VARCHAR NOT NULL,
+    line INTEGER,
+    return_type VARCHAR,
+    confidence FLOAT DEFAULT 0.85,
+    stage TINYINT NOT NULL,
+    reason VARCHAR
+);
+`;
+const AUXILIARY_TABLES_DDL = `
+CREATE TABLE IF NOT EXISTS cortex_embeddings (
+    node_id VARCHAR PRIMARY KEY,
+    vector FLOAT[384],
+    text_hash VARCHAR
+);
+
+CREATE TABLE IF NOT EXISTS cortex_health_snapshots (
+    timestamp TIMESTAMP,
+    metrics JSON
+);
+
+CREATE TABLE IF NOT EXISTS cortex_temporal_snapshots (
+    commit_hash VARCHAR,
+    timestamp TIMESTAMP,
+    node_counts JSON,
+    edge_counts JSON,
+    community_hash VARCHAR,
+    top_pagerank JSON,
+    hotspot_rankings JSON
+);
+
+CREATE TABLE IF NOT EXISTS cortex_flows (
+    id VARCHAR PRIMARY KEY,
+    name VARCHAR,
+    entry_point_id VARCHAR,
+    node_ids VARCHAR[],
+    has_async BOOLEAN DEFAULT false,
+    has_error_path BOOLEAN DEFAULT false
+);
+
+CREATE TABLE IF NOT EXISTS cortex_meta (
+    key VARCHAR PRIMARY KEY,
+    value VARCHAR
+);
+`;
+const INDEXES_DDL = `
+CREATE INDEX IF NOT EXISTS idx_calls_source ON edges_calls(source_id);
+CREATE INDEX IF NOT EXISTS idx_calls_target ON edges_calls(target_id);
+CREATE INDEX IF NOT EXISTS idx_imports_source ON edges_imports(source_id);
+CREATE INDEX IF NOT EXISTS idx_imports_target ON edges_imports(target_id);
+CREATE INDEX IF NOT EXISTS idx_extends_source ON edges_extends(source_id);
+CREATE INDEX IF NOT EXISTS idx_extends_target ON edges_extends(target_id);
+CREATE INDEX IF NOT EXISTS idx_implements_source ON edges_implements(source_id);
+CREATE INDEX IF NOT EXISTS idx_implements_target ON edges_implements(target_id);
+CREATE INDEX IF NOT EXISTS idx_contains_source ON edges_contains(source_id);
+CREATE INDEX IF NOT EXISTS idx_contains_target ON edges_contains(target_id);
+CREATE INDEX IF NOT EXISTS idx_flows_to_source ON edges_flows_to(source_id);
+CREATE INDEX IF NOT EXISTS idx_flows_to_target ON edges_flows_to(target_id);
+CREATE INDEX IF NOT EXISTS idx_reads_source ON edges_reads(source_id);
+CREATE INDEX IF NOT EXISTS idx_reads_target ON edges_reads(target_id);
+CREATE INDEX IF NOT EXISTS idx_writes_source ON edges_writes(source_id);
+CREATE INDEX IF NOT EXISTS idx_writes_target ON edges_writes(target_id);
+CREATE INDEX IF NOT EXISTS idx_returns_source ON edges_returns(source_id);
+CREATE INDEX IF NOT EXISTS idx_returns_target ON edges_returns(target_id);
+CREATE INDEX IF NOT EXISTS idx_fn_file ON nodes_function(file_path);
+CREATE INDEX IF NOT EXISTS idx_class_file ON nodes_class(file_path);
+CREATE INDEX IF NOT EXISTS idx_method_file ON nodes_method(file_path);
+CREATE INDEX IF NOT EXISTS idx_iface_file ON nodes_interface(file_path);
+CREATE INDEX IF NOT EXISTS idx_type_file ON nodes_type(file_path);
+CREATE INDEX IF NOT EXISTS idx_var_file ON nodes_variable(file_path);
+`;
+const STAGE4_TABLES_DDL = `
+CREATE TABLE IF NOT EXISTS type_constraints (
+    symbol_id VARCHAR NOT NULL,
+    type_name VARCHAR NOT NULL,
+    source VARCHAR NOT NULL,
+    confidence FLOAT DEFAULT 0.85,
+    file_path VARCHAR NOT NULL,
+    line INTEGER,
+    UNIQUE(symbol_id, type_name, source)
+);
+
+CREATE TABLE IF NOT EXISTS generic_instantiations (
+    symbol_id VARCHAR NOT NULL,
+    generic_name VARCHAR NOT NULL,
+    type_arguments VARCHAR[],
+    file_path VARCHAR NOT NULL,
+    line INTEGER
+);
+
+CREATE INDEX IF NOT EXISTS idx_constraints_symbol ON type_constraints(symbol_id);
+CREATE INDEX IF NOT EXISTS idx_constraints_type ON type_constraints(type_name);
+CREATE INDEX IF NOT EXISTS idx_generic_symbol ON generic_instantiations(symbol_id);
+`;
+const SYMBOLS_VIEW_DDL = `
+CREATE OR REPLACE VIEW symbols AS
+    SELECT id, name, file_path, line_start, line_end, 'function' AS kind FROM nodes_function
+    UNION ALL
+    SELECT id, name, file_path, line_start, line_end, 'class' AS kind FROM nodes_class
+    UNION ALL
+    SELECT id, name, file_path, line_start, line_end, 'method' AS kind FROM nodes_method
+    UNION ALL
+    SELECT id, name, file_path, line_start, line_end, 'interface' AS kind FROM nodes_interface
+    UNION ALL
+    SELECT id, name, file_path, line_start, line_end, 'type' AS kind FROM nodes_type
+    UNION ALL
+    SELECT id, name, file_path, line_start, line_end, 'variable' AS kind FROM nodes_variable;
+`;
+export async function createCortexSchema(db) {
+    await db.exec(NODE_TABLES_DDL);
+    await db.exec(EDGE_TABLES_DDL);
+    await db.exec(AUXILIARY_TABLES_DDL);
+    await db.exec(INDEXES_DDL);
+    await db.exec(STAGE4_TABLES_DDL);
+    try {
+        await db.exec('DROP TABLE IF EXISTS symbols;');
+    }
+    catch {
+        /* */
+    }
+    try {
+        await db.exec('DROP VIEW IF EXISTS symbols;');
+    }
+    catch {
+        /* */
+    }
+    await db.exec(SYMBOLS_VIEW_DDL);
+}
+export async function refreshSymbolsTable(db) {
+    try {
+        await db.exec('DROP VIEW IF EXISTS symbols;');
+    }
+    catch {
+        /* may be a table */
+    }
+    try {
+        await db.exec('DROP TABLE IF EXISTS symbols;');
+    }
+    catch {
+        /* may be a view */
+    }
+    await db.exec(`
+        CREATE TABLE symbols AS
+            SELECT id, name, file_path, line_start, line_end, 'function' AS kind FROM nodes_function
+            UNION ALL
+            SELECT id, name, file_path, line_start, line_end, 'class' AS kind FROM nodes_class
+            UNION ALL
+            SELECT id, name, file_path, line_start, line_end, 'method' AS kind FROM nodes_method
+            UNION ALL
+            SELECT id, name, file_path, line_start, line_end, 'interface' AS kind FROM nodes_interface
+            UNION ALL
+            SELECT id, name, file_path, line_start, line_end, 'type' AS kind FROM nodes_type
+            UNION ALL
+            SELECT id, name, file_path, line_start, line_end, 'variable' AS kind FROM nodes_variable;
+    `);
+}
+//# sourceMappingURL=schema.js.map

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

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

@@ -0,0 +1,7 @@
+import { CortexRepository } from './repository.js';
+import type { StageResult } from './types.js';
+export declare function runStage0(repo: CortexRepository, rootDir: string, options?: {
+    force?: boolean;
+    targetFiles?: string[];
+}): Promise<StageResult>;
+//# sourceMappingURL=stage-0-structure.d.ts.map

package/dist/src/cortex/stage-0-structure.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/cortex/stage-0-structure.js

@@ -0,0 +1,119 @@
+import path from 'node:path';
+import { readFileSync } from 'node:fs';
+import { walkFiles } from '#utils/files.js';
+import { detectLanguage } from '#core/languages.js';
+import { hashFileContent } from '#utils/files.js';
+const RE_EXPORT_PATTERN = /^\s*export\s+(\*|\{[^}]*\})\s+from\s+['"][^'"]+['"]\s*;?\s*$/;
+const EMPTY_OR_COMMENT = /^\s*($|\/\/|\/\*|\*)/;
+function isBarrelFile(content) {
+    const lines = content.split('\n');
+    let hasExport = false;
+    for (const line of lines) {
+        if (EMPTY_OR_COMMENT.test(line))
+            continue;
+        if (RE_EXPORT_PATTERN.test(line)) {
+            hasExport = true;
+            continue;
+        }
+        return false;
+    }
+    return hasExport;
+}
+export async function runStage0(repo, rootDir, options) {
+    const start = Date.now();
+    const errors = [];
+    let filesProcessed = 0;
+    let nodesCreated = 0;
+    let edgesCreated = 0;
+    const absolutePaths = options?.targetFiles
+        ? options.targetFiles.map((f) => path.resolve(rootDir, f))
+        : await walkFiles(rootDir);
+    const fileNodes = [];
+    const moduleNodes = new Map();
+    const containsEdges = [];
+    for (const absPath of absolutePaths) {
+        const relPath = path.relative(rootDir, absPath);
+        const fileId = `file:${relPath}`;
+        const language = detectLanguage(absPath);
+        let content;
+        try {
+            content = readFileSync(absPath, 'utf-8');
+        }
+        catch (err) {
+            errors.push({
+                filePath: relPath,
+                stage: 0,
+                message: err instanceof Error ? err.message : String(err),
+            });
+            continue;
+        }
+        const hash = hashFileContent(absPath, content);
+        if (!options?.force && !(await repo.isFileChanged(fileId, hash))) {
+            continue;
+        }
+        filesProcessed++;
+        fileNodes.push({
+            id: fileId,
+            path: relPath,
+            hash,
+            language,
+            depthLevel: 0,
+            lastIndexed: new Date(),
+        });
+        const dir = path.dirname(relPath);
+        const moduleId = `module:${dir === '.' ? relPath : dir}`;
+        if (dir === '.') {
+            const barrel = language === 'typescript' || language === 'javascript'
+                ? isBarrelFile(content)
+                : false;
+            if (!moduleNodes.has(moduleId)) {
+                moduleNodes.set(moduleId, {
+                    id: `module:${relPath}`,
+                    path: relPath,
+                    isBarrel: barrel,
+                });
+            }
+            else if (barrel) {
+                moduleNodes.get(moduleId).isBarrel = true;
+            }
+        }
+        if (dir !== '.') {
+            if (!moduleNodes.has(moduleId)) {
+                moduleNodes.set(moduleId, {
+                    id: moduleId,
+                    path: dir,
+                    isBarrel: false,
+                });
+            }
+        }
+        containsEdges.push({
+            sourceId: dir === '.' ? `module:${relPath}` : moduleId,
+            targetId: fileId,
+            confidence: 1.0,
+            stage: 0,
+            reason: null,
+        });
+    }
+    for (const node of fileNodes) {
+        await repo.upsertFileNode(node);
+        nodesCreated++;
+    }
+    const modules = Array.from(moduleNodes.values());
+    if (modules.length > 0) {
+        await repo.insertModuleNodes(modules);
+        nodesCreated += modules.length;
+    }
+    if (containsEdges.length > 0) {
+        await repo.insertContainsEdges(containsEdges);
+        edgesCreated += containsEdges.length;
+    }
+    return {
+        stage: 0,
+        filesProcessed,
+        nodesCreated,
+        edgesCreated,
+        durationMs: Date.now() - start,
+        errors,
+    };
+}
+//# sourceMappingURL=stage-0-structure.js.map

package/dist/src/cortex/stage-0-structure.js.map

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package/dist/src/cortex/stage-1-symbols.d.ts

@@ -0,0 +1,7 @@
+import { CortexRepository } from './repository.js';
+import type { StageResult } from './types.js';
+export declare function runStage1(repo: CortexRepository, rootDir: string, options?: {
+    force?: boolean;
+    targetFiles?: string[];
+}): Promise<StageResult>;
+//# sourceMappingURL=stage-1-symbols.d.ts.map

package/dist/src/cortex/stage-1-symbols.d.ts.map

@@ -0,0 +1 @@
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