@zbigniewsobiecki/squint 1.0.0

package/dist/commands/symbols/verify.js

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+import { Flags } from '@oclif/core';
+import chalk from 'chalk';
+import { LlmFlags, SharedFlags, readSourceAsString } from '../_shared/index.js';
+import { BaseLlmCommand } from '../llm/_shared/base-llm-command.js';
+import { filterCoverageForAspects } from '../llm/_shared/coverage.js';
+import { parseCombinedCsv } from '../llm/_shared/csv.js';
+import { completeWithLogging } from '../llm/_shared/llm-utils.js';
+import { buildSystemPrompt, buildUserPromptEnhanced, } from '../llm/_shared/prompts.js';
+import { verifyAnnotationContent } from '../llm/_shared/verify/content-verifier.js';
+import { checkAnnotationCoverage } from '../llm/_shared/verify/coverage-checker.js';
+export default class Verify extends BaseLlmCommand {
+    static description = 'Verify existing symbol annotations';
+    static examples = [
+        '<%= config.bin %> symbols verify --aspect purpose',
+        '<%= config.bin %> symbols verify --aspect purpose --aspect domain',
+        '<%= config.bin %> symbols verify --aspect purpose --fix',
+        '<%= config.bin %> symbols verify --aspect purpose --batch-size 10',
+    ];
+    static flags = {
+        database: SharedFlags.database,
+        json: SharedFlags.json,
+        ...LlmFlags,
+        aspect: Flags.string({
+            char: 'a',
+            description: 'Metadata key to verify (can be repeated)',
+            required: true,
+            multiple: true,
+        }),
+        fix: Flags.boolean({
+            description: 'Auto-fix structural issues found during verification',
+            default: false,
+        }),
+        'batch-size': Flags.integer({
+            char: 'b',
+            description: 'Number of symbols per LLM call',
+            default: 10,
+        }),
+        'max-iterations': Flags.integer({
+            description: 'Maximum iterations (0 = unlimited)',
+            default: 0,
+        }),
+    };
+    async execute(ctx, flags) {
+        const { db, isJson, dryRun } = ctx;
+        const aspects = flags.aspect;
+        const batchSize = flags['batch-size'] || 10;
+        const maxIterations = flags['max-iterations'] || 0;
+        const shouldFix = flags.fix;
+        if (!isJson) {
+            this.log(chalk.bold('Annotation Verification'));
+            this.log(chalk.gray(`Aspects: ${aspects.join(', ')}`));
+            this.log('');
+        }
+        // Phase 1: Coverage check
+        if (!isJson) {
+            this.log(chalk.bold('Phase 1: Coverage Check'));
+        }
+        const phase1 = checkAnnotationCoverage(db, aspects);
+        const report = { phase1 };
+        if (!isJson) {
+            this.log(`  Definitions: ${phase1.stats.annotatedDefinitions}/${phase1.stats.totalDefinitions} annotated`);
+            if (phase1.stats.missingCount > 0) {
+                this.log(chalk.red(`  Missing: ${phase1.stats.missingCount} annotations`));
+            }
+            const errorIssues = phase1.issues.filter((i) => i.severity === 'error');
+            if (errorIssues.length > 0) {
+                this.log('');
+                for (const issue of errorIssues.slice(0, 20)) {
+                    this.log(`  ${chalk.red('ERR')} ${issue.definitionName || '?'} (${issue.filePath}:${issue.line}): ${issue.message}`);
+                }
+                if (errorIssues.length > 20) {
+                    this.log(chalk.gray(`  ... and ${errorIssues.length - 20} more`));
+                }
+            }
+            const warningIssues = phase1.issues.filter((i) => i.severity === 'warning');
+            if (warningIssues.length > 0) {
+                this.log('');
+                this.log(chalk.yellow(`  Warnings (${warningIssues.length}):`));
+                for (const issue of warningIssues.slice(0, 20)) {
+                    this.log(`    ${chalk.yellow('WARN')} [${issue.category}] ${issue.message}`);
+                }
+                if (warningIssues.length > 20) {
+                    this.log(chalk.gray(`    ... and ${warningIssues.length - 20} more`));
+                }
+            }
+            if (phase1.passed) {
+                this.log(chalk.green('  ✓ All definitions have all aspects annotated'));
+            }
+            else {
+                this.log(chalk.red('  ✗ Coverage check failed'));
+            }
+            this.log('');
+        }
+        // Auto-fix: correct suspect-pure annotations if --fix
+        if (shouldFix && !dryRun) {
+            const suspectPureIssues = phase1.issues.filter((i) => i.fixData?.action === 'set-pure-false');
+            if (suspectPureIssues.length > 0) {
+                let fixed = 0;
+                for (const issue of suspectPureIssues) {
+                    if (issue.definitionId) {
+                        db.metadata.set(issue.definitionId, 'pure', 'false');
+                        fixed++;
+                    }
+                }
+                if (!isJson) {
+                    this.log(chalk.green(`  Fixed: corrected ${fixed} pure annotations to "false"`));
+                    this.log('');
+                }
+            }
+            // Auto-fix: harmonize inconsistent domain tags (deterministic — pick most common)
+            const domainIssues = phase1.issues.filter((i) => i.fixData?.action === 'harmonize-domain');
+            if (domainIssues.length > 0) {
+                // Group by (name, kind) to find the most common domain variant
+                const defIds = domainIssues.map((i) => i.definitionId).filter((id) => id !== undefined);
+                const groups = new Map();
+                for (const defId of defIds) {
+                    const def = db.definitions.getById(defId);
+                    if (!def)
+                        continue;
+                    const domain = db.metadata.getValue(defId, 'domain');
+                    if (!domain)
+                        continue;
+                    const key = `${def.name}::${def.kind}`;
+                    if (!groups.has(key))
+                        groups.set(key, []);
+                    groups.get(key).push({ id: defId, domain });
+                }
+                let harmonized = 0;
+                for (const [, defs] of groups) {
+                    // Find the most common domain variant
+                    const counts = new Map();
+                    for (const { domain } of defs) {
+                        try {
+                            const parsed = JSON.parse(domain);
+                            const normalized = JSON.stringify([...parsed].sort());
+                            counts.set(normalized, (counts.get(normalized) ?? 0) + 1);
+                        }
+                        catch {
+                            // Skip
+                        }
+                    }
+                    let bestDomain = '';
+                    let bestCount = 0;
+                    for (const [domain, count] of counts) {
+                        if (count > bestCount) {
+                            bestCount = count;
+                            bestDomain = domain;
+                        }
+                    }
+                    if (!bestDomain)
+                        continue;
+                    // Apply the most common domain to all definitions in the group
+                    for (const { id, domain } of defs) {
+                        try {
+                            const normalized = JSON.stringify([...JSON.parse(domain)].sort());
+                            if (normalized !== bestDomain) {
+                                db.metadata.set(id, 'domain', bestDomain);
+                                harmonized++;
+                            }
+                        }
+                        catch {
+                            // Skip
+                        }
+                    }
+                }
+                if (harmonized > 0 && !isJson) {
+                    this.log(chalk.green(`  Fixed: harmonized ${harmonized} inconsistent domain annotations`));
+                    this.log('');
+                }
+            }
+        }
+        // If dry-run or Phase 1 failed, stop here
+        if (dryRun || !phase1.passed) {
+            if (isJson) {
+                this.log(JSON.stringify(report, null, 2));
+            }
+            else if (dryRun) {
+                this.log(chalk.yellow('Dry run — skipping Phase 2 (LLM content verification)'));
+            }
+            return;
+        }
+        // Phase 2: LLM content verification
+        if (!isJson) {
+            this.log(chalk.bold('Phase 2: Content Verification (LLM)'));
+        }
+        const phase2 = await verifyAnnotationContent(db, ctx, this, {
+            'batch-size': batchSize,
+            'max-iterations': maxIterations,
+        }, aspects);
+        report.phase2 = phase2;
+        if (!isJson) {
+            this.log(`  Checked: ${phase2.stats.checked} definitions in ${phase2.stats.batchesProcessed} batches`);
+            if (phase2.issues.length === 0) {
+                this.log(chalk.green('  ✓ All annotations passed content verification'));
+            }
+            else {
+                this.log(chalk.yellow(`  Found ${phase2.issues.length} issues:`));
+                for (const issue of phase2.issues) {
+                    const severity = issue.severity === 'error' ? chalk.red('ERR') : chalk.yellow('WARN');
+                    this.log(`  ${severity} ${issue.definitionName || '?'}: ${issue.message}`);
+                }
+            }
+        }
+        // LLM-based fix: reannotate definitions flagged as wrong
+        if (shouldFix && !dryRun && ctx.model && phase2) {
+            const reannotateIssues = phase2.issues.filter((i) => i.fixData?.action === 'reannotate-definition');
+            if (reannotateIssues.length > 0) {
+                if (!isJson) {
+                    this.log('');
+                    this.log(chalk.bold(`Fixing ${reannotateIssues.length} wrong annotations via LLM...`));
+                }
+                // Collect definition IDs to re-annotate
+                const defIdsToFix = reannotateIssues.map((i) => i.definitionId).filter((id) => id !== undefined);
+                const uniqueDefIds = [...new Set(defIdsToFix)];
+                // Build symbols for re-annotation (set() will overwrite existing values)
+                const symbolsToFix = uniqueDefIds
+                    .map((id) => db.definitions.getById(id))
+                    .filter((d) => d !== null)
+                    .map((d) => ({
+                    id: d.id,
+                    name: d.name,
+                    kind: d.kind,
+                    filePath: d.filePath,
+                    line: d.line,
+                    endLine: d.endLine,
+                    dependencyCount: 0,
+                }));
+                if (symbolsToFix.length > 0) {
+                    const enhancedSymbols = await this.enhanceSymbols(db, symbolsToFix, aspects, 50);
+                    const systemPrompt = buildSystemPrompt(aspects);
+                    const symbolContexts = enhancedSymbols.map((s) => ({
+                        id: s.id,
+                        name: s.name,
+                        kind: s.kind,
+                        filePath: s.filePath,
+                        line: s.line,
+                        endLine: s.endLine,
+                        sourceCode: s.sourceCode,
+                        isExported: s.isExported,
+                        dependencies: s.dependencies,
+                        relationshipsToAnnotate: [],
+                        incomingDependencies: s.incomingDependencies,
+                        incomingDependencyCount: s.incomingDependencyCount,
+                    }));
+                    const allCoverage = db.metadata.getAspectCoverage({});
+                    const totalSymbols = db.metadata.getFilteredCount({});
+                    const coverage = filterCoverageForAspects(allCoverage, aspects, totalSymbols);
+                    const userPrompt = buildUserPromptEnhanced(symbolContexts, aspects, coverage);
+                    try {
+                        const response = await completeWithLogging({
+                            model: ctx.model,
+                            systemPrompt,
+                            userPrompt,
+                            temperature: 0,
+                            command: this,
+                            isJson: ctx.isJson,
+                        });
+                        const parseResult = parseCombinedCsv(response);
+                        const validIds = new Set(uniqueDefIds);
+                        let fixedCount = 0;
+                        for (const row of parseResult.symbols) {
+                            if (!validIds.has(row.symbolId))
+                                continue;
+                            if (!aspects.includes(row.aspect))
+                                continue;
+                            if (!row.value || row.value.length < 2)
+                                continue;
+                            db.metadata.set(row.symbolId, row.aspect, row.value);
+                            fixedCount++;
+                        }
+                        if (fixedCount > 0 && !isJson) {
+                            this.log(chalk.green(`  Fixed: re-annotated ${fixedCount} definition aspects via LLM`));
+                        }
+                    }
+                    catch {
+                        // LLM error
+                    }
+                }
+            }
+        }
+        if (isJson) {
+            this.log(JSON.stringify(report, null, 2));
+        }
+    }
+    /**
+     * Enhance symbols with source code, dependency context, and relationships to annotate.
+     */
+    async enhanceSymbols(db, symbols, aspects, relationshipLimit) {
+        const enhanced = [];
+        for (const symbol of symbols) {
+            const sourceCode = await readSourceAsString(db.resolveFilePath(symbol.filePath), symbol.line, symbol.endLine);
+            // Get dependencies with all their metadata
+            const deps = db.dependencies.getWithMetadata(symbol.id, aspects[0]);
+            const dependencies = deps.map((dep) => {
+                // Get all metadata for this dependency
+                const metadata = db.metadata.get(dep.id);
+                let domains = null;
+                try {
+                    if (metadata.domain) {
+                        domains = JSON.parse(metadata.domain);
+                    }
+                }
+                catch {
+                    /* ignore */
+                }
+                return {
+                    id: dep.id,
+                    name: dep.name,
+                    kind: dep.kind,
+                    filePath: dep.filePath,
+                    line: dep.line,
+                    purpose: metadata.purpose || null,
+                    domains,
+                    role: metadata.role || null,
+                    pure: metadata.pure ? metadata.pure === 'true' : null,
+                };
+            });
+            // Get unannotated relationships from this symbol (handle missing table)
+            let unannotatedRels = [];
+            try {
+                const limit = relationshipLimit > 0 ? relationshipLimit : undefined;
+                unannotatedRels = db.relationships.getUnannotated({ fromDefinitionId: symbol.id, limit });
+            }
+            catch {
+                // Table doesn't exist - continue with empty relationships
+            }
+            // These are usage-based relationships (calls), so they're all 'uses' type
+            const relationshipsToAnnotate = unannotatedRels.map((rel) => ({
+                toId: rel.toDefinitionId,
+                toName: rel.toName,
+                toKind: rel.toKind,
+                usageLine: rel.fromLine, // Use fromLine as approximate usage location
+                relationshipType: 'uses',
+            }));
+            // Get incoming dependencies (who uses this symbol)
+            const incomingDeps = db.dependencies.getIncoming(symbol.id, 5);
+            const incomingDependencyCount = db.dependencies.getIncomingCount(symbol.id);
+            const incomingDependencies = incomingDeps.map((inc) => ({
+                id: inc.id,
+                name: inc.name,
+                kind: inc.kind,
+                filePath: inc.filePath,
+            }));
+            // Get the definition to check if it's exported
+            const defInfo = db.definitions.getById(symbol.id);
+            const isExported = defInfo?.isExported ?? false;
+            enhanced.push({
+                ...symbol,
+                sourceCode,
+                isExported,
+                dependencies,
+                relationshipsToAnnotate,
+                incomingDependencies,
+                incomingDependencyCount,
+            });
+        }
+        return enhanced;
+    }
+}
+//# sourceMappingURL=verify.js.map

package/dist/commands/symbols/verify.js.map

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package/dist/db/connection.d.ts

@@ -0,0 +1,14 @@
+import Database from 'better-sqlite3';
+/**
+ * Create a new database connection with WAL mode enabled.
+ */
+export declare function createConnection(dbPath: string): Database.Database;
+/**
+ * Initialize the database schema, dropping any existing tables.
+ */
+export declare function initializeSchema(db: Database.Database): void;
+/**
+ * Close the database connection.
+ */
+export declare function closeConnection(db: Database.Database): void;
+//# sourceMappingURL=connection.d.ts.map

package/dist/db/connection.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"connection.d.ts","sourceRoot":"","sources":["../../src/db/connection.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AAGtC;;GAEG;AACH,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,GAAG,QAAQ,CAAC,QAAQ,CAIlE;AAED;;GAEG;AACH,wBAAgB,gBAAgB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,IAAI,CAgB5D;AAED;;GAEG;AACH,wBAAgB,eAAe,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,IAAI,CAE3D"}

package/dist/db/connection.js

@@ -0,0 +1,37 @@
+import Database from 'better-sqlite3';
+import { SCHEMA } from './schema.js';
+/**
+ * Create a new database connection with WAL mode enabled.
+ */
+export function createConnection(dbPath) {
+    const db = new Database(dbPath);
+    db.pragma('journal_mode = WAL');
+    return db;
+}
+/**
+ * Initialize the database schema, dropping any existing tables.
+ */
+export function initializeSchema(db) {
+    db.exec(`
+    DROP TABLE IF EXISTS flows;
+    DROP TABLE IF EXISTS module_members;
+    DROP TABLE IF EXISTS modules;
+    DROP TABLE IF EXISTS domains;
+    DROP TABLE IF EXISTS relationship_annotations;
+    DROP TABLE IF EXISTS definition_metadata;
+    DROP TABLE IF EXISTS usages;
+    DROP TABLE IF EXISTS symbols;
+    DROP TABLE IF EXISTS imports;
+    DROP TABLE IF EXISTS definitions;
+    DROP TABLE IF EXISTS files;
+    DROP TABLE IF EXISTS metadata;
+  `);
+    db.exec(SCHEMA);
+}
+/**
+ * Close the database connection.
+ */
+export function closeConnection(db) {
+    db.close();
+}
+//# sourceMappingURL=connection.js.map

package/dist/db/connection.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"connection.js","sourceRoot":"","sources":["../../src/db/connection.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,gBAAgB,CAAC;AACtC,OAAO,EAAE,MAAM,EAAE,MAAM,aAAa,CAAC;AAErC;;GAEG;AACH,MAAM,UAAU,gBAAgB,CAAC,MAAc;IAC7C,MAAM,EAAE,GAAG,IAAI,QAAQ,CAAC,MAAM,CAAC,CAAC;IAChC,EAAE,CAAC,MAAM,CAAC,oBAAoB,CAAC,CAAC;IAChC,OAAO,EAAE,CAAC;AACZ,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,gBAAgB,CAAC,EAAqB;IACpD,EAAE,CAAC,IAAI,CAAC;;;;;;;;;;;;;GAaP,CAAC,CAAC;IACH,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;AAClB,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,eAAe,CAAC,EAAqB;IACnD,EAAE,CAAC,KAAK,EAAE,CAAC;AACb,CAAC"}

package/dist/db/database-facade.d.ts

@@ -0,0 +1,125 @@
+import type { Definition } from '../parser/definition-extractor.js';
+import type { FileReference, ImportedSymbol, SymbolUsage } from '../parser/reference-extractor.js';
+import { type CallsiteResult, type FileInsert, type IIndexWriter } from './schema.js';
+import { CallGraphService } from './repositories/call-graph-service.js';
+import { DefinitionRepository } from './repositories/definition-repository.js';
+import { DependencyRepository } from './repositories/dependency-repository.js';
+import { DomainRepository } from './repositories/domain-repository.js';
+import { FeatureRepository } from './repositories/feature-repository.js';
+import { FileRepository } from './repositories/file-repository.js';
+import { FlowRepository } from './repositories/flow-repository.js';
+import { GraphRepository } from './repositories/graph-repository.js';
+import { InteractionAnalysis } from './repositories/interaction-analysis.js';
+import { InteractionRepository } from './repositories/interaction-repository.js';
+import { MetadataRepository } from './repositories/metadata-repository.js';
+import { ModuleRepository } from './repositories/module-repository.js';
+import { RelationshipRepository } from './repositories/relationship-repository.js';
+/**
+ * Database access layer that owns the connection and exposes repositories.
+ * Implements IIndexWriter for the parse/indexing pipeline.
+ */
+export declare class IndexDatabase implements IIndexWriter {
+    private conn;
+    private _sourceDirectory;
+    readonly files: FileRepository;
+    readonly definitions: DefinitionRepository;
+    readonly metadata: MetadataRepository;
+    readonly dependencies: DependencyRepository;
+    readonly relationships: RelationshipRepository;
+    readonly domains: DomainRepository;
+    readonly modules: ModuleRepository;
+    readonly interactions: InteractionRepository;
+    readonly features: FeatureRepository;
+    readonly flows: FlowRepository;
+    readonly graph: GraphRepository;
+    readonly callGraph: CallGraphService;
+    readonly interactionAnalysis: InteractionAnalysis;
+    constructor(dbPath: string);
+    initialize(): void;
+    close(): void;
+    getSourceDirectory(): string;
+    resolveFilePath(dbPath: string): string;
+    toRelativePath(absolutePath: string): string;
+    setMetadata(key: string, value: string): void;
+    insertFile(file: FileInsert): number;
+    insertDefinition(fileId: number, def: Definition): number;
+    insertReference(fromFileId: number, toFileId: number | null, ref: FileReference): number;
+    insertSymbol(refId: number | null, defId: number | null, sym: ImportedSymbol, fileId?: number): number;
+    insertUsage(symbolId: number, usage: SymbolUsage): void;
+    getDefinitionByName(fileId: number, name: string): number | null;
+    getDefinitionCount(): number;
+    getReferenceCount(): number;
+    getUsageCount(): number;
+    getCallsites(definitionId: number): CallsiteResult[];
+    getCallsitesForFile(fileId: number): CallsiteResult[];
+    getCallsiteCount(): number;
+    /**
+     * Get overall database stats (cross-repo aggregation)
+     */
+    getStats(): {
+        files: number;
+        definitions: number;
+        imports: number;
+        usages: number;
+        callsites: number;
+        modules: number;
+        assignedSymbols: number;
+        unassignedSymbols: number;
+        flows: number;
+        interactions: number;
+        relationships: number;
+    };
+    /**
+     * Get exported definitions that are not called by anything (entry points)
+     */
+    getRootDefinitions(): Array<{
+        id: number;
+        name: string;
+        kind: string;
+        filePath: string;
+        line: number;
+    }>;
+    /**
+     * Find ghost rows: rows referencing entities that no longer exist.
+     * Each query is wrapped in try/catch since tables may not exist.
+     */
+    findGhostRows(): {
+        ghostRelationships: Array<{
+            id: number;
+            table: string;
+        }>;
+        ghostMembers: Array<{
+            definitionId: number;
+            table: string;
+        }>;
+        ghostEntryPoints: Array<{
+            id: number;
+            table: string;
+        }>;
+        ghostEntryModules: Array<{
+            id: number;
+            table: string;
+        }>;
+        ghostInteractions: Array<{
+            id: number;
+            table: string;
+        }>;
+        ghostSubflows: Array<{
+            rowid: number;
+            table: string;
+        }>;
+    };
+    /**
+     * Delete a ghost row by table and primary key.
+     * Uses an allowlist of table names to prevent injection.
+     */
+    deleteGhostRow(table: string, id: number): boolean;
+    /**
+     * Remove stale file entries (files that no longer exist on disk).
+     */
+    cleanStaleFiles(): {
+        removed: number;
+        paths: string[];
+    };
+}
+//# sourceMappingURL=database-facade.d.ts.map

package/dist/db/database-facade.d.ts.map

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