@grafema/util 0.3.0-beta

package/dist/index.d.ts

@@ -0,0 +1,75 @@
+/**
+ * @grafema/util - Query, config, and guarantee utilities for Grafema
+ *
+ * This package contains the live query layer, configuration, diagnostics,
+ * and guarantee management. Analysis is handled by grafema-orchestrator (Rust).
+ */
+export { GrafemaError, ConfigError, FileAccessError, LanguageError, DatabaseError, PluginError, AnalysisError, ValidationError, StrictModeError, StrictModeFailure, } from './errors/GrafemaError.js';
+export type { ErrorContext, GrafemaErrorJSON, ResolutionStep, ResolutionFailureReason, } from './errors/GrafemaError.js';
+export { ConsoleLogger, FileLogger, MultiLogger, createLogger } from './logging/Logger.js';
+export type { Logger, LogLevel } from './logging/Logger.js';
+export { DiagnosticCollector, DiagnosticReporter, DiagnosticWriter } from './diagnostics/index.js';
+export type { Diagnostic, DiagnosticInput, ReportOptions, SummaryStats } from './diagnostics/index.js';
+export { DIAGNOSTIC_CATEGORIES, CODE_TO_CATEGORY, getCategoryForCode, getCodesForCategory } from './diagnostics/index.js';
+export type { DiagnosticCategory, DiagnosticCategoryKey, CodeCategoryInfo } from './diagnostics/index.js';
+export { loadConfig, DEFAULT_CONFIG, validateVersion, validateServices, validatePatterns, validateWorkspace, validateRouting, } from './config/index.js';
+export type { GrafemaConfig } from './config/index.js';
+export { GRAFEMA_VERSION, getSchemaVersion } from './version.js';
+export { getOnboardingInstruction } from './instructions/index.js';
+export { GraphBackend, typeToKind, edgeTypeToNumber } from './core/GraphBackend.js';
+export type { Node, Edge, EdgeType, AttrQuery, GraphStats, GraphExport } from './core/GraphBackend.js';
+export { RFDBClient } from '@grafema/rfdb-client';
+export { RFDBServerBackend } from './storage/backends/RFDBServerBackend.js';
+export { computeSemanticId, parseSemanticId, computeDiscriminator, computeSemanticIdV2, parseSemanticIdV2, computeContentHash } from './core/SemanticId.js';
+export type { Location, ScopeContext, SemanticIdOptions, ParsedSemanticId, LocatedItem, ParsedSemanticIdV2, ContentHashHints } from './core/SemanticId.js';
+export { isGrafemaUri, encodeFragment, decodeFragment, toGrafemaUri, parseGrafemaUri, toCompactSemanticId, normalizeSemanticId } from './core/GrafemaUri.js';
+export type { ParsedGrafemaUri } from './core/GrafemaUri.js';
+export { GuaranteeManager } from './core/GuaranteeManager.js';
+export type { GuaranteeGraph } from './core/GuaranteeManager.js';
+export { calculateFileHash, calculateFileHashAsync, calculateContentHash } from './core/HashUtils.js';
+export { findBinary, findAnalyzerBinary, findRfdbBinary, findOrchestratorBinary, getBinaryNotFoundMessage, getPlatformDir, getPlatformPackageName } from './utils/findRfdbBinary.js';
+export type { FindBinaryOptions, BinaryName } from './utils/findRfdbBinary.js';
+export { ensureBinary, downloadBinary, isDownloadable, findInGrafemaBin, getGrafemaBinDir } from './utils/lazyDownload.js';
+export { startRfdbServer, checkExistingServer } from './utils/startRfdbServer.js';
+export type { StartRfdbServerOptions } from './utils/startRfdbServer.js';
+export { resolveModulePath, isRelativeImport, resolveRelativeSpecifier, DEFAULT_EXTENSIONS, DEFAULT_INDEX_FILES } from './utils/moduleResolution.js';
+export type { ModuleResolutionOptions } from './utils/moduleResolution.js';
+export { resolveNodeFile } from './utils/resolveNodeFile.js';
+export { levenshtein, checkTypoAgainstKnownTypes, resetKnownNodeTypes, getKnownNodeTypes } from './storage/backends/typeValidation.js';
+export { PathValidator } from './validation/PathValidator.js';
+export type { PathValidationResult, EndpointDiff } from './validation/PathValidator.js';
+export { VersionManager, versionManager } from './core/VersionManager.js';
+export type { VersionedNode, VersionConstants, EnrichOptions, ModifiedNodeInfo, ChangesSummary, ClassifyChangesResult } from './core/VersionManager.js';
+export { GraphFreshnessChecker } from './core/GraphFreshnessChecker.js';
+export type { FreshnessGraph, FreshnessResult, StaleModule } from './core/GraphFreshnessChecker.js';
+export { IncrementalReanalyzer } from './core/IncrementalReanalyzer.js';
+export type { ReanalysisOptions, ReanalysisProgress, ReanalysisResult } from './core/IncrementalReanalyzer.js';
+export { CoverageAnalyzer } from './core/CoverageAnalyzer.js';
+export type { CoverageResult } from './core/CoverageAnalyzer.js';
+export { FileExplainer } from './core/FileExplainer.js';
+export type { FileExplainResult, EnhancedNode } from './core/FileExplainer.js';
+export { FileOverview } from './core/FileOverview.js';
+export type { FileOverviewResult, ImportInfo, ExportInfo, FunctionOverview, ClassOverview, VariableOverview, } from './core/FileOverview.js';
+export { ResourceRegistryImpl } from './core/ResourceRegistry.js';
+export { GraphAPI } from './api/GraphAPI.js';
+export { GuaranteeAPI } from './api/GuaranteeAPI.js';
+export type { GuaranteeGraphBackend } from './api/GuaranteeAPI.js';
+export { isGuaranteeType, isGrafemaType } from './core/nodes/NodeKind.js';
+export { IssueNode, type IssueNodeRecord, type IssueSeverity, type IssueType } from './core/nodes/IssueNode.js';
+export { GuaranteeNode } from './core/nodes/GuaranteeNode.js';
+export type { GuaranteeNodeRecord, GuaranteeNodeOptions, GuaranteePriority, GuaranteeStatus, GuaranteeType, } from './core/nodes/GuaranteeNode.js';
+export { InterfaceSchemaExtractor, GraphSchemaExtractor } from './schema/index.js';
+export type { InterfaceSchema, PropertySchema, ExtractOptions, GraphSchema, NodeTypeSchema, EdgeTypeSchema, GraphExtractOptions, } from './schema/index.js';
+export { KnowledgeBase, SemanticAddressResolver, parseSemanticAddress, parseFrontmatter, parseKBNode, serializeKBNode, parseEdgesFile, appendEdge, parseYamlArrayFile, GitIngest, parseGitLog, normalizeAuthors, getChurn, getCoChanges, getOwnership, getArchaeology } from './knowledge/index.js';
+export type { ResolverBackend } from './knowledge/index.js';
+export type { KBNodeType, KBLifecycle, KBScope, KBNodeBase, KBDecision, KBFact, KBSession, KBNode, KBEdge, KBStats, KBQueryFilter, ParsedSemanticAddress, ResolvedAddress, DanglingCodeRef, } from './knowledge/index.js';
+export type { RawCommit, FileChange, AuthorEntry, CommitEntry, IngestResult, Meta } from './knowledge/index.js';
+export type { ChurnEntry, CoChangeEntry, OwnershipEntry, ArchaeologyEntry } from './knowledge/index.js';
+export { findCallsInFunction, findContainingFunction, traceValues, aggregateValues, NONDETERMINISTIC_PATTERNS, NONDETERMINISTIC_OBJECTS } from './queries/index.js';
+export { traceDataflow, traceForwardBFS, traceBackwardBFS } from './queries/index.js';
+export { buildNodeContext, getNodeDisplayName, formatEdgeMetadata, STRUCTURAL_EDGE_TYPES } from './queries/index.js';
+export type { CallInfo, CallerInfo, FindCallsOptions, TracedValue, ValueSource, UnknownReason, TraceValuesOptions, ValueSetResult, TraceValuesGraphBackend, NondeterministicPattern, EdgeWithNode, EdgeGroup, SourcePreview, NodeContext, BuildNodeContextOptions, DataflowNode, DataflowEdge, DataflowBackend, TraceDataflowOptions, TraceDataflowResult, } from './queries/index.js';
+export { EDGE_ARCHETYPE_MAP, lookupEdge, generateLegend, PERSPECTIVES, renderNotation, extractSubgraph, shortenName, renderTraceNarrative } from './notation/index.js';
+export type { Archetype, EdgeMapping, DescribeOptions, SubgraphData, NotationBlock, NotationLine, TraceDetail, TraceNarrativeOptions, } from './notation/index.js';
+export type * from '@grafema/types';
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

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package/dist/index.js

@@ -0,0 +1,76 @@
+/**
+ * @grafema/util - Query, config, and guarantee utilities for Grafema
+ *
+ * This package contains the live query layer, configuration, diagnostics,
+ * and guarantee management. Analysis is handled by grafema-orchestrator (Rust).
+ */
+// Error types
+export { GrafemaError, ConfigError, FileAccessError, LanguageError, DatabaseError, PluginError, AnalysisError, ValidationError, StrictModeError, StrictModeFailure, } from './errors/GrafemaError.js';
+// Logging
+export { ConsoleLogger, FileLogger, MultiLogger, createLogger } from './logging/Logger.js';
+// Diagnostics
+export { DiagnosticCollector, DiagnosticReporter, DiagnosticWriter } from './diagnostics/index.js';
+export { DIAGNOSTIC_CATEGORIES, CODE_TO_CATEGORY, getCategoryForCode, getCodesForCategory } from './diagnostics/index.js';
+// Config
+export { loadConfig, DEFAULT_CONFIG, validateVersion, validateServices, validatePatterns, validateWorkspace, validateRouting, } from './config/index.js';
+// Version
+export { GRAFEMA_VERSION, getSchemaVersion } from './version.js';
+// Instructions (for AI agents)
+export { getOnboardingInstruction } from './instructions/index.js';
+// Graph backend
+export { GraphBackend, typeToKind, edgeTypeToNumber } from './core/GraphBackend.js';
+// RFDB
+export { RFDBClient } from '@grafema/rfdb-client';
+export { RFDBServerBackend } from './storage/backends/RFDBServerBackend.js';
+// Core utilities
+export { computeSemanticId, parseSemanticId, computeDiscriminator, computeSemanticIdV2, parseSemanticIdV2, computeContentHash } from './core/SemanticId.js';
+// URI format
+export { isGrafemaUri, encodeFragment, decodeFragment, toGrafemaUri, parseGrafemaUri, toCompactSemanticId, normalizeSemanticId } from './core/GrafemaUri.js';
+export { GuaranteeManager } from './core/GuaranteeManager.js';
+// Hash utilities
+export { calculateFileHash, calculateFileHashAsync, calculateContentHash } from './core/HashUtils.js';
+// Binary finder utilities
+export { findBinary, findAnalyzerBinary, findRfdbBinary, findOrchestratorBinary, getBinaryNotFoundMessage, getPlatformDir, getPlatformPackageName } from './utils/findRfdbBinary.js';
+// Lazy download
+export { ensureBinary, downloadBinary, isDownloadable, findInGrafemaBin, getGrafemaBinDir } from './utils/lazyDownload.js';
+// RFDB server lifecycle
+export { startRfdbServer, checkExistingServer } from './utils/startRfdbServer.js';
+// Module resolution utilities
+export { resolveModulePath, isRelativeImport, resolveRelativeSpecifier, DEFAULT_EXTENSIONS, DEFAULT_INDEX_FILES } from './utils/moduleResolution.js';
+// Node file path resolution
+export { resolveNodeFile } from './utils/resolveNodeFile.js';
+// Type validation and path validation
+export { levenshtein, checkTypoAgainstKnownTypes, resetKnownNodeTypes, getKnownNodeTypes } from './storage/backends/typeValidation.js';
+export { PathValidator } from './validation/PathValidator.js';
+// Version management
+export { VersionManager, versionManager } from './core/VersionManager.js';
+// Freshness checking and incremental reanalysis
+export { GraphFreshnessChecker } from './core/GraphFreshnessChecker.js';
+export { IncrementalReanalyzer } from './core/IncrementalReanalyzer.js';
+// Coverage
+export { CoverageAnalyzer } from './core/CoverageAnalyzer.js';
+// File analysis utilities
+export { FileExplainer } from './core/FileExplainer.js';
+export { FileOverview } from './core/FileOverview.js';
+// Resource system
+export { ResourceRegistryImpl } from './core/ResourceRegistry.js';
+// API
+export { GraphAPI } from './api/GraphAPI.js';
+export { GuaranteeAPI } from './api/GuaranteeAPI.js';
+// Node kinds
+export { isGuaranteeType, isGrafemaType } from './core/nodes/NodeKind.js';
+// Issue nodes (detected problems)
+export { IssueNode } from './core/nodes/IssueNode.js';
+// Guarantee nodes (contract-based)
+export { GuaranteeNode } from './core/nodes/GuaranteeNode.js';
+// Schema extraction
+export { InterfaceSchemaExtractor, GraphSchemaExtractor } from './schema/index.js';
+// Knowledge Base
+export { KnowledgeBase, SemanticAddressResolver, parseSemanticAddress, parseFrontmatter, parseKBNode, serializeKBNode, parseEdgesFile, appendEdge, parseYamlArrayFile, GitIngest, parseGitLog, normalizeAuthors, getChurn, getCoChanges, getOwnership, getArchaeology } from './knowledge/index.js';
+// Graph Query Utilities
+export { findCallsInFunction, findContainingFunction, traceValues, aggregateValues, NONDETERMINISTIC_PATTERNS, NONDETERMINISTIC_OBJECTS } from './queries/index.js';
+export { traceDataflow, traceForwardBFS, traceBackwardBFS } from './queries/index.js';
+export { buildNodeContext, getNodeDisplayName, formatEdgeMetadata, STRUCTURAL_EDGE_TYPES } from './queries/index.js';
+// Notation — DSL rendering engine
+export { EDGE_ARCHETYPE_MAP, lookupEdge, generateLegend, PERSPECTIVES, renderNotation, extractSubgraph, shortenName, renderTraceNarrative } from './notation/index.js';
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
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package/dist/instructions/index.d.ts

@@ -0,0 +1,8 @@
+/**
+ * Get the onboarding instruction document.
+ *
+ * Returns the full markdown text of the onboarding procedure
+ * that guides an AI agent through project study and configuration.
+ */
+export declare function getOnboardingInstruction(): string;
+//# sourceMappingURL=index.d.ts.map

package/dist/instructions/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/instructions/index.ts"],"names":[],"mappings":"AAYA;;;;;GAKG;AACH,wBAAgB,wBAAwB,IAAI,MAAM,CAEjD"}

package/dist/instructions/index.js

@@ -0,0 +1,20 @@
+/**
+ * Grafema instruction documents for AI agents.
+ *
+ * Instructions are markdown documents that guide agent behavior.
+ * They are read at runtime from the installed package.
+ */
+import { readFileSync } from 'fs';
+import { join, dirname } from 'path';
+import { fileURLToPath } from 'url';
+const __dirname = dirname(fileURLToPath(import.meta.url));
+/**
+ * Get the onboarding instruction document.
+ *
+ * Returns the full markdown text of the onboarding procedure
+ * that guides an AI agent through project study and configuration.
+ */
+export function getOnboardingInstruction() {
+    return readFileSync(join(__dirname, 'onboarding.md'), 'utf-8');
+}
+//# sourceMappingURL=index.js.map

package/dist/instructions/index.js.map

@@ -0,0 +1 @@
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package/dist/instructions/onboarding.md

@@ -0,0 +1,133 @@
+# Grafema Project Onboarding
+
+## Goal
+Study the target project and create a `.grafema/config.yaml` that correctly
+describes its services, entry points, and analysis configuration.
+
+## Prerequisites
+- The project directory exists and contains source code
+- Node.js 18+ installed
+- Run `grafema init` to create `.grafema/` directory if it doesn't exist
+
+## Step 1: Initial Reconnaissance
+
+Use `read_project_structure` to get the directory tree.
+
+Look for:
+- `package.json` in root and subdirectories (indicates JS/TS packages)
+- `pnpm-workspace.yaml`, `lerna.json`, root `package.json` with `workspaces`
+  field (workspace/monorepo indicators)
+- `tsconfig.json` files (TypeScript project)
+- `Dockerfile`, `docker-compose.yml`, `k8s/`, `apps.json` (deployment configs
+  that may reveal service boundaries)
+- Directories named `apps/`, `packages/`, `services/`, `pkg/`, `modules/`
+  (common monorepo structures)
+
+## Step 2: Identify Services
+
+A "service" in Grafema is an independently analyzable unit of code with its
+own entry point. Typically:
+- A standalone application (API server, web app, CLI tool)
+- A package in a monorepo that other packages depend on
+- A microservice in a deployment configuration
+
+For each potential service, determine:
+1. **Name** — human-readable identifier (e.g., "backend", "dashboard")
+2. **Path** — directory path relative to project root
+3. **Entry point** — the main source file (prefer TypeScript source over
+   compiled output)
+
+### How to find entry points
+Check in order:
+1. `package.json` "source" field (TypeScript source entry)
+2. `package.json` "main" field, but look for `.ts` equivalent in `src/`
+3. Common patterns: `src/index.ts`, `src/main.ts`, `src/app.ts`,
+   `src/server.ts`, `index.ts`
+4. For React apps: `src/App.tsx`, `src/index.tsx`
+5. Check `bin` field in package.json for CLI tools
+
+### When to ask the user
+- "I found [X] that looks like [description]. Should I include it as a
+  service?"
+- "This directory has multiple potential entry points: [list].
+  Which should I use?"
+- "I found deployment configuration mentioning services not visible in
+  the code structure. Should I investigate?"
+
+## Step 3: Run Auto-Discovery (Optional)
+
+Use `discover_services` to see what Grafema's built-in detection finds.
+Compare with your own findings from Steps 1-2. Note discrepancies —
+auto-discovery may miss services or misidentify entry points.
+
+## Step 4: Configure File Patterns
+
+The Rust orchestrator has a built-in analysis pipeline — no plugin
+configuration needed. Focus on:
+
+- **`include`** — glob patterns for source files to analyze
+  (e.g., `src/**/*.{ts,tsx,js,jsx}`)
+- **`exclude`** — patterns to skip (tests, generated code, dist)
+- **`services`** — for monorepos, explicit service definitions
+
+The minimal config generated by `grafema init` works for most projects.
+
+## Step 5: Write Configuration
+
+Edit `.grafema/config.yaml` directly. Minimal format:
+
+```yaml
+version: "0.3"
+root: ".."
+include:
+  - "src/**/*.{ts,tsx,js,jsx}"
+exclude:
+  - "**/*.test.*"
+  - "**/node_modules/**"
+  - "**/dist/**"
+```
+
+For monorepos, add services:
+
+```yaml
+services:
+  - name: "api"
+    path: "packages/api"
+    entryPoint: "src/index.ts"
+  - name: "web"
+    path: "packages/web"
+```
+
+Note: `root` is relative to `.grafema/` directory, so `".."` points to
+the project root.
+
+## Step 6: Verify
+
+Run `analyze_project` to build the graph. Then check:
+- `get_stats` — are node/edge counts reasonable for the project size?
+- `get_coverage` — are the expected files analyzed?
+
+If coverage is low or results are unexpected, iterate:
+revisit services, entry points, or include/exclude patterns.
+
+## Common Patterns
+
+### Monorepo with workspaces
+Look for `pnpm-workspace.yaml` or `workspaces` in root `package.json`.
+Each workspace package is typically a service. Use `read_project_structure`
+with depth=2 to see the package layout.
+
+### Legacy project with multiple entry points
+Look for `scripts` in `package.json`, `bin` field, or multiple files
+in `src/` that look like entry points (contain `app.listen()`,
+`createServer()`, `express()`).
+
+### Microservices with shared deployment
+Look for `docker-compose.yml`, Kubernetes configs, or similar
+deployment manifests that list services. Cross-reference with
+code directories.
+
+### Single-package project
+If there is only one `package.json` at the root and no monorepo
+structure, the project is likely a single service. The service path
+is `.` (root), and the entry point is determined from `package.json`.

package/dist/knowledge/KnowledgeBase.d.ts

@@ -0,0 +1,113 @@
+/**
+ * KnowledgeBase — in-memory index over git-tracked knowledge files.
+ *
+ * Scans knowledge/ directory, parses markdown files with YAML frontmatter,
+ * builds an in-memory index for fast lookups. All mutations also write to disk.
+ */
+import type { KBNode, KBNodeType, KBDecision, KBFact, KBEdge, KBStats, KBQueryFilter, ResolvedAddress, DanglingCodeRef } from './types.js';
+import type { ResolverBackend } from './SemanticAddressResolver.js';
+export declare class KnowledgeBase {
+    private knowledgeDir;
+    private nodes;
+    private edges;
+    private loaded;
+    private resolver;
+    constructor(knowledgeDir: string);
+    /**
+     * Wire up a code graph backend for resolving semantic addresses.
+     * Creates a SemanticAddressResolver that lazily resolves `relates_to`
+     * and `applies_to` addresses to current code node IDs.
+     */
+    setBackend(backend: ResolverBackend): void;
+    /**
+     * Bump the resolver's generation counter, marking all cached resolutions stale.
+     * Call after re-analysis so next resolve() re-queries the code graph.
+     */
+    invalidateResolutionCache(): void;
+    /**
+     * Resolve all code addresses in a node's relates_to (and applies_to for decisions).
+     * KB-internal addresses (kb:...) pass through without backend query.
+     * Returns empty array if no resolver is set.
+     */
+    resolveReferences(node: KBNode): Promise<ResolvedAddress[]>;
+    /**
+     * Find all KB nodes with code addresses that don't resolve to graph nodes.
+     * Returns pairs of (KB node ID, dangling address).
+     */
+    getDanglingCodeRefs(): Promise<DanglingCodeRef[]>;
+    /**
+     * Scan knowledge directory recursively, parse all .md files, build index.
+     * Malformed files are skipped with console.warn, don't crash.
+     * Missing directory succeeds with empty index.
+     */
+    load(): Promise<void>;
+    /**
+     * Get a node by its semantic ID.
+     */
+    getNode(id: string): KBNode | undefined;
+    /**
+     * Query nodes with filters. All filters are AND-combined.
+     * When include_dangling_only is true, only returns nodes with dangling code refs.
+     * Note: include_dangling_only requires a resolver backend; without one it returns empty.
+     */
+    queryNodes(filter: KBQueryFilter): Promise<KBNode[]>;
+    /**
+     * Find active decisions that apply to a given module/semantic address.
+     * Uses string includes matching on applies_to entries.
+     */
+    activeDecisionsFor(module: string): Promise<KBDecision[]>;
+    /**
+     * Add a new node to the knowledge base.
+     * Creates the .md file on disk and updates the in-memory index.
+     *
+     * @param params - Node properties. `id` and `filePath` are auto-generated.
+     * @returns The created node.
+     */
+    addNode(params: {
+        type: KBNodeType;
+        content: string;
+        slug?: string;
+        subtype?: string;
+        scope?: 'global' | 'project' | 'module';
+        projections?: string[];
+        source?: string;
+        relates_to?: string[];
+        status?: KBDecision['status'];
+        effective_from?: string;
+        applies_to?: string[];
+        confidence?: KBFact['confidence'];
+        task_id?: string;
+        session_path?: string;
+        produced?: string[];
+    }): Promise<KBNode>;
+    /**
+     * Supersede an existing fact with a new version.
+     * Creates new fact, updates old fact with superseded_by.
+     */
+    supersedeFact(oldId: string, newContent: string, newSlug?: string): Promise<{
+        old: KBFact;
+        new: KBFact;
+    }>;
+    /**
+     * Add an edge to the knowledge graph.
+     */
+    addEdge(edge: KBEdge): void;
+    /**
+     * Get edges, optionally filtered by node ID (from or to).
+     */
+    getEdges(nodeId?: string): KBEdge[];
+    /**
+     * Get statistics about the knowledge base.
+     * Includes dangling code references if a resolver backend is available.
+     */
+    getStats(): Promise<KBStats>;
+    /**
+     * Recursively scan directory for files with given extension.
+     */
+    private scanFiles;
+    /**
+     * Generate a slug from content (first line, simplified).
+     */
+    private generateSlug;
+}
+//# sourceMappingURL=KnowledgeBase.d.ts.map

package/dist/knowledge/KnowledgeBase.d.ts.map

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