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@ev3lynx/md-analyzer - npm Package Compare versions

Comparing version

0.1.4

0.1.6

+2

dist/cli/index.d.ts

		#!/usr/bin/env node
		export {};

+207

dist/cli/index.js

		#!/usr/bin/env node
		"use strict";
		var __createBinding = (this && this.__createBinding) \|\| (Object.create ? (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		var desc = Object.getOwnPropertyDescriptor(m, k);
		if (!desc \|\| ("get" in desc ? !m.__esModule : desc.writable \|\| desc.configurable)) {
		desc = { enumerable: true, get: function() { return m[k]; } };
		}
		Object.defineProperty(o, k2, desc);
		}) : (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		o[k2] = m[k];
		}));
		var __setModuleDefault = (this && this.__setModuleDefault) \|\| (Object.create ? (function(o, v) {
		Object.defineProperty(o, "default", { enumerable: true, value: v });
		}) : function(o, v) {
		o["default"] = v;
		});
		var __importStar = (this && this.__importStar) \|\| (function () {
		var ownKeys = function(o) {
		ownKeys = Object.getOwnPropertyNames \|\| function (o) {
		var ar = [];
		for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
		return ar;
		};
		return ownKeys(o);
		};
		return function (mod) {
		if (mod && mod.__esModule) return mod;
		var result = {};
		if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
		__setModuleDefault(result, mod);
		return result;
		};
		})();
		Object.defineProperty(exports, "__esModule", { value: true });
		const commander_1 = require("commander");
		const path = __importStar(require("path"));
		const fs = __importStar(require("fs"));
		const zod_1 = require("zod");
		const schema_js_1 = require("../core/schema.js");
		const config_js_1 = require("../utils/config.js");
		const analyzer_js_1 = require("../core/analyzer.js");
		const graph_js_1 = require("../core/graph.js");
		const search_js_1 = require("../core/search.js");
		const health_js_1 = require("../core/health.js");
		const session_js_1 = require("../core/session.js");
		const output_js_1 = require("./output.js");
		const pkgVersion = JSON.parse(fs.readFileSync(path.join(__dirname, '..', '..', 'package.json'), 'utf-8')).version;
		const program = new commander_1.Command();
		program
		.name('md-analyzer')
		.description('Markdown document analyzer for AI agents - extract metadata, headings, links, tables, tokens, formatting counts, and key points from .md files')
		.version(pkgVersion, '--version, -v', 'Show version number')
		.arguments('[directory]')
		.option('--json', 'Output as JSON')
		.option('--search <kw>', 'Search keyword in content')
		.option('--filter <k=v>', 'Filter by metadata field')
		.option('--rank', 'Rank results by relevance')
		.option('--graph', 'Document relationship graph')
		.option('--deps', 'Dependency graph (DAG order + levels)')
		.option('--orphans', 'Find unreferenced docs')
		.option('--backlinks <doc>', 'Find docs linking to <doc>')
		.option('--keypoints', 'Quick overview (single-shot)')
		.option('--lint-fragments', 'Fragment health check')
		.option('--session', 'Token budget report')
		.option('--budget <n>', 'Set token budget limit', parseInt, 100000)
		.option('--max-results <n>', 'Limit output', parseInt, 0)
		.addHelpText('after', `

		Examples:
		md-analyzer /path/to/docs --keypoints --json
		md-analyzer . --search "task" --rank --json
		md-analyzer . --session --budget 50000 --json
		md-analyzer . --orphans --json
		md-analyzer . --lint-fragments --json
		md-analyzer . --deps --json`);
		program.action(async (directory, options) => {
		const startTime = Date.now();
		let parsed;
		try {
		parsed = schema_js_1.CliOptions.parse({ directory, ...options });
		}
		catch (e) {
		if (e instanceof zod_1.z.ZodError) {
		console.error('Invalid arguments:');
		for (const issue of e.issues) {
		console.error(' ' + issue.path.join('.') + ': ' + issue.message);
		}
		}
		else {
		console.error('Unexpected error:', e instanceof Error ? e.message : e);
		}
		process.exit(1);
		}
		const configPath = (0, config_js_1.resolveConfigPath)();
		const config = (0, config_js_1.getTomlConfig)(configPath);
		const targetArg = parsed.directory \|\| process.env['MD_ANALYZER_DEFAULT_DIR'] \|\| config.default_directory \|\| process.cwd();
		let mdFiles = [];
		let scanErrors = [];
		try {
		const stat = fs.statSync(targetArg);
		if (stat.isFile()) {
		if (targetArg.endsWith('.md'))
		mdFiles = [targetArg];
		else {
		scanErrors.push('not_a_markdown_file: ' + targetArg);
		if (!parsed.json)
		console.log('Not a .md file: ' + targetArg + '\n');
		}
		}
		else if (stat.isDirectory()) {
		if (!parsed.json)
		console.log('Scanning: ' + targetArg + '\n');
		const scanned = (0, analyzer_js_1.scanMarkdownFiles)(targetArg);
		mdFiles = scanned.files;
		scanErrors = scanned.errors;
		if (!parsed.json) {
		console.log('Found ' + mdFiles.length + ' .md files\n');
		if (scanErrors.length > 0)
		console.log('Warnings: ' + scanErrors.length + ' directories skipped\n');
		}
		}
		else {
		scanErrors.push('unsupported_path_type: ' + targetArg);
		}
		}
		catch {
		scanErrors.push('path_not_found: ' + targetArg);
		}
		let results = await Promise.all(mdFiles.map(file => (0, analyzer_js_1.analyzeFileWithMicromark)(file).catch(() => (0, analyzer_js_1.analyzeFile)(file))));
		if (scanErrors.length > 0 && results.length > 0) {
		if (!results[0].stats.errors)
		results[0].stats.errors = [];
		results[0].stats.errors.push(...scanErrors);
		}
		if (parsed.filter && parsed.filter.includes('=')) {
		const [key, value] = parsed.filter.split('=');
		results = (0, search_js_1.filterByMetadata)(results, key, value);
		if (!parsed.json)
		console.log('Filtered by ' + key + '=' + value + ': ' + results.length + ' results\n');
		}
		if (parsed.search) {
		results = (0, search_js_1.searchContent)(results, parsed.search);
		if (!parsed.json)
		console.log('Search "' + parsed.search + '": ' + results.length + ' results\n');
		}
		if (parsed.rank && parsed.search) {
		results = (0, search_js_1.rankByRelevance)(results, parsed.search);
		if (!parsed.json)
		console.log('Ranked by relevance to "' + parsed.search + '"\n');
		}
		let limitedResults = results;
		if (parsed.maxResults > 0 && results.length > parsed.maxResults) {
		if (!parsed.json)
		console.log('Warning: Limiting output to ' + parsed.maxResults + ' of ' + results.length + ' results\n');
		limitedResults = results.slice(0, parsed.maxResults);
		}
		const session = (0, session_js_1.loadSession)();
		const updatedSession = (0, session_js_1.updateSessionStats)(results, session);
		(0, session_js_1.saveSession)(updatedSession);
		const tokensThisCall = results.reduce((sum, r) => sum + r.stats.tokens, 0);
		if (parsed.session)
		console.log(JSON.stringify((0, session_js_1.getTokenBudgetReport)(updatedSession, parsed.budget), null, 2));
		else if (parsed.keypoints)
		console.log(JSON.stringify(limitedResults.map(doc => (0, output_js_1.extractKeyPoints)(doc)), null, 2));
		else if (parsed.lintFragments)
		console.log(JSON.stringify((0, health_js_1.getFragmentHealth)(limitedResults), null, 2));
		else if (parsed.deps) {
		const graph = (0, graph_js_1.buildGraph)(limitedResults);
		console.log(JSON.stringify({ nodes: Object.keys(graph.nodes), edges: graph.edges, tokensThisCall }, null, 2));
		}
		else if (parsed.orphans) {
		const orphans = (0, graph_js_1.findOrphans)((0, graph_js_1.buildGraph)(limitedResults));
		console.log(JSON.stringify({ orphans, count: orphans.length, tokensThisCall }, null, 2));
		}
		else if (parsed.backlinks) {
		const backlinks = (0, graph_js_1.findBacklinks)(limitedResults, parsed.backlinks);
		console.log(JSON.stringify({ target: parsed.backlinks, backlinks, count: backlinks.length, tokensThisCall }, null, 2));
		}
		else if (parsed.graph)
		console.log(JSON.stringify((0, graph_js_1.buildGraph)(limitedResults), null, 2));
		else {
		if (!parsed.json) {
		console.log('\nTokens this call: ' + tokensThisCall);
		console.log('Total session tokens: ' + updatedSession.totalTokens + '\n');
		}
		console.log(JSON.stringify(limitedResults, null, 2));
		}
		const usedFlags = process.argv.slice(2).filter(a => a.startsWith('--')).map(a => a.replace(/=.*/, ''));
		const mode = parsed.deps ? 'deps' : parsed.lintFragments ? 'lint-fragments' : parsed.session ? 'session' : parsed.keypoints ? 'keypoints' : parsed.orphans ? 'orphans' : parsed.backlinks ? 'backlinks' : parsed.graph ? 'graph' : parsed.search ? 'search' : 'default';
		(0, output_js_1.writeRunLog)({
		timestamp: new Date().toISOString(),
		sessionId: updatedSession.sessionId,
		directory: targetArg,
		flags: usedFlags,
		filesFound: mdFiles.length,
		filesProcessed: results.length,
		tokensThisCall,
		totalSessionTokens: updatedSession.totalTokens,
		errors: scanErrors,
		durationMs: Date.now() - startTime,
		mode
		});
		});
		program.parse();
		//# sourceMappingURL=index.js.map

+1

dist/cli/index.js.map

+3

dist/cli/output.d.ts

		import type { AnalysisResult, RunLog } from '../types/index.js';
		export declare function extractKeyPoints(doc: AnalysisResult): object;
		export declare function writeRunLog(log: RunLog): void;

+71

dist/cli/output.js

		"use strict";
		var __createBinding = (this && this.__createBinding) \|\| (Object.create ? (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		var desc = Object.getOwnPropertyDescriptor(m, k);
		if (!desc \|\| ("get" in desc ? !m.__esModule : desc.writable \|\| desc.configurable)) {
		desc = { enumerable: true, get: function() { return m[k]; } };
		}
		Object.defineProperty(o, k2, desc);
		}) : (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		o[k2] = m[k];
		}));
		var __setModuleDefault = (this && this.__setModuleDefault) \|\| (Object.create ? (function(o, v) {
		Object.defineProperty(o, "default", { enumerable: true, value: v });
		}) : function(o, v) {
		o["default"] = v;
		});
		var __importStar = (this && this.__importStar) \|\| (function () {
		var ownKeys = function(o) {
		ownKeys = Object.getOwnPropertyNames \|\| function (o) {
		var ar = [];
		for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
		return ar;
		};
		return ownKeys(o);
		};
		return function (mod) {
		if (mod && mod.__esModule) return mod;
		var result = {};
		if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
		__setModuleDefault(result, mod);
		return result;
		};
		})();
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.extractKeyPoints = extractKeyPoints;
		exports.writeRunLog = writeRunLog;
		const fs = __importStar(require("fs"));
		const path = __importStar(require("path"));
		const constants_js_1 = require("../utils/constants.js");
		function extractKeyPoints(doc) {
		return {
		fileName: doc.fileName, title: doc.headings[0]?.text \|\| doc.fileName, level: doc.headings[0]?.level \|\| 1,
		summary: {
		totalHeadings: doc.stats.totalHeadings, totalLinks: doc.stats.totalLinks, totalWikilinks: doc.stats.totalWikilinks,
		totalTokens: doc.stats.tokens, wordCount: doc.stats.wordCount,
		boldCount: doc.stats.boldCount ?? 0, italicCount: doc.stats.italicCount ?? 0, bulletCount: doc.stats.bulletCount ?? 0
		},
		keyHeadings: doc.headings.slice(0, 10).map((h, i) => ({
		level: h.level, text: h.text, line: h.line,
		tokens: doc.sections?.[i]?.tokens ?? 0
		})),
		importantLinks: doc.links.filter(l => !l.isInternal).slice(0, 3).map(l => ({ text: l.text, url: l.url })),
		internalReferences: doc.links.filter(l => l.isInternal && l.fileName).slice(0, 5).map(l => l.fileName),
		metadata: doc.metadata, readingTime: Math.ceil(doc.stats.wordCount / 200) + ' min'
		};
		}
		function writeRunLog(log) {
		try {
		if (!fs.existsSync(constants_js_1.LOG_DIR))
		fs.mkdirSync(constants_js_1.LOG_DIR, { recursive: true });
		const logFile = path.join(constants_js_1.LOG_DIR, `${log.sessionId}.json`);
		const existing = fs.existsSync(logFile) ? JSON.parse(fs.readFileSync(logFile, 'utf-8')) : [];
		existing.push(log);
		fs.writeFileSync(logFile, JSON.stringify(existing, null, 2));
		}
		catch (e) {
		console.error('run_log_write_error:', e instanceof Error ? e.message : e);
		}
		}
		//# sourceMappingURL=output.js.map

+1

dist/cli/output.js.map

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+7

dist/core/analyzer.d.ts

		import type { AnalysisResult } from '../types/index.js';
		export declare function scanMarkdownFiles(dir: string): {
		files: string[];
		errors: string[];
		};
		export declare function analyzeFile(filePath: string): AnalysisResult;
		export declare function analyzeFileWithMicromark(filePath: string): Promise<AnalysisResult>;

+202

dist/core/analyzer.js

		"use strict";
		var __createBinding = (this && this.__createBinding) \|\| (Object.create ? (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		var desc = Object.getOwnPropertyDescriptor(m, k);
		if (!desc \|\| ("get" in desc ? !m.__esModule : desc.writable \|\| desc.configurable)) {
		desc = { enumerable: true, get: function() { return m[k]; } };
		}
		Object.defineProperty(o, k2, desc);
		}) : (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		o[k2] = m[k];
		}));
		var __setModuleDefault = (this && this.__setModuleDefault) \|\| (Object.create ? (function(o, v) {
		Object.defineProperty(o, "default", { enumerable: true, value: v });
		}) : function(o, v) {
		o["default"] = v;
		});
		var __importStar = (this && this.__importStar) \|\| (function () {
		var ownKeys = function(o) {
		ownKeys = Object.getOwnPropertyNames \|\| function (o) {
		var ar = [];
		for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
		return ar;
		};
		return ownKeys(o);
		};
		return function (mod) {
		if (mod && mod.__esModule) return mod;
		var result = {};
		if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
		__setModuleDefault(result, mod);
		return result;
		};
		})();
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.scanMarkdownFiles = scanMarkdownFiles;
		exports.analyzeFile = analyzeFile;
		exports.analyzeFileWithMicromark = analyzeFileWithMicromark;
		const fs = __importStar(require("fs"));
		const path = __importStar(require("path"));
		const js_tiktoken_1 = require("js-tiktoken");
		const constants_js_1 = require("../utils/constants.js");
		const extractors_js_1 = require("./extractors.js");
		const counters_js_1 = require("./counters.js");
		const micromark_walk_js_1 = require("./micromark-walk.js");
		const hybrid_merge_js_1 = require("./hybrid-merge.js");
		function scanMarkdownFiles(dir) {
		const files = [], errors = [];
		function walk(dir) {
		let entries;
		try {
		entries = fs.readdirSync(dir, { withFileTypes: true });
		}
		catch (e) {
		errors.push(`permission_denied: ${dir}`);
		console.error('scan_error:', e instanceof Error ? e.message : e);
		return;
		}
		for (const entry of entries) {
		if (entry.name.startsWith('.') \|\| constants_js_1.SKIP_DIRS.has(entry.name))
		continue;
		const fullPath = path.join(dir, entry.name);
		try {
		if (entry.isDirectory())
		walk(fullPath);
		else if (entry.isFile() && entry.name.endsWith('.md'))
		files.push(fullPath);
		}
		catch (e) {
		errors.push(`access_error: ${fullPath}`);
		console.error('access_error:', e instanceof Error ? e.message : e);
		}
		}
		}
		try {
		walk(dir);
		}
		catch (e) {
		errors.push(`scan_error: ${e instanceof Error ? e.message : 'unknown'}`);
		console.error('walk_error:', e instanceof Error ? e.message : e);
		}
		return { files, errors };
		}
		function computeSections(content, headings) {
		const bodyLines = content.split('\n');
		return headings.map((h, i) => {
		const startIdx = h.line - 1;
		const endIdx = i + 1 < headings.length ? headings[i + 1].line - 1 : bodyLines.length;
		const sectionText = bodyLines.slice(startIdx, endIdx).join('\n');
		let tokens = 0;
		try {
		tokens = (0, js_tiktoken_1.encodingForModel)('gpt-4').encode(sectionText).length;
		}
		catch (e) {
		console.error('section_token_fallback:', e instanceof Error ? e.message : e);
		tokens = Math.ceil(sectionText.length / 4);
		}
		return { line: h.line, tokens };
		});
		}
		function buildBaseResult(filePath, content, errors) {
		const { metadata, content: markdownContent } = (0, extractors_js_1.extractFrontmatter)(content);
		const fragmentMeta = (0, extractors_js_1.extractFragmentMeta)(metadata);
		const headings = (0, extractors_js_1.extractHeadings)(markdownContent);
		const links = (0, extractors_js_1.extractLinks)(markdownContent);
		const wikilinks = (0, extractors_js_1.extractWikilinks)(markdownContent);
		const tables = (0, extractors_js_1.extractTables)(markdownContent);
		const counts = (0, counters_js_1.countStats)(markdownContent);
		if (counts.tokens === 0 && !errors.includes('token_count_fallback')) {
		errors.push('token_count_fallback: tiktoken unavailable');
		}
		const sections = computeSections(markdownContent, headings);
		const fileName = path.basename(filePath, '.md');
		return {
		file: filePath, fileName, metadata, fragmentMeta, headings, sections, links, wikilinks, tables,
		stats: {
		totalHeadings: headings.length, totalLinks: links.length,
		internalLinks: links.filter(l => l.isInternal).length,
		externalLinks: links.filter(l => !l.isInternal).length,
		totalWikilinks: wikilinks.length, wordCount: counts.wordCount,
		charCount: counts.charCount, lineCount: counts.lineCount,
		codeBlocks: counts.codeBlocks, tables: tables.length,
		tokens: counts.tokens, errors: errors.length > 0 ? errors : undefined
		}
		};
		}
		function analyzeFile(filePath) {
		const errors = [];
		let content = '';
		try {
		content = fs.readFileSync(filePath, 'utf-8');
		}
		catch (e) {
		errors.push(`file_read_error: ${e instanceof Error ? e.message : 'unknown'}`);
		return {
		file: filePath, fileName: path.basename(filePath, '.md'), metadata: null, fragmentMeta: null,
		headings: [], sections: [], links: [], wikilinks: [], tables: [],
		stats: { totalHeadings: 0, totalLinks: 0, internalLinks: 0, externalLinks: 0, totalWikilinks: 0, wordCount: 0, charCount: 0, lineCount: 0, codeBlocks: 0, tables: 0, tokens: 0, errors }
		};
		}
		return buildBaseResult(filePath, content, errors);
		}
		async function analyzeFileWithMicromark(filePath) {
		const errors = [];
		let content = '';
		try {
		content = fs.readFileSync(filePath, 'utf-8');
		}
		catch (e) {
		errors.push(`file_read_error: ${e instanceof Error ? e.message : 'unknown'}`);
		return {
		file: filePath, fileName: path.basename(filePath, '.md'), metadata: null, fragmentMeta: null,
		headings: [], sections: [], links: [], wikilinks: [], tables: [],
		stats: { totalHeadings: 0, totalLinks: 0, internalLinks: 0, externalLinks: 0, totalWikilinks: 0, wordCount: 0, charCount: 0, lineCount: 0, codeBlocks: 0, tables: 0, tokens: 0, errors }
		};
		}
		const { content: markdownContent } = (0, extractors_js_1.extractFrontmatter)(content);
		if (!(await (0, micromark_walk_js_1.isMicromarkAvailable)())) {
		errors.push('micromark_unavailable');
		return buildBaseResult(filePath, content, errors);
		}
		try {
		const [regions, mmLinks, mmHeadings, mmTables, mmFormatting] = await Promise.all([
		(0, micromark_walk_js_1.walkCodeBlocks)(markdownContent),
		(0, micromark_walk_js_1.walkLinks)(markdownContent),
		(0, micromark_walk_js_1.walkHeadings)(markdownContent),
		(0, micromark_walk_js_1.walkTables)(markdownContent),
		(0, micromark_walk_js_1.walkFormatting)(markdownContent)
		]);
		if (mmLinks === null)
		errors.push('walkLinks_failed');
		if (mmHeadings === null)
		errors.push('walkHeadings_failed');
		if (mmTables === null)
		errors.push('walkTables_failed');
		if (mmFormatting === null)
		errors.push('walkFormatting_failed');
		const safeRegions = regions ?? [];
		const result = buildBaseResult(filePath, content, errors);
		result.links = (0, hybrid_merge_js_1.filterMicromarkLinks)(mmLinks ?? [], safeRegions);
		result.stats.totalLinks = result.links.length;
		result.stats.internalLinks = result.links.filter(l => l.isInternal).length;
		result.stats.externalLinks = result.links.filter(l => !l.isInternal).length;
		result.headings = (0, hybrid_merge_js_1.filterMicromarkHeadings)(mmHeadings ?? [], safeRegions, markdownContent);
		result.sections = computeSections(markdownContent, result.headings);
		result.stats.totalHeadings = result.headings.length;
		result.tables = (0, hybrid_merge_js_1.filterMicromarkTables)(mmTables ?? [], safeRegions, markdownContent);
		result.stats.tables = result.tables.length;
		result.stats.codeBlocks = (0, hybrid_merge_js_1.countCodeBlocks)(regions);
		const fmt = (0, hybrid_merge_js_1.countFormatting)(mmFormatting, markdownContent, safeRegions);
		result.stats.boldCount = fmt.boldCount;
		result.stats.italicCount = fmt.italicCount;
		result.stats.bulletCount = fmt.bulletCount;
		result.stats.errors = errors.length > 0 ? errors : undefined;
		return result;
		}
		catch (e) {
		errors.push(`micromark_pipeline_failed: ${e instanceof Error ? e.message : 'unknown'}`);
		return buildBaseResult(filePath, content, errors);
		}
		}
		//# sourceMappingURL=analyzer.js.map

+1

dist/core/analyzer.js.map

+7

dist/core/counters.d.ts

		export declare function countStats(content: string): {
		wordCount: number;
		charCount: number;
		lineCount: number;
		codeBlocks: number;
		tokens: number;
		};

+20

dist/core/counters.js

		"use strict";
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.countStats = countStats;
		const js_tiktoken_1 = require("js-tiktoken");
		function countStats(content) {
		const wordCount = content.split(/\s+/).filter(w => w.length > 0).length;
		const charCount = content.length;
		const lineCount = content.split('\n').length;
		const codeBlocks = (content.match(/```[\s\S]*?```/g) \|\| []).length;
		let tokens = 0;
		try {
		tokens = (0, js_tiktoken_1.encodingForModel)('gpt-4').encode(content).length;
		}
		catch (e) {
		console.error('token_count_fallback: tiktoken unavailable, using estimate:', e instanceof Error ? e.message : e);
		tokens = Math.ceil(charCount / 4);
		}
		return { wordCount, charCount, lineCount, codeBlocks, tokens };
		}
		//# sourceMappingURL=counters.js.map

+1

dist/core/counters.js.map

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+13

dist/core/extractors.d.ts

		import type { Link, Wikilink, Heading, Table, FragmentMeta } from '../types/index.js';
		export declare function extractFrontmatter(content: string): {
		metadata: Record<string, unknown> \| null;
		content: string;
		};
		export declare function extractFragmentMeta(metadata: Record<string, unknown> \| null): FragmentMeta \| null;
		/** @deprecated Use walkHeadings from micromark-walk.js instead (token-accurate) */
		export declare function extractHeadings(content: string): Heading[];
		/** @deprecated Use walkLinks from micromark-walk.js instead (token-accurate) */
		export declare function extractLinks(content: string): Link[];
		export declare function extractWikilinks(content: string): Wikilink[];
		/** @deprecated Use walkTables from micromark-walk.js instead (uses GFM spec) */
		export declare function extractTables(content: string): Table[];

+131

dist/core/extractors.js

		"use strict";
		var __createBinding = (this && this.__createBinding) \|\| (Object.create ? (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		var desc = Object.getOwnPropertyDescriptor(m, k);
		if (!desc \|\| ("get" in desc ? !m.__esModule : desc.writable \|\| desc.configurable)) {
		desc = { enumerable: true, get: function() { return m[k]; } };
		}
		Object.defineProperty(o, k2, desc);
		}) : (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		o[k2] = m[k];
		}));
		var __setModuleDefault = (this && this.__setModuleDefault) \|\| (Object.create ? (function(o, v) {
		Object.defineProperty(o, "default", { enumerable: true, value: v });
		}) : function(o, v) {
		o["default"] = v;
		});
		var __importStar = (this && this.__importStar) \|\| (function () {
		var ownKeys = function(o) {
		ownKeys = Object.getOwnPropertyNames \|\| function (o) {
		var ar = [];
		for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
		return ar;
		};
		return ownKeys(o);
		};
		return function (mod) {
		if (mod && mod.__esModule) return mod;
		var result = {};
		if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
		__setModuleDefault(result, mod);
		return result;
		};
		})();
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.extractFrontmatter = extractFrontmatter;
		exports.extractFragmentMeta = extractFragmentMeta;
		exports.extractHeadings = extractHeadings;
		exports.extractLinks = extractLinks;
		exports.extractWikilinks = extractWikilinks;
		exports.extractTables = extractTables;
		const path = __importStar(require("path"));
		const yaml = __importStar(require("js-yaml"));
		function extractFrontmatter(content) {
		const frontmatterRegex = /^---\s\n([\s\S]?)\n---\s*\n/;
		const match = content.match(frontmatterRegex);
		if (!match)
		return { metadata: null, content };
		try {
		const parsed = yaml.load(match[1]);
		const metadata = parsed && typeof parsed === 'object' ? parsed : null;
		return { metadata, content: content.substring(match[0].length) };
		}
		catch (e) {
		console.error('frontmatter_parse_error:', e instanceof Error ? e.message : e);
		return { metadata: null, content };
		}
		}
		function extractFragmentMeta(metadata) {
		if (!metadata)
		return null;
		const dependsRaw = metadata.depends_on;
		const depends = Array.isArray(dependsRaw) ? dependsRaw.map(String) : (typeof dependsRaw === 'string' ? [dependsRaw] : []);
		const tags = Array.isArray(metadata.tags) ? metadata.tags.map(String) : (typeof metadata.tags === 'string' ? [metadata.tags] : []);
		return {
		title: String(metadata.title \|\| ''),
		description: metadata.description ? String(metadata.description) : null,
		tags,
		depends_on: depends,
		status: metadata.status ? String(metadata.status) : null,
		source: metadata.source ? String(metadata.source) : null,
		order: metadata.order != null ? Number(metadata.order) : null,
		date_iso: metadata.date_iso ? String(metadata.date_iso) : null,
		};
		}
		/** @deprecated Use walkHeadings from micromark-walk.js instead (token-accurate) */
		function extractHeadings(content) {
		const headings = [];
		const headingRegex = /^(#{1,6})\s+(.+)$/gm;
		let match;
		while ((match = headingRegex.exec(content)) !== null) {
		const line = content.substring(0, match.index).split('\n').length;
		headings.push({ level: match[1].length, text: match[2].trim(), line });
		}
		return headings;
		}
		/** @deprecated Use walkLinks from micromark-walk.js instead (token-accurate) */
		function extractLinks(content) {
		const links = [];
		const linkRegex = /\[([^\]]+)\]$([^)]+)$/g;
		let match;
		while ((match = linkRegex.exec(content)) !== null) {
		const url = match[2].trim();
		const isInternal = url.startsWith('#') \|\| (!url.startsWith('http') && !url.startsWith('//'));
		let fileName = null;
		if (isInternal && !url.startsWith('#')) {
		const baseName = path.basename(url, '.md');
		if (baseName && baseName !== url)
		fileName = baseName;
		}
		links.push({ text: match[1].trim(), url, isInternal, fileName });
		}
		return links;
		}
		function extractWikilinks(content) {
		const wikilinks = [];
		const wikiRegex = /\[\[([^\]\|]+)(?:\\|([^\]]+))?\]\]/g;
		let match;
		while ((match = wikiRegex.exec(content)) !== null) {
		wikilinks.push({ target: match[1].trim(), display: match[2]?.trim() \|\| null });
		}
		return wikilinks;
		}
		/** @deprecated Use walkTables from micromark-walk.js instead (uses GFM spec) */
		function extractTables(content) {
		const tables = [];
		const tableRegex = /\\|(.+)\\|\n\\|[-:\s\|]+\\|\n((?:\\|.+\\|\n?)+)/g;
		let match;
		while ((match = tableRegex.exec(content)) !== null) {
		const headers = match[1].split('\|').map(h => h.trim()).filter(h => h);
		const rows = [];
		match[2].trim().split('\n').forEach(row => {
		const cells = row.split('\|').map(c => c.trim()).filter(c => c);
		if (cells.length > 0)
		rows.push(cells);
		});
		tables.push({ headers, rows });
		}
		return tables;
		}
		//# sourceMappingURL=extractors.js.map

+1

dist/core/extractors.js.map

+4

dist/core/graph.d.ts

		import type { AnalysisResult, Graph } from '../types/index.js';
		export declare function buildGraph(results: AnalysisResult[]): Graph;
		export declare function findOrphans(graph: Graph, excludeOrphansWithDeps?: Set<string>): string[];
		export declare function findBacklinks(results: AnalysisResult[], targetFileName: string): string[];

+65

dist/core/graph.js

		"use strict";
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.buildGraph = buildGraph;
		exports.findOrphans = findOrphans;
		exports.findBacklinks = findBacklinks;
		function addEdge(graph, edges, source, target, type) {
		if (!graph[source])
		graph[source] = { inbound: [], outbound: [] };
		if (!graph[target])
		graph[target] = { inbound: [], outbound: [] };
		if (!graph[source].outbound.includes(target))
		graph[source].outbound.push(target);
		if (!graph[target].inbound.includes(source))
		graph[target].inbound.push(source);
		edges.push({ source, target, type });
		}
		function buildGraph(results) {
		const graph = {}, edges = [];
		results.forEach(doc => {
		const source = doc.fileName;
		if (!graph[source])
		graph[source] = { inbound: [], outbound: [] };
		doc.links.forEach(link => {
		if (link.isInternal && link.fileName)
		addEdge(graph, edges, source, link.fileName, 'link');
		});
		doc.wikilinks.forEach(w => {
		const slug = w.target.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+\|-+$/g, '');
		if (slug !== source && results.some(r => r.fileName === slug))
		addEdge(graph, edges, source, slug, 'wikilink');
		});
		if (doc.fragmentMeta) {
		doc.fragmentMeta.depends_on.forEach(dep => {
		const depName = dep.replace(/\.md$/, '');
		if (depName !== source && results.some(r => r.fileName === depName))
		addEdge(graph, edges, source, depName, 'depends_on');
		});
		}
		});
		return { nodes: graph, edges };
		}
		function findOrphans(graph, excludeOrphansWithDeps) {
		return Object.keys(graph.nodes).filter(node => {
		if (excludeOrphansWithDeps?.has(node))
		return false;
		return graph.nodes[node].inbound.length === 0 && graph.nodes[node].outbound.length === 0;
		});
		}
		function findBacklinks(results, targetFileName) {
		const backlinks = [];
		results.forEach(doc => {
		doc.links.forEach(link => {
		if (link.isInternal && link.fileName === targetFileName && !backlinks.includes(doc.fileName)) {
		backlinks.push(doc.fileName);
		}
		});
		doc.wikilinks.forEach(w => {
		const slug = w.target.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+\|-+$/g, '');
		if (slug === targetFileName && !backlinks.includes(doc.fileName))
		backlinks.push(doc.fileName);
		});
		});
		return backlinks;
		}
		//# sourceMappingURL=graph.js.map

+1

dist/core/graph.js.map

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+2

dist/core/health.d.ts

		import type { AnalysisResult } from '../types/index.js';
		export declare function getFragmentHealth(results: AnalysisResult[]): object;

+31

dist/core/health.js

		"use strict";
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.getFragmentHealth = getFragmentHealth;
		function getFragmentHealth(results) {
		const total = results.length;
		const withFrontmatter = results.filter(r => r.fragmentMeta).length;
		const withDeps = results.filter(r => r.fragmentMeta && r.fragmentMeta.depends_on.length > 0).length;
		const withWikilinks = results.filter(r => r.stats.totalWikilinks > 0).length;
		const withStatus = results.filter(r => r.fragmentMeta && r.fragmentMeta.status).length;
		const withDescription = results.filter(r => r.fragmentMeta && r.fragmentMeta.description).length;
		const withSource = results.filter(r => r.fragmentMeta && r.fragmentMeta.source).length;
		const noTitle = results.filter(r => r.fragmentMeta && !r.fragmentMeta.title).length;
		const issues = [];
		for (const r of results) {
		const fileIssues = [];
		if (!r.fragmentMeta)
		fileIssues.push('no_frontmatter');
		else {
		if (!r.fragmentMeta.title)
		fileIssues.push('empty_title');
		if (!r.fragmentMeta.source)
		fileIssues.push('no_source');
		if (r.fragmentMeta.depends_on.length === 0 && r.stats.totalWikilinks > 0)
		fileIssues.push('wikilinks_no_depends_on');
		}
		if (fileIssues.length > 0)
		issues.push({ file: r.fileName, issues: fileIssues });
		}
		return { total, withFrontmatter, withDeps, withWikilinks, withStatus, withDescription, withSource, noTitle, filesWithIssues: issues.length, issues };
		}
		//# sourceMappingURL=health.js.map

+1

dist/core/health.js.map

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+11

dist/core/hybrid-merge.d.ts

		import type { CodeBlockRegion, FormattingCounts, MicromarkLink } from './micromark-walk.js';
		import type { Link, Heading, Table } from '../types/index.js';
		export declare function filterMicromarkLinks(links: MicromarkLink[], regions: CodeBlockRegion[]): Link[];
		export declare function filterMicromarkHeadings(headings: Heading[], regions: CodeBlockRegion[], content: string): Heading[];
		export declare function filterMicromarkTables(tables: Table[], regions: CodeBlockRegion[], content: string): Table[];
		export declare function countCodeBlocks(regions: CodeBlockRegion[] \| null): number;
		export declare function countFormatting(counts: FormattingCounts \| null, content: string, regions: CodeBlockRegion[]): {
		boldCount: number;
		italicCount: number;
		bulletCount: number;
		};

+122

dist/core/hybrid-merge.js

		"use strict";
		var __createBinding = (this && this.__createBinding) \|\| (Object.create ? (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		var desc = Object.getOwnPropertyDescriptor(m, k);
		if (!desc \|\| ("get" in desc ? !m.__esModule : desc.writable \|\| desc.configurable)) {
		desc = { enumerable: true, get: function() { return m[k]; } };
		}
		Object.defineProperty(o, k2, desc);
		}) : (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		o[k2] = m[k];
		}));
		var __setModuleDefault = (this && this.__setModuleDefault) \|\| (Object.create ? (function(o, v) {
		Object.defineProperty(o, "default", { enumerable: true, value: v });
		}) : function(o, v) {
		o["default"] = v;
		});
		var __importStar = (this && this.__importStar) \|\| (function () {
		var ownKeys = function(o) {
		ownKeys = Object.getOwnPropertyNames \|\| function (o) {
		var ar = [];
		for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
		return ar;
		};
		return ownKeys(o);
		};
		return function (mod) {
		if (mod && mod.__esModule) return mod;
		var result = {};
		if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
		__setModuleDefault(result, mod);
		return result;
		};
		})();
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.filterMicromarkLinks = filterMicromarkLinks;
		exports.filterMicromarkHeadings = filterMicromarkHeadings;
		exports.filterMicromarkTables = filterMicromarkTables;
		exports.countCodeBlocks = countCodeBlocks;
		exports.countFormatting = countFormatting;
		const path = __importStar(require("path"));
		function isInsideBlock(offset, regions) {
		if (regions.length === 0)
		return false;
		return regions.some(r => offset >= r.start && offset < r.end);
		}
		function filterMicromarkLinks(links, regions) {
		if (!links \|\| links.length === 0)
		return [];
		return links
		.filter(ml => {
		if (regions.length === 0)
		return true;
		return !isInsideBlock(ml.start, regions);
		})
		.map(ml => ({
		text: ml.text,
		url: ml.url,
		isInternal: ml.url.startsWith('#') \|\| (!ml.url.startsWith('http') && !ml.url.startsWith('//')),
		fileName: (() => {
		if (!ml.url.startsWith('#') && !ml.url.startsWith('http') && !ml.url.startsWith('//')) {
		const baseName = path.basename(ml.url, '.md');
		if (baseName && baseName !== ml.url)
		return baseName;
		}
		return null;
		})(),
		isImage: ml.isImage \|\| undefined
		}));
		}
		function filterMicromarkHeadings(headings, regions, content) {
		if (!headings \|\| headings.length === 0)
		return [];
		if (regions.length === 0)
		return headings;
		return headings.filter(h => {
		const idx = content.indexOf(h.text);
		return idx === -1 \|\| !isInsideBlock(idx, regions);
		});
		}
		function filterMicromarkTables(tables, regions, content) {
		if (!tables \|\| tables.length === 0)
		return [];
		if (regions.length === 0)
		return tables;
		return tables.filter(t => {
		const idx = content.indexOf(t.headers.join('\|'));
		return idx === -1 \|\| !isInsideBlock(idx, regions);
		});
		}
		function countCodeBlocks(regions) {
		return regions ? regions.length : -1;
		}
		function isInsideAnyBlock(offset, regions) {
		return regions.some(r => offset >= r.start && offset < r.end);
		}
		function countFormatting(counts, content, regions) {
		if (!counts)
		return { boldCount: 0, italicCount: 0, bulletCount: 0 };
		if (regions.length === 0) {
		return {
		boldCount: counts.bold + counts.boldItalic,
		italicCount: counts.italic,
		bulletCount: counts.bullet
		};
		}
		const boldItalicRe = /\\\(.+?)\\\/g;
		const boldRe = /(?<!\)\\(?!\)(.+?)\\/g;
		const italicRe = /(?<!\)\(?!\)(.+?)(?<!\)\(?!\)/g;
		const bulletRe = /^[ \t][-+][ \t]/gm;
		const isInCode = (offset) => isInsideAnyBlock(offset, regions);
		const boldItalicCount = [...content.matchAll(boldItalicRe)].filter(m => !isInCode(m.index)).length;
		const boldCount = [...content.matchAll(boldRe)].filter(m => !isInCode(m.index)).length;
		const italicCount = [...content.matchAll(italicRe)].filter(m => !isInCode(m.index)).length;
		const bulletCount = [...content.matchAll(bulletRe)].filter(m => !isInCode(m.index)).length;
		return {
		boldCount: boldCount + boldItalicCount,
		italicCount,
		bulletCount
		};
		}
		//# sourceMappingURL=hybrid-merge.js.map

+1

dist/core/hybrid-merge.js.map

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+26

dist/core/micromark-walk.d.ts

		export interface CodeBlockRegion {
		start: number;
		end: number;
		}
		export interface FormattingCounts {
		bold: number;
		italic: number;
		boldItalic: number;
		bullet: number;
		}
		export interface MicromarkLink {
		text: string;
		url: string;
		start: number;
		end: number;
		isImage: boolean;
		isAutolink: boolean;
		isReference: boolean;
		}
		import type { Heading, Table } from '../types/index.js';
		export declare function isMicromarkAvailable(): Promise<boolean>;
		export declare function walkCodeBlocks(content: string): Promise<CodeBlockRegion[] \| null>;
		export declare function walkLinks(content: string): Promise<MicromarkLink[] \| null>;
		export declare function walkHeadings(content: string): Promise<Heading[] \| null>;
		export declare function walkFormatting(content: string): Promise<FormattingCounts \| null>;
		export declare function walkTables(content: string): Promise<Table[] \| null>;

+323

dist/core/micromark-walk.js

		"use strict";
		var __createBinding = (this && this.__createBinding) \|\| (Object.create ? (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		var desc = Object.getOwnPropertyDescriptor(m, k);
		if (!desc \|\| ("get" in desc ? !m.__esModule : desc.writable \|\| desc.configurable)) {
		desc = { enumerable: true, get: function() { return m[k]; } };
		}
		Object.defineProperty(o, k2, desc);
		}) : (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		o[k2] = m[k];
		}));
		var __setModuleDefault = (this && this.__setModuleDefault) \|\| (Object.create ? (function(o, v) {
		Object.defineProperty(o, "default", { enumerable: true, value: v });
		}) : function(o, v) {
		o["default"] = v;
		});
		var __importStar = (this && this.__importStar) \|\| (function () {
		var ownKeys = function(o) {
		ownKeys = Object.getOwnPropertyNames \|\| function (o) {
		var ar = [];
		for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
		return ar;
		};
		return ownKeys(o);
		};
		return function (mod) {
		if (mod && mod.__esModule) return mod;
		var result = {};
		if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
		__setModuleDefault(result, mod);
		return result;
		};
		})();
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.isMicromarkAvailable = isMicromarkAvailable;
		exports.walkCodeBlocks = walkCodeBlocks;
		exports.walkLinks = walkLinks;
		exports.walkHeadings = walkHeadings;
		exports.walkFormatting = walkFormatting;
		exports.walkTables = walkTables;
		let micromarkModule = null;
		async function getMicromark() {
		if (micromarkModule === null) {
		try {
		micromarkModule = await Promise.resolve().then(() => __importStar(require('micromark')));
		}
		catch {
		micromarkModule = false;
		}
		}
		return micromarkModule;
		}
		async function isMicromarkAvailable() {
		const mm = await getMicromark();
		return mm !== false;
		}
		function parseEvents(content, extensions) {
		const mm = micromarkModule;
		if (!mm)
		throw new Error('micromark not loaded');
		if (!content)
		return [];
		const opts = extensions && extensions.length > 0 ? { extensions } : {};
		return mm.postprocess(mm.parse(opts).document().write(mm.preprocess()(content, 'utf-8', true)));
		}
		async function walkCodeBlocks(content) {
		const mm = await getMicromark();
		if (!mm)
		return null;
		try {
		const events = parseEvents(content);
		const regions = [];
		let depth = 0;
		let currentStart = 0;
		for (const ev of events) {
		const token = ev[1];
		if (token.type === 'codeFenced' \|\| token.type === 'codeIndented') {
		if (ev[0] === 'enter') {
		if (depth === 0)
		currentStart = token.start.offset;
		depth++;
		}
		else {
		depth--;
		if (depth === 0 && token.end) {
		regions.push({ start: currentStart, end: token.end.offset });
		}
		}
		}
		}
		return regions;
		}
		catch (e) {
		console.error('walkCodeBlocks_error:', e instanceof Error ? e.message : e);
		return null;
		}
		}
		async function walkLinks(content) {
		const mm = await getMicromark();
		if (!mm)
		return null;
		try {
		const events = parseEvents(content);
		const definitions = new Map();
		for (const ev of events) {
		if (ev[0] === 'enter' && ev[1].type === 'definitionLabelString') {
		const name = content.slice(ev[1].start.offset, ev[1].end?.offset ?? ev[1].start.offset).toLowerCase();
		definitions.set(name, '');
		}
		else if (ev[0] === 'enter' && ev[1].type === 'definitionDestinationString') {
		const url = content.slice(ev[1].start.offset, ev[1].end?.offset ?? ev[1].start.offset);
		let lastName = '';
		for (const [k, v] of definitions) {
		if (!v) {
		lastName = k;
		break;
		}
		}
		if (lastName)
		definitions.set(lastName, url);
		}
		}
		const links = [];
		let current = null;
		for (const ev of events) {
		const token = ev[1];
		const slice = (t) => content.slice(t.start.offset, t.end?.offset ?? t.start.offset);
		if (ev[0] === 'enter' && (token.type === 'link' \|\| token.type === 'image' \|\| token.type === 'autolink')) {
		current = { type: token.type, start: token.start.offset, text: '', url: '', hasRef: false };
		}
		if (current && ev[0] === 'enter') {
		if (token.type === 'labelText') {
		current.text = slice(token);
		}
		else if (token.type === 'resourceDestinationString') {
		current.url = slice(token);
		}
		else if (token.type === 'referenceString') {
		current.hasRef = true;
		current.url = definitions.get(slice(token).toLowerCase()) ?? slice(token);
		}
		else if (token.type === 'autolinkEmail' \|\| token.type === 'autolinkProtocol') {
		current.url = slice(token);
		if (!current.text)
		current.text = current.url;
		}
		}
		if (ev[0] === 'exit' && current && token.type === current.type) {
		if (token.end && (current.text \|\| current.url)) {
		links.push({
		text: current.text \|\| current.url,
		url: current.url \|\| current.text,
		start: current.start,
		end: token.end.offset,
		isImage: current.type === 'image',
		isAutolink: current.type === 'autolink',
		isReference: current.hasRef
		});
		}
		current = null;
		}
		}
		return links;
		}
		catch (e) {
		console.error('walkLinks_error:', e instanceof Error ? e.message : e);
		return null;
		}
		}
		function offsetToLine(content, offset) {
		let line = 1;
		for (let i = 0; i < offset && i < content.length; i++) {
		if (content[i] === '\n')
		line++;
		}
		return line;
		}
		async function walkHeadings(content) {
		const mm = await getMicromark();
		if (!mm)
		return null;
		try {
		const events = parseEvents(content);
		const headings = [];
		let current = null;
		for (const ev of events) {
		const token = ev[1];
		const slice = (t) => content.slice(t.start.offset, t.end?.offset ?? t.start.offset);
		if (ev[0] === 'enter') {
		if (token.type === 'setextHeadingText') {
		current = { level: 0, text: slice(token), start: token.start.offset };
		}
		else if (token.type === 'setextHeadingLineSequence') {
		if (current)
		current.level = slice(token).startsWith('=') ? 1 : 2;
		}
		else if (token.type === 'atxHeadingSequence') {
		current = { level: slice(token).length, text: '', start: token.start.offset };
		}
		else if (token.type === 'atxHeadingText') {
		if (current)
		current.text = slice(token);
		}
		}
		if (ev[0] === 'exit' && current && (token.type === 'atxHeading' \|\| token.type === 'setextHeading')) {
		headings.push({
		level: current.level,
		text: current.text.trim(),
		line: offsetToLine(content, current.start)
		});
		current = null;
		}
		}
		return headings.length > 0 ? headings : null;
		}
		catch (e) {
		console.error('walkHeadings_error:', e instanceof Error ? e.message : e);
		return null;
		}
		}
		async function walkFormatting(content) {
		const mm = await getMicromark();
		if (!mm)
		return null;
		try {
		const boldItalicRe = /\\\(.+?)\\\/g;
		const boldRe = /(?<!\)\\(?!\)(.+?)\\/g;
		const italicRe = /(?<!\)\(?!\)(.+?)(?<!\)\(?!\)/g;
		const bulletRe = /^[ \t][-+][ \t]/gm;
		const boldItalicMatches = [...content.matchAll(boldItalicRe)];
		const boldMatches = [...content.matchAll(boldRe)];
		const italicMatches = [...content.matchAll(italicRe)];
		const bulletMatches = [...content.matchAll(bulletRe)];
		return {
		bold: boldMatches.length,
		italic: italicMatches.length,
		boldItalic: boldItalicMatches.length,
		bullet: bulletMatches.length
		};
		}
		catch (e) {
		console.error('walkFormatting_error:', e instanceof Error ? e.message : e);
		return null;
		}
		}
		async function walkTables(content) {
		const mm = await getMicromark();
		if (!mm)
		return null;
		try {
		const gfm = await Promise.resolve().then(() => __importStar(require('micromark-extension-gfm')));
		const events = parseEvents(content, [gfm.gfm()]);
		const tables = [];
		let currentTable = null;
		let inHead = false;
		let inBody = false;
		let currentRow = null;
		let currentCell = null;
		for (const ev of events) {
		const token = ev[1];
		const slice = (t) => content.slice(t.start.offset, t.end?.offset ?? t.start.offset);
		if (ev[0] === 'enter') {
		if (token.type === 'table') {
		currentTable = { headers: [], rows: [] };
		}
		else if (token.type === 'tableHead') {
		inHead = true;
		}
		else if (token.type === 'tableBody') {
		inBody = true;
		}
		else if (token.type === 'tableRow' && (inHead \|\| inBody)) {
		currentRow = [];
		}
		else if (token.type === 'tableHeader' && inHead) {
		currentCell = '';
		}
		else if (token.type === 'tableData' && inBody) {
		currentCell = '';
		}
		else if (token.type === 'tableContent' && currentCell !== null) {
		currentCell = slice(token);
		}
		}
		if (ev[0] === 'exit') {
		if (token.type === 'tableHeader' && inHead && currentCell !== null) {
		if (currentRow)
		currentRow.push(currentCell);
		currentCell = null;
		}
		else if (token.type === 'tableData' && inBody && currentCell !== null) {
		if (currentRow)
		currentRow.push(currentCell);
		currentCell = null;
		}
		else if (token.type === 'tableRow' && currentRow !== null) {
		if (inHead)
		currentTable.headers = currentRow;
		else if (inBody)
		currentTable.rows.push(currentRow);
		currentRow = null;
		}
		else if (token.type === 'tableHead') {
		inHead = false;
		}
		else if (token.type === 'tableBody') {
		inBody = false;
		}
		else if (token.type === 'table' && currentTable) {
		tables.push(currentTable);
		currentTable = null;
		}
		}
		}
		return tables.length > 0 ? tables : null;
		}
		catch (e) {
		console.error('walkTables_error:', e instanceof Error ? e.message : e);
		return null;
		}
		}
		//# sourceMappingURL=micromark-walk.js.map

+1

dist/core/micromark-walk.js.map

+26

dist/core/schema.d.ts

		import { z } from 'zod';
		export declare const CliOptions: z.ZodObject<{
		directory: z.ZodOptional<z.ZodString>;
		json: z.ZodDefault<z.ZodBoolean>;
		search: z.ZodOptional<z.ZodString>;
		filter: z.ZodOptional<z.ZodString>;
		rank: z.ZodDefault<z.ZodBoolean>;
		graph: z.ZodDefault<z.ZodBoolean>;
		deps: z.ZodDefault<z.ZodBoolean>;
		orphans: z.ZodDefault<z.ZodBoolean>;
		backlinks: z.ZodOptional<z.ZodString>;
		keypoints: z.ZodDefault<z.ZodBoolean>;
		lintFragments: z.ZodDefault<z.ZodBoolean>;
		session: z.ZodDefault<z.ZodBoolean>;
		budget: z.ZodDefault<z.ZodNumber>;
		maxResults: z.ZodDefault<z.ZodNumber>;
		}, z.core.$strip>;
		export type CliOptions = z.infer<typeof CliOptions>;
		export declare const AnalyzerConfigSchema: z.ZodObject<{
		default_directory: z.ZodDefault<z.ZodString>;
		default_budget: z.ZodDefault<z.ZodNumber>;
		max_tokens: z.ZodDefault<z.ZodNumber>;
		max_results_default: z.ZodDefault<z.ZodNumber>;
		session_file: z.ZodDefault<z.ZodString>;
		}, z.core.$strip>;
		export type AnalyzerConfig = z.infer<typeof AnalyzerConfigSchema>;

+28

dist/core/schema.js

		"use strict";
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.AnalyzerConfigSchema = exports.CliOptions = void 0;
		const zod_1 = require("zod");
		exports.CliOptions = zod_1.z.object({
		directory: zod_1.z.string().optional(),
		json: zod_1.z.boolean().default(false),
		search: zod_1.z.string().min(1, 'Search keyword cannot be empty').optional(),
		filter: zod_1.z.string().regex(/^[^=]+=.+$/, 'Filter must be in format key=value').optional(),
		rank: zod_1.z.boolean().default(false),
		graph: zod_1.z.boolean().default(false),
		deps: zod_1.z.boolean().default(false),
		orphans: zod_1.z.boolean().default(false),
		backlinks: zod_1.z.string().min(1, 'Backlinks target cannot be empty').optional(),
		keypoints: zod_1.z.boolean().default(false),
		lintFragments: zod_1.z.boolean().default(false),
		session: zod_1.z.boolean().default(false),
		budget: zod_1.z.number().int().positive('Budget must be a positive integer').default(100000),
		maxResults: zod_1.z.number().int().nonnegative('max-results must be non-negative').default(0),
		});
		exports.AnalyzerConfigSchema = zod_1.z.object({
		default_directory: zod_1.z.string().default(''),
		default_budget: zod_1.z.number().int().positive().default(100000),
		max_tokens: zod_1.z.number().int().positive().default(200000),
		max_results_default: zod_1.z.number().int().nonnegative().default(20),
		session_file: zod_1.z.string().default('/tmp/md-analyzer-session.json'),
		});
		//# sourceMappingURL=schema.js.map

+1

dist/core/schema.js.map

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+4

dist/core/search.d.ts

		import type { AnalysisResult } from '../types/index.js';
		export declare function searchContent(results: AnalysisResult[], keyword: string): AnalysisResult[];
		export declare function filterByMetadata(results: AnalysisResult[], key: string, value: string): AnalysisResult[];
		export declare function rankByRelevance(results: AnalysisResult[], keyword: string): AnalysisResult[];

+58

dist/core/search.js

		"use strict";
		var __createBinding = (this && this.__createBinding) \|\| (Object.create ? (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		var desc = Object.getOwnPropertyDescriptor(m, k);
		if (!desc \|\| ("get" in desc ? !m.__esModule : desc.writable \|\| desc.configurable)) {
		desc = { enumerable: true, get: function() { return m[k]; } };
		}
		Object.defineProperty(o, k2, desc);
		}) : (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		o[k2] = m[k];
		}));
		var __setModuleDefault = (this && this.__setModuleDefault) \|\| (Object.create ? (function(o, v) {
		Object.defineProperty(o, "default", { enumerable: true, value: v });
		}) : function(o, v) {
		o["default"] = v;
		});
		var __importStar = (this && this.__importStar) \|\| (function () {
		var ownKeys = function(o) {
		ownKeys = Object.getOwnPropertyNames \|\| function (o) {
		var ar = [];
		for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
		return ar;
		};
		return ownKeys(o);
		};
		return function (mod) {
		if (mod && mod.__esModule) return mod;
		var result = {};
		if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
		__setModuleDefault(result, mod);
		return result;
		};
		})();
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.searchContent = searchContent;
		exports.filterByMetadata = filterByMetadata;
		exports.rankByRelevance = rankByRelevance;
		const fs = __importStar(require("fs"));
		function searchContent(results, keyword) {
		const kw = keyword.toLowerCase();
		return results.filter(doc => {
		const content = fs.readFileSync(doc.file, 'utf-8').toLowerCase();
		return content.includes(kw);
		});
		}
		function filterByMetadata(results, key, value) {
		return results.filter(doc => doc.metadata && String(doc.metadata[key] \|\| '') === value);
		}
		function rankByRelevance(results, keyword) {
		const kw = keyword.toLowerCase();
		return [...results].sort((a, b) => {
		const countA = (fs.readFileSync(a.file, 'utf-8').toLowerCase().match(new RegExp(kw, 'g')) \|\| []).length;
		const countB = (fs.readFileSync(b.file, 'utf-8').toLowerCase().match(new RegExp(kw, 'g')) \|\| []).length;
		return countB - countA;
		});
		}
		//# sourceMappingURL=search.js.map

+1

dist/core/search.js.map

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+5

dist/core/session.d.ts

		import type { AnalysisResult, SessionStats } from '../types/index.js';
		export declare function loadSession(): SessionStats;
		export declare function saveSession(session: SessionStats): void;
		export declare function updateSessionStats(results: AnalysisResult[], session: SessionStats): SessionStats;
		export declare function getTokenBudgetReport(session: SessionStats, budget: number): object;

+66

dist/core/session.js

		"use strict";
		var __createBinding = (this && this.__createBinding) \|\| (Object.create ? (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		var desc = Object.getOwnPropertyDescriptor(m, k);
		if (!desc \|\| ("get" in desc ? !m.__esModule : desc.writable \|\| desc.configurable)) {
		desc = { enumerable: true, get: function() { return m[k]; } };
		}
		Object.defineProperty(o, k2, desc);
		}) : (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		o[k2] = m[k];
		}));
		var __setModuleDefault = (this && this.__setModuleDefault) \|\| (Object.create ? (function(o, v) {
		Object.defineProperty(o, "default", { enumerable: true, value: v });
		}) : function(o, v) {
		o["default"] = v;
		});
		var __importStar = (this && this.__importStar) \|\| (function () {
		var ownKeys = function(o) {
		ownKeys = Object.getOwnPropertyNames \|\| function (o) {
		var ar = [];
		for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
		return ar;
		};
		return ownKeys(o);
		};
		return function (mod) {
		if (mod && mod.__esModule) return mod;
		var result = {};
		if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
		__setModuleDefault(result, mod);
		return result;
		};
		})();
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.loadSession = loadSession;
		exports.saveSession = saveSession;
		exports.updateSessionStats = updateSessionStats;
		exports.getTokenBudgetReport = getTokenBudgetReport;
		const fs = __importStar(require("fs"));
		const constants_js_1 = require("../utils/constants.js");
		function loadSession() {
		try {
		return JSON.parse(fs.readFileSync(constants_js_1.SESSION_FILE, 'utf-8'));
		}
		catch (e) {
		console.error('session_load: new session created');
		return { sessionId: `session-${Date.now()}`, calls: 0, totalTokens: 0, filesProcessed: 0, startTime: new Date().toISOString() };
		}
		}
		function saveSession(session) {
		fs.writeFileSync(constants_js_1.SESSION_FILE, JSON.stringify(session, null, 2));
		}
		function updateSessionStats(results, session) {
		const tokensThisCall = results.reduce((sum, r) => sum + r.stats.tokens, 0);
		return { ...session, calls: session.calls + 1, totalTokens: session.totalTokens + tokensThisCall, filesProcessed: session.filesProcessed + results.length };
		}
		function getTokenBudgetReport(session, budget) {
		const remaining = budget - session.totalTokens;
		const percentUsed = Math.round((session.totalTokens / budget) * 100);
		return {
		sessionId: session.sessionId, totalCalls: session.calls, totalTokens: session.totalTokens, budget, remaining,
		percentUsed: percentUsed + '%', status: percentUsed >= 100 ? 'EXCEEDED' : percentUsed >= 80 ? 'WARNING' : 'OK'
		};
		}
		//# sourceMappingURL=session.js.map

+1

dist/core/session.js.map

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+10

dist/index.d.ts

		export { analyzeFile, analyzeFileWithMicromark, scanMarkdownFiles } from './core/analyzer.js';
		export { buildGraph, findOrphans, findBacklinks } from './core/graph.js';
		export { searchContent, filterByMetadata, rankByRelevance } from './core/search.js';
		export { getFragmentHealth } from './core/health.js';
		export { loadSession, saveSession, updateSessionStats, getTokenBudgetReport } from './core/session.js';
		export { countStats } from './core/counters.js';
		export { extractFrontmatter, extractFragmentMeta, extractHeadings, extractLinks, extractWikilinks, extractTables } from './core/extractors.js';
		export { CliOptions, AnalyzerConfigSchema } from './core/schema.js';
		export type { AnalyzerConfig } from './core/schema.js';
		export type { Link, Wikilink, Heading, Table, FragmentMeta, Stats, SectionInfo, AnalysisResult, GraphNode, Graph, SessionStats, RunLog } from './types/index.js';

+35

dist/index.js

		"use strict";
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.AnalyzerConfigSchema = exports.CliOptions = exports.extractTables = exports.extractWikilinks = exports.extractLinks = exports.extractHeadings = exports.extractFragmentMeta = exports.extractFrontmatter = exports.countStats = exports.getTokenBudgetReport = exports.updateSessionStats = exports.saveSession = exports.loadSession = exports.getFragmentHealth = exports.rankByRelevance = exports.filterByMetadata = exports.searchContent = exports.findBacklinks = exports.findOrphans = exports.buildGraph = exports.scanMarkdownFiles = exports.analyzeFileWithMicromark = exports.analyzeFile = void 0;
		var analyzer_js_1 = require("./core/analyzer.js");
		Object.defineProperty(exports, "analyzeFile", { enumerable: true, get: function () { return analyzer_js_1.analyzeFile; } });
		Object.defineProperty(exports, "analyzeFileWithMicromark", { enumerable: true, get: function () { return analyzer_js_1.analyzeFileWithMicromark; } });
		Object.defineProperty(exports, "scanMarkdownFiles", { enumerable: true, get: function () { return analyzer_js_1.scanMarkdownFiles; } });
		var graph_js_1 = require("./core/graph.js");
		Object.defineProperty(exports, "buildGraph", { enumerable: true, get: function () { return graph_js_1.buildGraph; } });
		Object.defineProperty(exports, "findOrphans", { enumerable: true, get: function () { return graph_js_1.findOrphans; } });
		Object.defineProperty(exports, "findBacklinks", { enumerable: true, get: function () { return graph_js_1.findBacklinks; } });
		var search_js_1 = require("./core/search.js");
		Object.defineProperty(exports, "searchContent", { enumerable: true, get: function () { return search_js_1.searchContent; } });
		Object.defineProperty(exports, "filterByMetadata", { enumerable: true, get: function () { return search_js_1.filterByMetadata; } });
		Object.defineProperty(exports, "rankByRelevance", { enumerable: true, get: function () { return search_js_1.rankByRelevance; } });
		var health_js_1 = require("./core/health.js");
		Object.defineProperty(exports, "getFragmentHealth", { enumerable: true, get: function () { return health_js_1.getFragmentHealth; } });
		var session_js_1 = require("./core/session.js");
		Object.defineProperty(exports, "loadSession", { enumerable: true, get: function () { return session_js_1.loadSession; } });
		Object.defineProperty(exports, "saveSession", { enumerable: true, get: function () { return session_js_1.saveSession; } });
		Object.defineProperty(exports, "updateSessionStats", { enumerable: true, get: function () { return session_js_1.updateSessionStats; } });
		Object.defineProperty(exports, "getTokenBudgetReport", { enumerable: true, get: function () { return session_js_1.getTokenBudgetReport; } });
		var counters_js_1 = require("./core/counters.js");
		Object.defineProperty(exports, "countStats", { enumerable: true, get: function () { return counters_js_1.countStats; } });
		var extractors_js_1 = require("./core/extractors.js");
		Object.defineProperty(exports, "extractFrontmatter", { enumerable: true, get: function () { return extractors_js_1.extractFrontmatter; } });
		Object.defineProperty(exports, "extractFragmentMeta", { enumerable: true, get: function () { return extractors_js_1.extractFragmentMeta; } });
		Object.defineProperty(exports, "extractHeadings", { enumerable: true, get: function () { return extractors_js_1.extractHeadings; } });
		Object.defineProperty(exports, "extractLinks", { enumerable: true, get: function () { return extractors_js_1.extractLinks; } });
		Object.defineProperty(exports, "extractWikilinks", { enumerable: true, get: function () { return extractors_js_1.extractWikilinks; } });
		Object.defineProperty(exports, "extractTables", { enumerable: true, get: function () { return extractors_js_1.extractTables; } });
		var schema_js_1 = require("./core/schema.js");
		Object.defineProperty(exports, "CliOptions", { enumerable: true, get: function () { return schema_js_1.CliOptions; } });
		Object.defineProperty(exports, "AnalyzerConfigSchema", { enumerable: true, get: function () { return schema_js_1.AnalyzerConfigSchema; } });
		//# sourceMappingURL=index.js.map

+1

dist/index.js.map

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+102

dist/types/index.d.ts

		export interface Link {
		text: string;
		url: string;
		isInternal: boolean;
		fileName: string \| null;
		isImage?: boolean;
		}
		export interface Wikilink {
		target: string;
		display: string \| null;
		}
		export interface Heading {
		level: number;
		text: string;
		line: number;
		}
		export interface Table {
		headers: string[];
		rows: string[][];
		}
		export interface FragmentMeta {
		title: string;
		description: string \| null;
		tags: string[];
		depends_on: string[];
		status: string \| null;
		source: string \| null;
		order: number \| null;
		date_iso: string \| null;
		}
		export interface Stats {
		totalHeadings: number;
		totalLinks: number;
		internalLinks: number;
		externalLinks: number;
		totalWikilinks: number;
		wordCount: number;
		charCount: number;
		lineCount: number;
		codeBlocks: number;
		tables: number;
		tokens: number;
		boldCount?: number;
		italicCount?: number;
		bulletCount?: number;
		errors?: string[];
		}
		export interface SectionInfo {
		line: number;
		tokens: number;
		}
		export interface AnalysisResult {
		file: string;
		fileName: string;
		metadata: Record<string, unknown> \| null;
		fragmentMeta: FragmentMeta \| null;
		headings: Heading[];
		sections: SectionInfo[];
		links: Link[];
		wikilinks: Wikilink[];
		tables: Table[];
		stats: Stats;
		}
		export interface GraphNode {
		inbound: string[];
		outbound: string[];
		}
		export interface Graph {
		nodes: Record<string, GraphNode>;
		edges: {
		source: string;
		target: string;
		type: string;
		}[];
		}
		export interface SessionStats {
		sessionId: string;
		calls: number;
		totalTokens: number;
		filesProcessed: number;
		startTime: string;
		}
		export interface RunLog {
		timestamp: string;
		sessionId: string;
		directory: string;
		flags: string[];
		filesFound: number;
		filesProcessed: number;
		tokensThisCall: number;
		totalSessionTokens: number;
		errors: string[];
		durationMs: number;
		mode: string;
		}
		export interface AnalyzerConfig {
		default_directory: string;
		default_budget: number;
		max_tokens: number;
		max_results_default: number;
		session_file: string;
		}

+3

dist/types/index.js

		"use strict";
		Object.defineProperty(exports, "__esModule", { value: true });
		//# sourceMappingURL=index.js.map

+1

dist/types/index.js.map

{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/types/index.ts"],"names":[],"mappings":""}

+3

dist/utils/config.d.ts

		import type { AnalyzerConfig } from '../core/schema.js';
		export declare function getTomlConfig(tomlPath: string): AnalyzerConfig;
		export declare function resolveConfigPath(): string;

+91

dist/utils/config.js

		"use strict";
		var __createBinding = (this && this.__createBinding) \|\| (Object.create ? (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		var desc = Object.getOwnPropertyDescriptor(m, k);
		if (!desc \|\| ("get" in desc ? !m.__esModule : desc.writable \|\| desc.configurable)) {
		desc = { enumerable: true, get: function() { return m[k]; } };
		}
		Object.defineProperty(o, k2, desc);
		}) : (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		o[k2] = m[k];
		}));
		var __setModuleDefault = (this && this.__setModuleDefault) \|\| (Object.create ? (function(o, v) {
		Object.defineProperty(o, "default", { enumerable: true, value: v });
		}) : function(o, v) {
		o["default"] = v;
		});
		var __importStar = (this && this.__importStar) \|\| (function () {
		var ownKeys = function(o) {
		ownKeys = Object.getOwnPropertyNames \|\| function (o) {
		var ar = [];
		for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
		return ar;
		};
		return ownKeys(o);
		};
		return function (mod) {
		if (mod && mod.__esModule) return mod;
		var result = {};
		if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
		__setModuleDefault(result, mod);
		return result;
		};
		})();
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.getTomlConfig = getTomlConfig;
		exports.resolveConfigPath = resolveConfigPath;
		const fs = __importStar(require("fs"));
		const path = __importStar(require("path"));
		const schema_js_1 = require("../core/schema.js");
		const DEFAULT_CONFIG = schema_js_1.AnalyzerConfigSchema.parse({});
		function getTomlConfig(tomlPath) {
		try {
		const content = fs.readFileSync(tomlPath, 'utf-8');
		const config = {};
		let inConfigSection = false;
		content.split('\n').forEach(line => {
		const trimmed = line.trim();
		if (trimmed === '[tool.md-analyzer.config]') {
		inConfigSection = true;
		return;
		}
		if (inConfigSection) {
		if (trimmed.startsWith('[')) {
		inConfigSection = false;
		return;
		}
		if (trimmed.includes('=')) {
		const separatorIdx = trimmed.indexOf('=');
		const key = trimmed.substring(0, separatorIdx).trim();
		const value = trimmed.substring(separatorIdx + 1).trim().replace(/^["']\|["']$/g, '');
		config[key] = value;
		}
		}
		});
		return {
		default_directory: config['default_directory'] \|\| DEFAULT_CONFIG.default_directory,
		default_budget: parseInt(config['default_budget'] \|\| '', 10) \|\| DEFAULT_CONFIG.default_budget,
		max_tokens: parseInt(config['max_tokens'] \|\| '', 10) \|\| DEFAULT_CONFIG.max_tokens,
		max_results_default: parseInt(config['max_results_default'] \|\| '', 10) \|\| DEFAULT_CONFIG.max_results_default,
		session_file: config['session_file'] \|\| DEFAULT_CONFIG.session_file,
		};
		}
		catch (e) {
		console.error('config_load_error: could not read hooks.toml:', e instanceof Error ? e.message : e);
		return { ...DEFAULT_CONFIG };
		}
		}
		function resolveConfigPath() {
		const candidates = [
		path.join(__dirname, '..', '..', 'hooks.toml'),
		path.join(__dirname, '..', 'hooks.toml'),
		path.join(process.cwd(), 'hooks.toml'),
		];
		for (const candidate of candidates) {
		if (fs.existsSync(candidate))
		return candidate;
		}
		return candidates[0];
		}
		//# sourceMappingURL=config.js.map

+1

dist/utils/config.js.map

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+3

dist/utils/constants.d.ts

		export declare const SKIP_DIRS: Set<string>;
		export declare const SESSION_FILE = "/tmp/md-analyzer-session.json";
		export declare const LOG_DIR: string;

+45

dist/utils/constants.js

		"use strict";
		var __createBinding = (this && this.__createBinding) \|\| (Object.create ? (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		var desc = Object.getOwnPropertyDescriptor(m, k);
		if (!desc \|\| ("get" in desc ? !m.__esModule : desc.writable \|\| desc.configurable)) {
		desc = { enumerable: true, get: function() { return m[k]; } };
		}
		Object.defineProperty(o, k2, desc);
		}) : (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		o[k2] = m[k];
		}));
		var __setModuleDefault = (this && this.__setModuleDefault) \|\| (Object.create ? (function(o, v) {
		Object.defineProperty(o, "default", { enumerable: true, value: v });
		}) : function(o, v) {
		o["default"] = v;
		});
		var __importStar = (this && this.__importStar) \|\| (function () {
		var ownKeys = function(o) {
		ownKeys = Object.getOwnPropertyNames \|\| function (o) {
		var ar = [];
		for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
		return ar;
		};
		return ownKeys(o);
		};
		return function (mod) {
		if (mod && mod.__esModule) return mod;
		var result = {};
		if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
		__setModuleDefault(result, mod);
		return result;
		};
		})();
		Object.defineProperty(exports, "__esModule", { value: true });
		exports.LOG_DIR = exports.SESSION_FILE = exports.SKIP_DIRS = void 0;
		const path = __importStar(require("path"));
		exports.SKIP_DIRS = new Set([
		'node_modules', '.git', '.svn', '.hg',
		'services', 'data', 'appendonlydir',
		'dist', 'build', '__pycache__', '.next', 'coverage'
		]);
		exports.SESSION_FILE = '/tmp/md-analyzer-session.json';
		exports.LOG_DIR = path.join(__dirname, '..', '..', 'log');
		//# sourceMappingURL=constants.js.map

+1

dist/utils/constants.js.map

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+150

src/cli/index.ts

		#!/usr/bin/env node
		import { Command } from 'commander'
		import * as path from 'path'
		import * as fs from 'fs'
		import { z } from 'zod'
		import { CliOptions } from '../core/schema.js'
		import { getTomlConfig, resolveConfigPath } from '../utils/config.js'
		import { scanMarkdownFiles, analyzeFile } from '../core/analyzer.js'
		import { buildGraph, findOrphans, findBacklinks } from '../core/graph.js'
		import { searchContent, filterByMetadata, rankByRelevance } from '../core/search.js'
		import { getFragmentHealth } from '../core/health.js'
		import { loadSession, saveSession, updateSessionStats, getTokenBudgetReport } from '../core/session.js'
		import { extractKeyPoints, writeRunLog } from './output.js'

		const pkgVersion: string = JSON.parse(
		fs.readFileSync(path.join(__dirname, '..', '..', 'package.json'), 'utf-8')
		).version

		const program = new Command()

		program
		.name('md-analyzer')
		.description('Markdown document analyzer for AI agents - extract metadata, headings, links, tables, tokens, and key points from .md files')
		.version(pkgVersion, '--version, -v', 'Show version number')
		.arguments('[directory]')
		.option('--json', 'Output as JSON')
		.option('--search <kw>', 'Search keyword in content')
		.option('--filter <k=v>', 'Filter by metadata field')
		.option('--rank', 'Rank results by relevance')
		.option('--graph', 'Document relationship graph')
		.option('--deps', 'Dependency graph (DAG order + levels)')
		.option('--orphans', 'Find unreferenced docs')
		.option('--backlinks <doc>', 'Find docs linking to <doc>')
		.option('--keypoints', 'Quick overview (single-shot)')
		.option('--lint-fragments', 'Fragment health check')
		.option('--session', 'Token budget report')
		.option('--budget <n>', 'Set token budget limit', parseInt, 100000)
		.option('--max-results <n>', 'Limit output', parseInt, 0)
		.addHelpText('after', `

		Examples:
		md-analyzer /path/to/docs --keypoints --json
		md-analyzer . --search "task" --rank --json
		md-analyzer . --session --budget 50000 --json
		md-analyzer . --orphans --json
		md-analyzer . --lint-fragments --json
		md-analyzer . --deps --json`)

		program.action((directory: string \| undefined, options: Record<string, unknown>) => {
		const startTime = Date.now()

		let parsed: CliOptions
		try {
		parsed = CliOptions.parse({ directory, ...options })
		} catch (e: unknown) {
		if (e instanceof z.ZodError) {
		console.error('Invalid arguments:')
		for (const issue of e.issues) {
		console.error(' ' + issue.path.join('.') + ': ' + issue.message)
		}
		} else {
		console.error('Unexpected error:', e instanceof Error ? e.message : e)
		}
		process.exit(1)
		}

		const configPath = resolveConfigPath()
		const config = getTomlConfig(configPath)
		const targetDir = parsed.directory \|\| process.env['MD_ANALYZER_DEFAULT_DIR'] \|\| config.default_directory \|\| process.cwd()

		if (!parsed.json) console.log('Scanning: ' + targetDir + '\n')

		const { files: mdFiles, errors: scanErrors } = scanMarkdownFiles(targetDir)
		if (!parsed.json) {
		console.log('Found ' + mdFiles.length + ' .md files\n')
		if (scanErrors.length > 0) console.log('Warnings: ' + scanErrors.length + ' directories skipped\n')
		}

		let results = mdFiles.map(file => analyzeFile(file))
		if (scanErrors.length > 0 && results.length > 0) {
		if (!results[0].stats.errors) results[0].stats.errors = []
		results[0].stats.errors.push(...scanErrors)
		}

		if (parsed.filter && parsed.filter.includes('=')) {
		const [key, value] = parsed.filter.split('=')
		results = filterByMetadata(results, key, value)
		if (!parsed.json) console.log('Filtered by ' + key + '=' + value + ': ' + results.length + ' results\n')
		}

		if (parsed.search) {
		results = searchContent(results, parsed.search)
		if (!parsed.json) console.log('Search "' + parsed.search + '": ' + results.length + ' results\n')
		}

		if (parsed.rank && parsed.search) {
		results = rankByRelevance(results, parsed.search)
		if (!parsed.json) console.log('Ranked by relevance to "' + parsed.search + '"\n')
		}

		let limitedResults = results
		if (parsed.maxResults > 0 && results.length > parsed.maxResults) {
		if (!parsed.json) console.log('Warning: Limiting output to ' + parsed.maxResults + ' of ' + results.length + ' results\n')
		limitedResults = results.slice(0, parsed.maxResults)
		}

		const session = loadSession()
		const updatedSession = updateSessionStats(results, session)
		saveSession(updatedSession)
		const tokensThisCall = results.reduce((sum, r) => sum + r.stats.tokens, 0)

		if (parsed.session) console.log(JSON.stringify(getTokenBudgetReport(updatedSession, parsed.budget), null, 2))
		else if (parsed.keypoints) console.log(JSON.stringify(limitedResults.map(doc => extractKeyPoints(doc)), null, 2))
		else if (parsed.lintFragments) console.log(JSON.stringify(getFragmentHealth(limitedResults), null, 2))
		else if (parsed.deps) {
		const graph = buildGraph(limitedResults)
		console.log(JSON.stringify({ nodes: Object.keys(graph.nodes), edges: graph.edges, tokensThisCall }, null, 2))
		} else if (parsed.orphans) {
		const orphans = findOrphans(buildGraph(limitedResults))
		console.log(JSON.stringify({ orphans, count: orphans.length, tokensThisCall }, null, 2))
		} else if (parsed.backlinks) {
		const backlinks = findBacklinks(limitedResults, parsed.backlinks)
		console.log(JSON.stringify({ target: parsed.backlinks, backlinks, count: backlinks.length, tokensThisCall }, null, 2))
		} else if (parsed.graph) console.log(JSON.stringify(buildGraph(limitedResults), null, 2))
		else {
		if (!parsed.json) {
		console.log('\nTokens this call: ' + tokensThisCall)
		console.log('Total session tokens: ' + updatedSession.totalTokens + '\n')
		}
		console.log(JSON.stringify(limitedResults, null, 2))
		}

		const usedFlags = process.argv.slice(2).filter(a => a.startsWith('--')).map(a => a.replace(/=.*/, ''))
		const mode = parsed.deps ? 'deps' : parsed.lintFragments ? 'lint-fragments' : parsed.session ? 'session' : parsed.keypoints ? 'keypoints' : parsed.orphans ? 'orphans' : parsed.backlinks ? 'backlinks' : parsed.graph ? 'graph' : parsed.search ? 'search' : 'default'
		writeRunLog({
		timestamp: new Date().toISOString(),
		sessionId: updatedSession.sessionId,
		directory: targetDir,
		flags: usedFlags,
		filesFound: mdFiles.length,
		filesProcessed: results.length,
		tokensThisCall,
		totalSessionTokens: updatedSession.totalTokens,
		errors: scanErrors,
		durationMs: Date.now() - startTime,
		mode
		})
		})

		program.parse()

+33

src/cli/output.ts

		import * as fs from 'fs'
		import * as path from 'path'
		import { LOG_DIR } from '../utils/constants.js'
		import type { AnalysisResult, RunLog } from '../types/index.js'

		export function extractKeyPoints(doc: AnalysisResult): object {
		return {
		fileName: doc.fileName, title: doc.headings[0]?.text \|\| doc.fileName, level: doc.headings[0]?.level \|\| 1,
		summary: {
		totalHeadings: doc.stats.totalHeadings, totalLinks: doc.stats.totalLinks, totalWikilinks: doc.stats.totalWikilinks,
		totalTokens: doc.stats.tokens, wordCount: doc.stats.wordCount
		},
		keyHeadings: doc.headings.slice(0, 10).map((h, i) => ({
		level: h.level, text: h.text, line: h.line,
		tokens: doc.sections?.[i]?.tokens ?? 0
		})),
		importantLinks: doc.links.filter(l => !l.isInternal).slice(0, 3).map(l => ({ text: l.text, url: l.url })),
		internalReferences: doc.links.filter(l => l.isInternal && l.fileName).slice(0, 5).map(l => l.fileName),
		metadata: doc.metadata, readingTime: Math.ceil(doc.stats.wordCount / 200) + ' min'
		}
		}

		export function writeRunLog(log: RunLog): void {
		try {
		if (!fs.existsSync(LOG_DIR)) fs.mkdirSync(LOG_DIR, { recursive: true })
		const logFile = path.join(LOG_DIR, `${log.sessionId}.json`)
		const existing: RunLog[] = fs.existsSync(logFile) ? JSON.parse(fs.readFileSync(logFile, 'utf-8')) : []
		existing.push(log)
		fs.writeFileSync(logFile, JSON.stringify(existing, null, 2))
		} catch (e: unknown) {
		console.error('run_log_write_error:', e instanceof Error ? e.message : e)
		}
		}

+76

src/core/analyzer.ts

		import * as fs from 'fs'
		import * as path from 'path'
		import { encodingForModel } from 'js-tiktoken'
		import { SKIP_DIRS } from '../utils/constants.js'
		import { extractFrontmatter, extractFragmentMeta, extractHeadings, extractLinks, extractWikilinks, extractTables } from './extractors.js'
		import { countStats } from './counters.js'
		import type { AnalysisResult, SectionInfo } from '../types/index.js'

		export function scanMarkdownFiles(dir: string): { files: string[]; errors: string[] } {
		const files: string[] = [], errors: string[] = []
		function walk(dir: string): void {
		let entries
		try { entries = fs.readdirSync(dir, { withFileTypes: true }) }
		catch (e: unknown) { errors.push(`permission_denied: ${dir}`); console.error('scan_error:', e instanceof Error ? e.message : e); return }
		for (const entry of entries) {
		if (entry.name.startsWith('.') \|\| SKIP_DIRS.has(entry.name)) continue
		const fullPath = path.join(dir, entry.name)
		try {
		if (entry.isDirectory()) walk(fullPath)
		else if (entry.isFile() && entry.name.endsWith('.md')) files.push(fullPath)
		} catch (e: unknown) { errors.push(`access_error: ${fullPath}`); console.error('access_error:', e instanceof Error ? e.message : e) }
		}
		}
		try { walk(dir) } catch (e: unknown) { errors.push(`scan_error: ${e instanceof Error ? e.message : 'unknown'}`); console.error('walk_error:', e instanceof Error ? e.message : e) }
		return { files, errors }
		}

		function computeSections(content: string, headings: { line: number }[]): SectionInfo[] {
		const bodyLines = content.split('\n')
		return headings.map((h, i) => {
		const startIdx = h.line - 1
		const endIdx = i + 1 < headings.length ? headings[i + 1].line - 1 : bodyLines.length
		const sectionText = bodyLines.slice(startIdx, endIdx).join('\n')
		let tokens = 0
		try { tokens = encodingForModel('gpt-4').encode(sectionText).length }
		catch (e: unknown) {
		console.error('section_token_fallback:', e instanceof Error ? e.message : e)
		tokens = Math.ceil(sectionText.length / 4)
		}
		return { line: h.line, tokens }
		})
		}

		export function analyzeFile(filePath: string): AnalysisResult {
		const errors: string[] = []
		let content = ''
		try { content = fs.readFileSync(filePath, 'utf-8') }
		catch (e: unknown) {
		errors.push(`file_read_error: ${e instanceof Error ? e.message : 'unknown'}`)
		return {
		file: filePath, fileName: path.basename(filePath, '.md'), metadata: null, fragmentMeta: null,
		headings: [], sections: [], links: [], wikilinks: [], tables: [],
		stats: { totalHeadings: 0, totalLinks: 0, internalLinks: 0, externalLinks: 0, totalWikilinks: 0, wordCount: 0, charCount: 0, lineCount: 0, codeBlocks: 0, tables: 0, tokens: 0, errors }
		}
		}
		const { metadata, content: markdownContent } = extractFrontmatter(content)
		const fragmentMeta = extractFragmentMeta(metadata)
		const headings = extractHeadings(markdownContent)
		const links = extractLinks(markdownContent)
		const wikilinks = extractWikilinks(markdownContent)
		const tables = extractTables(markdownContent)
		const counts = countStats(markdownContent)
		if (counts.tokens === 0) errors.push('token_count_fallback: tiktoken unavailable')

		const sections = computeSections(markdownContent, headings)

		return {
		file: filePath, fileName: path.basename(filePath, '.md'), metadata, fragmentMeta, headings, sections, links, wikilinks, tables,
		stats: {
		totalHeadings: headings.length, totalLinks: links.length, internalLinks: links.filter(l => l.isInternal).length,
		externalLinks: links.filter(l => !l.isInternal).length, totalWikilinks: wikilinks.length, wordCount: counts.wordCount,
		charCount: counts.charCount, lineCount: counts.lineCount, codeBlocks: counts.codeBlocks, tables: tables.length,
		tokens: counts.tokens, errors: errors.length > 0 ? errors : undefined
		}
		}
		}

+16

src/core/counters.ts

		import { encodingForModel } from 'js-tiktoken'

		export function countStats(content: string): { wordCount: number; charCount: number; lineCount: number; codeBlocks: number; tokens: number } {
		const wordCount = content.split(/\s+/).filter(w => w.length > 0).length
		const charCount = content.length
		const lineCount = content.split('\n').length
		const codeBlocks = (content.match(/```[\s\S]*?```/g) \|\| []).length
		let tokens = 0
		try {
		tokens = encodingForModel('gpt-4').encode(content).length
		} catch (e: unknown) {
		console.error('token_count_fallback: tiktoken unavailable, using estimate:', e instanceof Error ? e.message : e)
		tokens = Math.ceil(charCount / 4)
		}
		return { wordCount, charCount, lineCount, codeBlocks, tokens }
		}

+88

src/core/extractors.ts

		import * as path from 'path'
		import * as yaml from 'js-yaml'
		import type { Link, Wikilink, Heading, Table, FragmentMeta } from '../types/index.js'

		export function extractFrontmatter(content: string): { metadata: Record<string, unknown> \| null; content: string } {
		const frontmatterRegex = /^---\s\n([\s\S]?)\n---\s*\n/
		const match = content.match(frontmatterRegex)
		if (!match) return { metadata: null, content }
		try {
		const parsed = yaml.load(match[1])
		const metadata = parsed && typeof parsed === 'object' ? parsed as Record<string, unknown> : null
		return { metadata, content: content.substring(match[0].length) }
		} catch (e: unknown) {
		console.error('frontmatter_parse_error:', e instanceof Error ? e.message : e)
		return { metadata: null, content }
		}
		}

		export function extractFragmentMeta(metadata: Record<string, unknown> \| null): FragmentMeta \| null {
		if (!metadata) return null
		const dependsRaw = metadata.depends_on
		const depends: string[] = Array.isArray(dependsRaw) ? dependsRaw.map(String) : (typeof dependsRaw === 'string' ? [dependsRaw] : [])
		const tags: string[] = Array.isArray(metadata.tags) ? metadata.tags.map(String) : (typeof metadata.tags === 'string' ? [metadata.tags] : [])
		return {
		title: String(metadata.title \|\| ''),
		description: metadata.description ? String(metadata.description) : null,
		tags,
		depends_on: depends,
		status: metadata.status ? String(metadata.status) : null,
		source: metadata.source ? String(metadata.source) : null,
		order: metadata.order != null ? Number(metadata.order) : null,
		date_iso: metadata.date_iso ? String(metadata.date_iso) : null,
		}
		}

		export function extractHeadings(content: string): Heading[] {
		const headings: Heading[] = []
		const headingRegex = /^(#{1,6})\s+(.+)$/gm
		let match: RegExpExecArray \| null
		while ((match = headingRegex.exec(content)) !== null) {
		const line = content.substring(0, match.index).split('\n').length
		headings.push({ level: match[1].length, text: match[2].trim(), line })
		}
		return headings
		}

		export function extractLinks(content: string): Link[] {
		const links: Link[] = []
		const linkRegex = /\[([^\]]+)\]$([^)]+)$/g
		let match: RegExpExecArray \| null
		while ((match = linkRegex.exec(content)) !== null) {
		const url = match[2].trim()
		const isInternal = url.startsWith('#') \|\| (!url.startsWith('http') && !url.startsWith('//'))
		let fileName: string \| null = null
		if (isInternal && !url.startsWith('#')) {
		const baseName = path.basename(url, '.md')
		if (baseName && baseName !== url) fileName = baseName
		}
		links.push({ text: match[1].trim(), url, isInternal, fileName })
		}
		return links
		}

		export function extractWikilinks(content: string): Wikilink[] {
		const wikilinks: Wikilink[] = []
		const wikiRegex = /\[\[([^\]\|]+)(?:\\|([^\]]+))?\]\]/g
		let match: RegExpExecArray \| null
		while ((match = wikiRegex.exec(content)) !== null) {
		wikilinks.push({ target: match[1].trim(), display: match[2]?.trim() \|\| null })
		}
		return wikilinks
		}

		export function extractTables(content: string): Table[] {
		const tables: Table[] = []
		const tableRegex = /\\|(.+)\\|\n\\|[-:\s\|]+\\|\n((?:\\|.+\\|\n?)+)/g
		let match: RegExpExecArray \| null
		while ((match = tableRegex.exec(content)) !== null) {
		const headers = match[1].split('\|').map(h => h.trim()).filter(h => h)
		const rows: string[][] = []
		match[2].trim().split('\n').forEach(row => {
		const cells = row.split('\|').map(c => c.trim()).filter(c => c)
		if (cells.length > 0) rows.push(cells)
		})
		tables.push({ headers, rows })
		}
		return tables
		}

+54

src/core/graph.ts

		import type { AnalysisResult, Graph, GraphNode } from '../types/index.js'

		function addEdge(graph: Record<string, GraphNode>, edges: { source: string; target: string; type: string }[], source: string, target: string, type: string): void {
		if (!graph[source]) graph[source] = { inbound: [], outbound: [] }
		if (!graph[target]) graph[target] = { inbound: [], outbound: [] }
		if (!graph[source].outbound.includes(target)) graph[source].outbound.push(target)
		if (!graph[target].inbound.includes(source)) graph[target].inbound.push(source)
		edges.push({ source, target, type })
		}

		export function buildGraph(results: AnalysisResult[]): Graph {
		const graph: Record<string, GraphNode> = {}, edges: { source: string; target: string; type: string }[] = []
		results.forEach(doc => {
		const source = doc.fileName
		if (!graph[source]) graph[source] = { inbound: [], outbound: [] }
		doc.links.forEach(link => {
		if (link.isInternal && link.fileName) addEdge(graph, edges, source, link.fileName, 'link')
		})
		doc.wikilinks.forEach(w => {
		const slug = w.target.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+\|-+$/g, '')
		if (slug !== source && results.some(r => r.fileName === slug)) addEdge(graph, edges, source, slug, 'wikilink')
		})
		if (doc.fragmentMeta) {
		doc.fragmentMeta.depends_on.forEach(dep => {
		const depName = dep.replace(/\.md$/, '')
		if (depName !== source && results.some(r => r.fileName === depName)) addEdge(graph, edges, source, depName, 'depends_on')
		})
		}
		})
		return { nodes: graph, edges }
		}

		export function findOrphans(graph: Graph, excludeOrphansWithDeps?: Set<string>): string[] {
		return Object.keys(graph.nodes).filter(node => {
		if (excludeOrphansWithDeps?.has(node)) return false
		return graph.nodes[node].inbound.length === 0 && graph.nodes[node].outbound.length === 0
		})
		}

		export function findBacklinks(results: AnalysisResult[], targetFileName: string): string[] {
		const backlinks: string[] = []
		results.forEach(doc => {
		doc.links.forEach(link => {
		if (link.isInternal && link.fileName === targetFileName && !backlinks.includes(doc.fileName)) {
		backlinks.push(doc.fileName)
		}
		})
		doc.wikilinks.forEach(w => {
		const slug = w.target.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+\|-+$/g, '')
		if (slug === targetFileName && !backlinks.includes(doc.fileName)) backlinks.push(doc.fileName)
		})
		})
		return backlinks
		}

+24

src/core/health.ts

		import type { AnalysisResult } from '../types/index.js'

		export function getFragmentHealth(results: AnalysisResult[]): object {
		const total = results.length
		const withFrontmatter = results.filter(r => r.fragmentMeta).length
		const withDeps = results.filter(r => r.fragmentMeta && r.fragmentMeta.depends_on.length > 0).length
		const withWikilinks = results.filter(r => r.stats.totalWikilinks > 0).length
		const withStatus = results.filter(r => r.fragmentMeta && r.fragmentMeta.status).length
		const withDescription = results.filter(r => r.fragmentMeta && r.fragmentMeta.description).length
		const withSource = results.filter(r => r.fragmentMeta && r.fragmentMeta.source).length
		const noTitle = results.filter(r => r.fragmentMeta && !r.fragmentMeta.title).length
		const issues: { file: string; issues: string[] }[] = []
		for (const r of results) {
		const fileIssues: string[] = []
		if (!r.fragmentMeta) fileIssues.push('no_frontmatter')
		else {
		if (!r.fragmentMeta.title) fileIssues.push('empty_title')
		if (!r.fragmentMeta.source) fileIssues.push('no_source')
		if (r.fragmentMeta.depends_on.length === 0 && r.stats.totalWikilinks > 0) fileIssues.push('wikilinks_no_depends_on')
		}
		if (fileIssues.length > 0) issues.push({ file: r.fileName, issues: fileIssues })
		}
		return { total, withFrontmatter, withDeps, withWikilinks, withStatus, withDescription, withSource, noTitle, filesWithIssues: issues.length, issues }
		}

+30

src/core/schema.ts

		import { z } from 'zod'

		export const CliOptions = z.object({
		directory: z.string().optional(),
		json: z.boolean().default(false),
		search: z.string().min(1, 'Search keyword cannot be empty').optional(),
		filter: z.string().regex(/^[^=]+=.+$/, 'Filter must be in format key=value').optional(),
		rank: z.boolean().default(false),
		graph: z.boolean().default(false),
		deps: z.boolean().default(false),
		orphans: z.boolean().default(false),
		backlinks: z.string().min(1, 'Backlinks target cannot be empty').optional(),
		keypoints: z.boolean().default(false),
		lintFragments: z.boolean().default(false),
		session: z.boolean().default(false),
		budget: z.number().int().positive('Budget must be a positive integer').default(100000),
		maxResults: z.number().int().nonnegative('max-results must be non-negative').default(0),
		})

		export type CliOptions = z.infer<typeof CliOptions>

		export const AnalyzerConfigSchema = z.object({
		default_directory: z.string().default(''),
		default_budget: z.number().int().positive().default(100000),
		max_tokens: z.number().int().positive().default(200000),
		max_results_default: z.number().int().nonnegative().default(20),
		session_file: z.string().default('/tmp/md-analyzer-session.json'),
		})

		export type AnalyzerConfig = z.infer<typeof AnalyzerConfigSchema>

+23

src/core/search.ts

		import * as fs from 'fs'
		import type { AnalysisResult } from '../types/index.js'

		export function searchContent(results: AnalysisResult[], keyword: string): AnalysisResult[] {
		const kw = keyword.toLowerCase()
		return results.filter(doc => {
		const content = fs.readFileSync(doc.file, 'utf-8').toLowerCase()
		return content.includes(kw)
		})
		}

		export function filterByMetadata(results: AnalysisResult[], key: string, value: string): AnalysisResult[] {
		return results.filter(doc => doc.metadata && String(doc.metadata[key] \|\| '') === value)
		}

		export function rankByRelevance(results: AnalysisResult[], keyword: string): AnalysisResult[] {
		const kw = keyword.toLowerCase()
		return [...results].sort((a, b) => {
		const countA = (fs.readFileSync(a.file, 'utf-8').toLowerCase().match(new RegExp(kw, 'g')) \|\| []).length
		const countB = (fs.readFileSync(b.file, 'utf-8').toLowerCase().match(new RegExp(kw, 'g')) \|\| []).length
		return countB - countA
		})
		}

+30

src/core/session.ts

		import * as fs from 'fs'
		import { SESSION_FILE } from '../utils/constants.js'
		import type { AnalysisResult, SessionStats } from '../types/index.js'

		export function loadSession(): SessionStats {
		try {
		return JSON.parse(fs.readFileSync(SESSION_FILE, 'utf-8'))
		} catch (e: unknown) {
		console.error('session_load: new session created')
		return { sessionId: `session-${Date.now()}`, calls: 0, totalTokens: 0, filesProcessed: 0, startTime: new Date().toISOString() }
		}
		}

		export function saveSession(session: SessionStats): void {
		fs.writeFileSync(SESSION_FILE, JSON.stringify(session, null, 2))
		}

		export function updateSessionStats(results: AnalysisResult[], session: SessionStats): SessionStats {
		const tokensThisCall = results.reduce((sum, r) => sum + r.stats.tokens, 0)
		return { ...session, calls: session.calls + 1, totalTokens: session.totalTokens + tokensThisCall, filesProcessed: session.filesProcessed + results.length }
		}

		export function getTokenBudgetReport(session: SessionStats, budget: number): object {
		const remaining = budget - session.totalTokens
		const percentUsed = Math.round((session.totalTokens / budget) * 100)
		return {
		sessionId: session.sessionId, totalCalls: session.calls, totalTokens: session.totalTokens, budget, remaining,
		percentUsed: percentUsed + '%', status: percentUsed >= 100 ? 'EXCEEDED' : percentUsed >= 80 ? 'WARNING' : 'OK'
		}
		}

+15

src/index.ts

		export { analyzeFile, scanMarkdownFiles } from './core/analyzer.js'
		export { buildGraph, findOrphans, findBacklinks } from './core/graph.js'
		export { searchContent, filterByMetadata, rankByRelevance } from './core/search.js'
		export { getFragmentHealth } from './core/health.js'
		export { loadSession, saveSession, updateSessionStats, getTokenBudgetReport } from './core/session.js'
		export { countStats } from './core/counters.js'
		export { extractFrontmatter, extractFragmentMeta, extractHeadings, extractLinks, extractWikilinks, extractTables } from './core/extractors.js'

		export { CliOptions, AnalyzerConfigSchema } from './core/schema.js'
		export type { AnalyzerConfig } from './core/schema.js'

		export type {
		Link, Wikilink, Heading, Table, FragmentMeta, Stats, SectionInfo,
		AnalysisResult, GraphNode, Graph, SessionStats, RunLog
		} from './types/index.js'

+106

src/types/index.ts

		export interface Link {
		text: string
		url: string
		isInternal: boolean
		fileName: string \| null
		}

		export interface Wikilink {
		target: string
		display: string \| null
		}

		export interface Heading {
		level: number
		text: string
		line: number
		}

		export interface Table {
		headers: string[]
		rows: string[][]
		}

		export interface FragmentMeta {
		title: string
		description: string \| null
		tags: string[]
		depends_on: string[]
		status: string \| null
		source: string \| null
		order: number \| null
		date_iso: string \| null
		}

		export interface Stats {
		totalHeadings: number
		totalLinks: number
		internalLinks: number
		externalLinks: number
		totalWikilinks: number
		wordCount: number
		charCount: number
		lineCount: number
		codeBlocks: number
		tables: number
		tokens: number
		errors?: string[]
		}

		export interface SectionInfo {
		line: number
		tokens: number
		}

		export interface AnalysisResult {
		file: string
		fileName: string
		metadata: Record<string, unknown> \| null
		fragmentMeta: FragmentMeta \| null
		headings: Heading[]
		sections: SectionInfo[]
		links: Link[]
		wikilinks: Wikilink[]
		tables: Table[]
		stats: Stats
		}

		export interface GraphNode {
		inbound: string[]
		outbound: string[]
		}

		export interface Graph {
		nodes: Record<string, GraphNode>
		edges: { source: string; target: string; type: string }[]
		}

		export interface SessionStats {
		sessionId: string
		calls: number
		totalTokens: number
		filesProcessed: number
		startTime: string
		}

		export interface RunLog {
		timestamp: string
		sessionId: string
		directory: string
		flags: string[]
		filesFound: number
		filesProcessed: number
		tokensThisCall: number
		totalSessionTokens: number
		errors: string[]
		durationMs: number
		mode: string
		}

		export interface AnalyzerConfig {
		default_directory: string
		default_budget: number
		max_tokens: number
		max_results_default: number
		session_file: string
		}

+49

src/utils/config.ts

		import * as fs from 'fs'
		import * as path from 'path'
		import { AnalyzerConfigSchema } from '../core/schema.js'
		import type { AnalyzerConfig } from '../core/schema.js'

		const DEFAULT_CONFIG: AnalyzerConfig = AnalyzerConfigSchema.parse({})

		export function getTomlConfig(tomlPath: string): AnalyzerConfig {
		try {
		const content = fs.readFileSync(tomlPath, 'utf-8')
		const config: Record<string, string> = {}
		let inConfigSection = false
		content.split('\n').forEach(line => {
		const trimmed = line.trim()
		if (trimmed === '[tool.md-analyzer.config]') { inConfigSection = true; return }
		if (inConfigSection) {
		if (trimmed.startsWith('[')) { inConfigSection = false; return }
		if (trimmed.includes('=')) {
		const separatorIdx = trimmed.indexOf('=')
		const key = trimmed.substring(0, separatorIdx).trim()
		const value = trimmed.substring(separatorIdx + 1).trim().replace(/^["']\|["']$/g, '')
		config[key] = value
		}
		}
		})
		return {
		default_directory: config['default_directory'] \|\| DEFAULT_CONFIG.default_directory,
		default_budget: parseInt(config['default_budget'] \|\| '', 10) \|\| DEFAULT_CONFIG.default_budget,
		max_tokens: parseInt(config['max_tokens'] \|\| '', 10) \|\| DEFAULT_CONFIG.max_tokens,
		max_results_default: parseInt(config['max_results_default'] \|\| '', 10) \|\| DEFAULT_CONFIG.max_results_default,
		session_file: config['session_file'] \|\| DEFAULT_CONFIG.session_file,
		}
		} catch (e: unknown) {
		console.error('config_load_error: could not read hooks.toml:', e instanceof Error ? e.message : e)
		return { ...DEFAULT_CONFIG }
		}
		}

		export function resolveConfigPath(): string {
		const candidates = [
		path.join(__dirname, '..', '..', 'hooks.toml'),
		path.join(__dirname, '..', 'hooks.toml'),
		path.join(process.cwd(), 'hooks.toml'),
		]
		for (const candidate of candidates) {
		if (fs.existsSync(candidate)) return candidate
		}
		return candidates[0]
		}

+11

src/utils/constants.ts

		import * as path from 'path'

		export const SKIP_DIRS = new Set([
		'node_modules', '.git', '.svn', '.hg',
		'services', 'data', 'appendonlydir',
		'dist', 'build', '__pycache__', '.next', 'coverage'
		])

		export const SESSION_FILE = '/tmp/md-analyzer-session.json'

		export const LOG_DIR = path.join(__dirname, '..', '..', 'log')

+9

-6

package.json

		{
		"name": "@ev3lynx/md-analyzer",
		"version": "0.1.4",
		"version": "0.1.6",
		"description": "Markdown document analyzer for AI agents - extract metadata, headings, links, tables, tokens, and key points",
		"main": "md-analyzer.js",
		"main": "dist/index.js",
		"types": "dist/index.d.ts",
		"bin": {
		"md-analyzer": "md-analyzer.js"
		"md-analyzer": "dist/cli/index.js"
		},
		@@ -15,3 +16,3 @@ "scripts": {
		"prepublish": "npm run build",
		"test": "node md-analyzer.js . --json"
		"test": "node dist/cli/index.js . --json"
		},
		@@ -41,5 +42,7 @@ "keywords": [
		"dependencies": {
		"commander": "^15.0.0",
		"js-tiktoken": "^1.0.0",
		"js-yaml": "^4.2.0",
		"micromark": "^4.0.0"
		"micromark": "^4.0.0",
		"zod": "^4.4.3"
		},
		@@ -55,3 +58,3 @@ "devDependencies": {
		"files": [
		"md-analyzer.js",
		"dist/",
		"src/",
		@@ -58,0 +61,0 @@ "hooks.toml",

-538

md-analyzer.js

		#!/usr/bin/env node
		"use strict";
		var __createBinding = (this && this.__createBinding) \|\| (Object.create ? (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		var desc = Object.getOwnPropertyDescriptor(m, k);
		if (!desc \|\| ("get" in desc ? !m.__esModule : desc.writable \|\| desc.configurable)) {
		desc = { enumerable: true, get: function() { return m[k]; } };
		}
		Object.defineProperty(o, k2, desc);
		}) : (function(o, m, k, k2) {
		if (k2 === undefined) k2 = k;
		o[k2] = m[k];
		}));
		var __setModuleDefault = (this && this.__setModuleDefault) \|\| (Object.create ? (function(o, v) {
		Object.defineProperty(o, "default", { enumerable: true, value: v });
		}) : function(o, v) {
		o["default"] = v;
		});
		var __importStar = (this && this.__importStar) \|\| (function () {
		var ownKeys = function(o) {
		ownKeys = Object.getOwnPropertyNames \|\| function (o) {
		var ar = [];
		for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
		return ar;
		};
		return ownKeys(o);
		};
		return function (mod) {
		if (mod && mod.__esModule) return mod;
		var result = {};
		if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
		__setModuleDefault(result, mod);
		return result;
		};
		})();
		Object.defineProperty(exports, "__esModule", { value: true });
		const fs = __importStar(require("fs"));
		const path = __importStar(require("path"));
		const js_tiktoken_1 = require("js-tiktoken");
		const yaml = __importStar(require("js-yaml"));
		const SKIP_DIRS = new Set([
		'node_modules', '.git', '.svn', '.hg',
		'services', 'data', 'appendonlydir',
		'dist', 'build', '__pycache__', '.next', 'coverage'
		]);
		function getTomlConfig(tomlPath) {
		try {
		const content = fs.readFileSync(tomlPath, 'utf-8');
		const config = {};
		let inConfigSection = false;
		content.split('\n').forEach(line => {
		const trimmed = line.trim();
		if (trimmed === '[tool.md-analyzer.config]') {
		inConfigSection = true;
		return;
		}
		if (inConfigSection) {
		if (trimmed.startsWith('[')) {
		inConfigSection = false;
		return;
		}
		if (trimmed.includes('=')) {
		const [key, ...valueParts] = trimmed.split('=');
		const value = valueParts.join('=').trim().replace(/^["']\|["']$/g, '');
		config[key.trim()] = value;
		}
		}
		});
		return config;
		}
		catch {
		return {};
		}
		}
		function extractFrontmatter(content) {
		const frontmatterRegex = /^---\s\n([\s\S]?)\n---\s*\n/;
		const match = content.match(frontmatterRegex);
		if (!match)
		return { metadata: null, content };
		try {
		const parsed = yaml.load(match[1]);
		const metadata = parsed && typeof parsed === 'object' ? parsed : null;
		return { metadata, content: content.substring(match[0].length) };
		}
		catch {
		return { metadata: null, content };
		}
		}
		function extractHeadings(content) {
		const headings = [];
		const headingRegex = /^(#{1,6})\s+(.+)$/gm;
		let match;
		while ((match = headingRegex.exec(content)) !== null) {
		const line = content.substring(0, match.index).split('\n').length;
		headings.push({ level: match[1].length, text: match[2].trim(), line });
		}
		return headings;
		}
		function extractLinks(content) {
		const links = [];
		const linkRegex = /\[([^\]]+)\]$([^)]+)$/g;
		let match;
		while ((match = linkRegex.exec(content)) !== null) {
		const url = match[2].trim();
		const isInternal = url.startsWith('#') \|\| (!url.startsWith('http') && !url.startsWith('//'));
		let fileName = null;
		if (isInternal && !url.startsWith('#')) {
		const baseName = path.basename(url, '.md');
		if (baseName && baseName !== url)
		fileName = baseName;
		}
		links.push({ text: match[1].trim(), url, isInternal, fileName });
		}
		return links;
		}
		function extractWikilinks(content) {
		const wikilinks = [];
		const wikiRegex = /\[\[([^\]\|]+)(?:\\|([^\]]+))?\]\]/g;
		let match;
		while ((match = wikiRegex.exec(content)) !== null) {
		wikilinks.push({ target: match[1].trim(), display: match[2]?.trim() \|\| null });
		}
		return wikilinks;
		}
		function extractFragmentMeta(metadata) {
		if (!metadata)
		return null;
		const dependsRaw = metadata.depends_on;
		const depends = Array.isArray(dependsRaw) ? dependsRaw.map(String) : (typeof dependsRaw === 'string' ? [dependsRaw] : []);
		const tags = Array.isArray(metadata.tags) ? metadata.tags.map(String) : (typeof metadata.tags === 'string' ? [metadata.tags] : []);
		return {
		title: String(metadata.title \|\| ''),
		description: metadata.description ? String(metadata.description) : null,
		tags,
		depends_on: depends,
		status: metadata.status ? String(metadata.status) : null,
		source: metadata.source ? String(metadata.source) : null,
		order: metadata.order != null ? Number(metadata.order) : null,
		date_iso: metadata.date_iso ? String(metadata.date_iso) : null,
		};
		}
		function extractTables(content) {
		const tables = [];
		const tableRegex = /\\|(.+)\\|\n\\|[-:\s\|]+\\|\n((?:\\|.+\\|\n?)+)/g;
		let match;
		while ((match = tableRegex.exec(content)) !== null) {
		const headers = match[1].split('\|').map(h => h.trim()).filter(h => h);
		const rows = [];
		match[2].trim().split('\n').forEach(row => {
		const cells = row.split('\|').map(c => c.trim()).filter(c => c);
		if (cells.length > 0)
		rows.push(cells);
		});
		tables.push({ headers, rows });
		}
		return tables;
		}
		function countStats(content) {
		const wordCount = content.split(/\s+/).filter(w => w.length > 0).length;
		const charCount = content.length;
		const lineCount = content.split('\n').length;
		const codeBlocks = (content.match(/```[\s\S]*?```/g) \|\| []).length;
		let tokens = 0;
		try {
		tokens = (0, js_tiktoken_1.encodingForModel)('gpt-4').encode(content).length;
		}
		catch {
		tokens = Math.ceil(charCount / 4);
		}
		return { wordCount, charCount, lineCount, codeBlocks, tokens };
		}
		function scanMarkdownFiles(dir) {
		const files = [], errors = [];
		function walk(dir) {
		let entries;
		try {
		entries = fs.readdirSync(dir, { withFileTypes: true });
		}
		catch (e) {
		errors.push(`permission_denied: ${dir}`);
		return;
		}
		for (const entry of entries) {
		if (entry.name.startsWith('.') \|\| SKIP_DIRS.has(entry.name))
		continue;
		const fullPath = path.join(dir, entry.name);
		try {
		if (entry.isDirectory())
		walk(fullPath);
		else if (entry.isFile() && entry.name.endsWith('.md'))
		files.push(fullPath);
		}
		catch (e) {
		errors.push(`access_error: ${fullPath}`);
		}
		}
		}
		try {
		walk(dir);
		}
		catch (e) {
		errors.push(`scan_error: ${e instanceof Error ? e.message : 'unknown'}`);
		}
		return { files, errors };
		}
		function analyzeFile(filePath) {
		const errors = [];
		let content = '';
		try {
		content = fs.readFileSync(filePath, 'utf-8');
		}
		catch (e) {
		errors.push(`file_read_error: ${e instanceof Error ? e.message : 'unknown'}`);
		return { file: filePath, fileName: path.basename(filePath, '.md'), metadata: null, fragmentMeta: null, headings: [], sections: [], links: [], wikilinks: [], tables: [],
		stats: { totalHeadings: 0, totalLinks: 0, internalLinks: 0, externalLinks: 0, totalWikilinks: 0, wordCount: 0, charCount: 0, lineCount: 0, codeBlocks: 0, tables: 0, tokens: 0, errors } };
		}
		const { metadata, content: markdownContent } = extractFrontmatter(content);
		const fragmentMeta = extractFragmentMeta(metadata);
		const headings = extractHeadings(markdownContent);
		const links = extractLinks(markdownContent);
		const wikilinks = extractWikilinks(markdownContent);
		const tables = extractTables(markdownContent);
		const counts = countStats(markdownContent);
		if (counts.tokens === 0)
		errors.push('token_count_fallback: tiktoken unavailable');
		const bodyLines = markdownContent.split('\n');
		const sections = headings.map((h, i) => {
		const startIdx = h.line - 1;
		const endIdx = i + 1 < headings.length ? headings[i + 1].line - 1 : bodyLines.length;
		const sectionText = bodyLines.slice(startIdx, endIdx).join('\n');
		let tokens = 0;
		try {
		tokens = (0, js_tiktoken_1.encodingForModel)('gpt-4').encode(sectionText).length;
		}
		catch {
		tokens = Math.ceil(sectionText.length / 4);
		}
		return { line: h.line, tokens };
		});
		return { file: filePath, fileName: path.basename(filePath, '.md'), metadata, fragmentMeta, headings, sections, links, wikilinks, tables,
		stats: { totalHeadings: headings.length, totalLinks: links.length, internalLinks: links.filter(l => l.isInternal).length,
		externalLinks: links.filter(l => !l.isInternal).length, totalWikilinks: wikilinks.length, wordCount: counts.wordCount,
		charCount: counts.charCount, lineCount: counts.lineCount, codeBlocks: counts.codeBlocks, tables: tables.length,
		tokens: counts.tokens, errors: errors.length > 0 ? errors : undefined } };
		}
		function addEdge(graph, edges, source, target, type) {
		if (!graph[source])
		graph[source] = { inbound: [], outbound: [] };
		if (!graph[target])
		graph[target] = { inbound: [], outbound: [] };
		if (!graph[source].outbound.includes(target))
		graph[source].outbound.push(target);
		if (!graph[target].inbound.includes(source))
		graph[target].inbound.push(source);
		edges.push({ source, target, type });
		}
		function buildGraph(results) {
		const graph = {}, edges = [];
		results.forEach(doc => {
		const source = doc.fileName;
		if (!graph[source])
		graph[source] = { inbound: [], outbound: [] };
		doc.links.forEach(link => {
		if (link.isInternal && link.fileName)
		addEdge(graph, edges, source, link.fileName, 'link');
		});
		doc.wikilinks.forEach(w => {
		const slug = w.target.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+\|-+$/g, '');
		if (slug !== source && results.some(r => r.fileName === slug))
		addEdge(graph, edges, source, slug, 'wikilink');
		});
		if (doc.fragmentMeta) {
		doc.fragmentMeta.depends_on.forEach(dep => {
		const depName = dep.replace(/\.md$/, '');
		if (depName !== source && results.some(r => r.fileName === depName))
		addEdge(graph, edges, source, depName, 'depends_on');
		});
		}
		});
		return { nodes: graph, edges };
		}
		function findOrphans(graph, excludeOrphansWithDeps) {
		return Object.keys(graph.nodes).filter(node => {
		if (excludeOrphansWithDeps?.has(node))
		return false;
		return graph.nodes[node].inbound.length === 0 && graph.nodes[node].outbound.length === 0;
		});
		}
		function findBacklinks(results, targetFileName) {
		const backlinks = [];
		results.forEach(doc => {
		doc.links.forEach(link => {
		if (link.isInternal && link.fileName === targetFileName && !backlinks.includes(doc.fileName)) {
		backlinks.push(doc.fileName);
		}
		});
		doc.wikilinks.forEach(w => {
		const slug = w.target.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+\|-+$/g, '');
		if (slug === targetFileName && !backlinks.includes(doc.fileName))
		backlinks.push(doc.fileName);
		});
		});
		return backlinks;
		}
		function searchContent(results, keyword) {
		const kw = keyword.toLowerCase();
		return results.filter(doc => {
		const content = fs.readFileSync(doc.file, 'utf-8').toLowerCase();
		return content.includes(kw);
		});
		}
		function filterByMetadata(results, key, value) {
		return results.filter(doc => doc.metadata && String(doc.metadata[key] \|\| '') === value);
		}
		function rankByRelevance(results, keyword) {
		const kw = keyword.toLowerCase();
		return [...results].sort((a, b) => {
		const countA = (fs.readFileSync(a.file, 'utf-8').toLowerCase().match(new RegExp(kw, 'g')) \|\| []).length;
		const countB = (fs.readFileSync(b.file, 'utf-8').toLowerCase().match(new RegExp(kw, 'g')) \|\| []).length;
		return countB - countA;
		});
		}
		function extractKeyPoints(doc) {
		return { fileName: doc.fileName, title: doc.headings[0]?.text \|\| doc.fileName, level: doc.headings[0]?.level \|\| 1,
		summary: { totalHeadings: doc.stats.totalHeadings, totalLinks: doc.stats.totalLinks, totalWikilinks: doc.stats.totalWikilinks, totalTokens: doc.stats.tokens, wordCount: doc.stats.wordCount },
		keyHeadings: doc.headings.slice(0, 10).map((h, i) => ({
		level: h.level, text: h.text, line: h.line,
		tokens: doc.sections?.[i]?.tokens ?? 0
		})),
		importantLinks: doc.links.filter(l => !l.isInternal).slice(0, 3).map(l => ({ text: l.text, url: l.url })),
		internalReferences: doc.links.filter(l => l.isInternal && l.fileName).slice(0, 5).map(l => l.fileName),
		metadata: doc.metadata, readingTime: Math.ceil(doc.stats.wordCount / 200) + ' min' };
		}
		const SESSION_FILE = '/tmp/md-analyzer-session.json';
		function loadSession() {
		try {
		return JSON.parse(fs.readFileSync(SESSION_FILE, 'utf-8'));
		}
		catch {
		return { sessionId: `session-${Date.now()}`, calls: 0, totalTokens: 0, filesProcessed: 0, startTime: new Date().toISOString() };
		}
		}
		function saveSession(session) { fs.writeFileSync(SESSION_FILE, JSON.stringify(session, null, 2)); }
		function updateSessionStats(results, session) {
		const tokensThisCall = results.reduce((sum, r) => sum + r.stats.tokens, 0);
		return { ...session, calls: session.calls + 1, totalTokens: session.totalTokens + tokensThisCall, filesProcessed: session.filesProcessed + results.length };
		}
		function getTokenBudgetReport(session, budget) {
		const remaining = budget - session.totalTokens;
		const percentUsed = Math.round((session.totalTokens / budget) * 100);
		return { sessionId: session.sessionId, totalCalls: session.calls, totalTokens: session.totalTokens, budget, remaining,
		percentUsed: percentUsed + '%', status: percentUsed >= 100 ? 'EXCEEDED' : percentUsed >= 80 ? 'WARNING' : 'OK' };
		}
		const LOG_DIR = path.join(__dirname, 'log');
		function writeRunLog(log) {
		try {
		if (!fs.existsSync(LOG_DIR))
		fs.mkdirSync(LOG_DIR, { recursive: true });
		const logFile = path.join(LOG_DIR, `${log.sessionId}.json`);
		const existing = fs.existsSync(logFile) ? JSON.parse(fs.readFileSync(logFile, 'utf-8')) : [];
		existing.push(log);
		fs.writeFileSync(logFile, JSON.stringify(existing, null, 2));
		}
		catch { }
		}
		function getPositionalArg(start) {
		for (let i = start; i < process.argv.length; i++) {
		if (!process.argv[i].startsWith('-'))
		return process.argv[i];
		}
		return '';
		}
		function getFlagArg(flag) {
		const idx = process.argv.indexOf(flag);
		return idx > 0 && idx + 1 < process.argv.length ? process.argv[idx + 1] : null;
		}
		function getFragmentHealth(results) {
		const total = results.length;
		const withFrontmatter = results.filter(r => r.fragmentMeta).length;
		const withDeps = results.filter(r => r.fragmentMeta && r.fragmentMeta.depends_on.length > 0).length;
		const withWikilinks = results.filter(r => r.stats.totalWikilinks > 0).length;
		const withStatus = results.filter(r => r.fragmentMeta && r.fragmentMeta.status).length;
		const withDescription = results.filter(r => r.fragmentMeta && r.fragmentMeta.description).length;
		const withSource = results.filter(r => r.fragmentMeta && r.fragmentMeta.source).length;
		const noTitle = results.filter(r => r.fragmentMeta && !r.fragmentMeta.title).length;
		const issues = [];
		for (const r of results) {
		const fileIssues = [];
		if (!r.fragmentMeta)
		fileIssues.push('no_frontmatter');
		else {
		if (!r.fragmentMeta.title)
		fileIssues.push('empty_title');
		if (!r.fragmentMeta.source)
		fileIssues.push('no_source');
		if (r.fragmentMeta.depends_on.length === 0 && r.stats.totalWikilinks > 0)
		fileIssues.push('wikilinks_no_depends_on');
		}
		if (fileIssues.length > 0)
		issues.push({ file: r.fileName, issues: fileIssues });
		}
		return { total, withFrontmatter, withDeps, withWikilinks, withStatus, withDescription, withSource, noTitle, filesWithIssues: issues.length, issues };
		}
		function main() {
		const startTime = Date.now();
		const configPath = path.join(__dirname, 'hooks.toml');
		const config = getTomlConfig(configPath);
		if (process.argv.includes('--help') \|\| process.argv.includes('-h')) {
		console.log(`md-analyzer - Markdown document analyzer for AI agents

		Usage: md-analyzer <directory> [options]

		Options:
		--json Output as JSON
		--search <kw> Search keyword in content
		--filter <k=v> Filter by metadata field
		--rank Rank results by relevance
		--graph Document relationship graph
		--deps Dependency graph (DAG order + levels)
		--orphans Find unreferenced docs
		--backlinks <doc> Find docs linking to <doc>
		--keypoints Quick overview (single-shot)
		--lint-fragments Fragment health check
		--session Token budget report
		--budget <n> Set token budget limit
		--max-results <n> Limit output
		--help, -h Show this help message

		Examples:
		md-analyzer /path/to/docs --keypoints --json
		md-analyzer . --search "task" --rank --json
		md-analyzer . --session --budget 50000 --json
		md-analyzer . --orphans --json
		md-analyzer . --lint-fragments --json
		md-analyzer . --deps --json`);
		process.exit(0);
		}
		const cliDir = getPositionalArg(2);
		const targetDir = cliDir \|\| process.env['MD_ANALYZER_DEFAULT_DIR'] \|\| config['default_directory'] \|\| process.cwd();
		const jsonOnly = process.argv.includes('--json');
		const graphMode = process.argv.includes('--graph');
		const orphansMode = process.argv.includes('--orphans');
		const rankMode = process.argv.includes('--rank');
		const sessionMode = process.argv.includes('--session');
		const keypointsMode = process.argv.includes('--keypoints');
		const depsMode = process.argv.includes('--deps');
		const lintFragmentsMode = process.argv.includes('--lint-fragments');
		const budget = parseInt(getFlagArg('--budget') \|\| '', 10) \|\| 100000;
		const maxResults = parseInt(getFlagArg('--max-results') \|\| '', 10) \|\| 0;
		const backlinksTarget = getFlagArg('--backlinks');
		const searchKeyword = getFlagArg('--search');
		const filterRaw = getFlagArg('--filter');
		const session = loadSession();
		if (!jsonOnly)
		console.log(`Scanning: ${targetDir}\n`);
		const { files: mdFiles, errors: scanErrors } = scanMarkdownFiles(targetDir);
		if (!jsonOnly) {
		console.log(`Found ${mdFiles.length} .md files\n`);
		if (scanErrors.length > 0)
		console.log(`Warnings: ${scanErrors.length} directories skipped\n`);
		}
		let results = mdFiles.map(file => analyzeFile(file));
		if (scanErrors.length > 0 && results.length > 0) {
		if (!results[0].stats.errors)
		results[0].stats.errors = [];
		results[0].stats.errors.push(...scanErrors);
		}
		if (filterRaw && filterRaw.includes('=')) {
		const [key, value] = filterRaw.split('=');
		results = filterByMetadata(results, key, value);
		if (!jsonOnly)
		console.log(`Filtered by ${key}=${value}: ${results.length} results\n`);
		}
		if (searchKeyword) {
		results = searchContent(results, searchKeyword);
		if (!jsonOnly)
		console.log(`Search "${searchKeyword}": ${results.length} results\n`);
		}
		if (rankMode && searchKeyword) {
		results = rankByRelevance(results, searchKeyword);
		if (!jsonOnly)
		console.log(`Ranked by relevance to "${searchKeyword}"\n`);
		}
		let limitedResults = results;
		if (maxResults > 0 && results.length > maxResults) {
		if (!jsonOnly)
		console.log(`Warning: Limiting output to ${maxResults} of ${results.length} results\n`);
		limitedResults = results.slice(0, maxResults);
		}
		const updatedSession = updateSessionStats(results, session);
		saveSession(updatedSession);
		const tokensThisCall = results.reduce((sum, r) => sum + r.stats.tokens, 0);
		if (sessionMode)
		console.log(JSON.stringify(getTokenBudgetReport(updatedSession, budget), null, 2));
		else if (keypointsMode)
		console.log(JSON.stringify(limitedResults.map(doc => extractKeyPoints(doc)), null, 2));
		else if (lintFragmentsMode)
		console.log(JSON.stringify(getFragmentHealth(limitedResults), null, 2));
		else if (depsMode) {
		const graph = buildGraph(limitedResults);
		console.log(JSON.stringify({ nodes: Object.keys(graph.nodes), edges: graph.edges, tokensThisCall }, null, 2));
		}
		else if (orphansMode) {
		const orphans = findOrphans(buildGraph(limitedResults));
		console.log(JSON.stringify({ orphans, count: orphans.length, tokensThisCall }, null, 2));
		}
		else if (backlinksTarget) {
		const backlinks = findBacklinks(limitedResults, backlinksTarget);
		console.log(JSON.stringify({ target: backlinksTarget, backlinks, count: backlinks.length, tokensThisCall }, null, 2));
		}
		else if (graphMode)
		console.log(JSON.stringify(buildGraph(limitedResults), null, 2));
		else {
		if (!jsonOnly) {
		console.log(`\nTokens this call: ${tokensThisCall}`);
		console.log(`Total session tokens: ${updatedSession.totalTokens}\n`);
		}
		;
		console.log(JSON.stringify(limitedResults, null, 2));
		}
		const flags = process.argv.slice(2).filter(a => a.startsWith('--')).map(a => a.replace(/=.*/, ''));
		const mode = depsMode ? 'deps' : lintFragmentsMode ? 'lint-fragments' : sessionMode ? 'session' : keypointsMode ? 'keypoints' : orphansMode ? 'orphans' : backlinksTarget ? 'backlinks' : graphMode ? 'graph' : searchKeyword ? 'search' : 'default';
		writeRunLog({
		timestamp: new Date().toISOString(),
		sessionId: updatedSession.sessionId,
		directory: targetDir,
		flags,
		filesFound: mdFiles.length,
		filesProcessed: results.length,
		tokensThisCall,
		totalSessionTokens: updatedSession.totalTokens,
		errors: scanErrors,
		durationMs: Date.now() - startTime,
		mode
		});
		}
		main();
		//# sourceMappingURL=md-analyzer.js.map

-498

src/md-analyzer.ts

		#!/usr/bin/env node
		import * as fs from 'fs'
		import * as path from 'path'
		import { encodingForModel } from 'js-tiktoken'
		import * as yaml from 'js-yaml'

		const SKIP_DIRS = new Set([
		'node_modules', '.git', '.svn', '.hg',
		'services', 'data', 'appendonlydir',
		'dist', 'build', '__pycache__', '.next', 'coverage'
		])

		interface Link { text: string; url: string; isInternal: boolean; fileName: string \| null }
		interface Wikilink { target: string; display: string \| null }
		interface Heading { level: number; text: string; line: number }
		interface Table { headers: string[]; rows: string[][] }
		interface FragmentMeta {
		title: string
		description: string \| null
		tags: string[]
		depends_on: string[]
		status: string \| null
		source: string \| null
		order: number \| null
		date_iso: string \| null
		}
		interface Stats {
		totalHeadings: number; totalLinks: number; internalLinks: number; externalLinks: number
		totalWikilinks: number; wordCount: number; charCount: number; lineCount: number
		codeBlocks: number; tables: number; tokens: number; errors?: string[]
		}
		interface SectionInfo { line: number; tokens: number }

		interface AnalysisResult {
		file: string; fileName: string
		metadata: Record<string, string> \| null
		fragmentMeta: FragmentMeta \| null
		headings: Heading[]; sections: SectionInfo[]
		links: Link[]; wikilinks: Wikilink[]; tables: Table[]
		stats: Stats
		}
		interface GraphNode { inbound: string[]; outbound: string[] }
		interface Graph { nodes: Record<string, GraphNode>; edges: { source: string; target: string; type: string }[] }
		interface SessionStats { sessionId: string; calls: number; totalTokens: number; filesProcessed: number; startTime: string }

		function getTomlConfig(tomlPath: string): Record<string, any> {
		try {
		const content = fs.readFileSync(tomlPath, 'utf-8')
		const config: Record<string, any> = {}
		let inConfigSection = false
		content.split('\n').forEach(line => {
		const trimmed = line.trim()
		if (trimmed === '[tool.md-analyzer.config]') { inConfigSection = true; return }
		if (inConfigSection) {
		if (trimmed.startsWith('[')) { inConfigSection = false; return }
		if (trimmed.includes('=')) {
		const [key, ...valueParts] = trimmed.split('=')
		const value = valueParts.join('=').trim().replace(/^["']\|["']$/g, '')
		config[key.trim()] = value
		}
		}
		})
		return config
		} catch { return {} }
		}

		function extractFrontmatter(content: string): { metadata: Record<string, any> \| null; content: string } {
		const frontmatterRegex = /^---\s\n([\s\S]?)\n---\s*\n/
		const match = content.match(frontmatterRegex)
		if (!match) return { metadata: null, content }
		try {
		const parsed = yaml.load(match[1])
		const metadata = parsed && typeof parsed === 'object' ? parsed as Record<string, any> : null
		return { metadata, content: content.substring(match[0].length) }
		} catch {
		return { metadata: null, content }
		}
		}

		function extractHeadings(content: string): Heading[] {
		const headings: Heading[] = []
		const headingRegex = /^(#{1,6})\s+(.+)$/gm
		let match
		while ((match = headingRegex.exec(content)) !== null) {
		const line = content.substring(0, match.index).split('\n').length
		headings.push({ level: match[1].length, text: match[2].trim(), line })
		}
		return headings
		}

		function extractLinks(content: string): Link[] {
		const links: Link[] = []
		const linkRegex = /\[([^\]]+)\]$([^)]+)$/g
		let match
		while ((match = linkRegex.exec(content)) !== null) {
		const url = match[2].trim()
		const isInternal = url.startsWith('#') \|\| (!url.startsWith('http') && !url.startsWith('//'))
		let fileName: string \| null = null
		if (isInternal && !url.startsWith('#')) {
		const baseName = path.basename(url, '.md')
		if (baseName && baseName !== url) fileName = baseName
		}
		links.push({ text: match[1].trim(), url, isInternal, fileName })
		}
		return links
		}

		function extractWikilinks(content: string): Wikilink[] {
		const wikilinks: Wikilink[] = []
		const wikiRegex = /\[\[([^\]\|]+)(?:\\|([^\]]+))?\]\]/g
		let match
		while ((match = wikiRegex.exec(content)) !== null) {
		wikilinks.push({ target: match[1].trim(), display: match[2]?.trim() \|\| null })
		}
		return wikilinks
		}

		function extractFragmentMeta(metadata: Record<string, any> \| null): FragmentMeta \| null {
		if (!metadata) return null
		const dependsRaw = metadata.depends_on
		const depends: string[] = Array.isArray(dependsRaw) ? dependsRaw.map(String) : (typeof dependsRaw === 'string' ? [dependsRaw] : [])
		const tags: string[] = Array.isArray(metadata.tags) ? metadata.tags.map(String) : (typeof metadata.tags === 'string' ? [metadata.tags] : [])
		return {
		title: String(metadata.title \|\| ''),
		description: metadata.description ? String(metadata.description) : null,
		tags,
		depends_on: depends,
		status: metadata.status ? String(metadata.status) : null,
		source: metadata.source ? String(metadata.source) : null,
		order: metadata.order != null ? Number(metadata.order) : null,
		date_iso: metadata.date_iso ? String(metadata.date_iso) : null,
		}
		}

		function extractTables(content: string): Table[] {
		const tables: Table[] = []
		const tableRegex = /\\|(.+)\\|\n\\|[-:\s\|]+\\|\n((?:\\|.+\\|\n?)+)/g
		let match
		while ((match = tableRegex.exec(content)) !== null) {
		const headers = match[1].split('\|').map(h => h.trim()).filter(h => h)
		const rows: string[][] = []
		match[2].trim().split('\n').forEach(row => {
		const cells = row.split('\|').map(c => c.trim()).filter(c => c)
		if (cells.length > 0) rows.push(cells)
		})
		tables.push({ headers, rows })
		}
		return tables
		}

		function countStats(content: string): { wordCount: number; charCount: number; lineCount: number; codeBlocks: number; tokens: number } {
		const wordCount = content.split(/\s+/).filter(w => w.length > 0).length
		const charCount = content.length
		const lineCount = content.split('\n').length
		const codeBlocks = (content.match(/```[\s\S]*?```/g) \|\| []).length
		let tokens = 0
		try { tokens = encodingForModel('gpt-4').encode(content).length } catch { tokens = Math.ceil(charCount / 4) }
		return { wordCount, charCount, lineCount, codeBlocks, tokens }
		}

		function scanMarkdownFiles(dir: string): { files: string[]; errors: string[] } {
		const files: string[] = [], errors: string[] = []
		function walk(dir: string): void {
		let entries
		try { entries = fs.readdirSync(dir, { withFileTypes: true }) }
		catch (e) { errors.push(`permission_denied: ${dir}`); return }
		for (const entry of entries) {
		if (entry.name.startsWith('.') \|\| SKIP_DIRS.has(entry.name)) continue
		const fullPath = path.join(dir, entry.name)
		try {
		if (entry.isDirectory()) walk(fullPath)
		else if (entry.isFile() && entry.name.endsWith('.md')) files.push(fullPath)
		} catch (e) { errors.push(`access_error: ${fullPath}`) }
		}
		}
		try { walk(dir) } catch (e) { errors.push(`scan_error: ${e instanceof Error ? e.message : 'unknown'}`) }
		return { files, errors }
		}

		function analyzeFile(filePath: string): AnalysisResult {
		const errors: string[] = []
		let content = ''
		try { content = fs.readFileSync(filePath, 'utf-8') }
		catch (e) {
		errors.push(`file_read_error: ${e instanceof Error ? e.message : 'unknown'}`)
		return { file: filePath, fileName: path.basename(filePath, '.md'), metadata: null, fragmentMeta: null, headings: [], sections: [], links: [], wikilinks: [], tables: [],
		stats: { totalHeadings: 0, totalLinks: 0, internalLinks: 0, externalLinks: 0, totalWikilinks: 0, wordCount: 0, charCount: 0, lineCount: 0, codeBlocks: 0, tables: 0, tokens: 0, errors } }
		}
		const { metadata, content: markdownContent } = extractFrontmatter(content)
		const fragmentMeta = extractFragmentMeta(metadata)
		const headings = extractHeadings(markdownContent)
		const links = extractLinks(markdownContent)
		const wikilinks = extractWikilinks(markdownContent)
		const tables = extractTables(markdownContent)
		const counts = countStats(markdownContent)
		if (counts.tokens === 0) errors.push('token_count_fallback: tiktoken unavailable')

		const bodyLines = markdownContent.split('\n')
		const sections = headings.map((h, i) => {
		const startIdx = h.line - 1
		const endIdx = i + 1 < headings.length ? headings[i + 1].line - 1 : bodyLines.length
		const sectionText = bodyLines.slice(startIdx, endIdx).join('\n')
		let tokens = 0
		try { tokens = encodingForModel('gpt-4').encode(sectionText).length }
		catch { tokens = Math.ceil(sectionText.length / 4) }
		return { line: h.line, tokens }
		})

		return { file: filePath, fileName: path.basename(filePath, '.md'), metadata, fragmentMeta, headings, sections, links, wikilinks, tables,
		stats: { totalHeadings: headings.length, totalLinks: links.length, internalLinks: links.filter(l => l.isInternal).length,
		externalLinks: links.filter(l => !l.isInternal).length, totalWikilinks: wikilinks.length, wordCount: counts.wordCount,
		charCount: counts.charCount, lineCount: counts.lineCount, codeBlocks: counts.codeBlocks, tables: tables.length,
		tokens: counts.tokens, errors: errors.length > 0 ? errors : undefined } }
		}

		function addEdge(graph: Record<string, GraphNode>, edges: { source: string; target: string; type: string }[], source: string, target: string, type: string): void {
		if (!graph[source]) graph[source] = { inbound: [], outbound: [] }
		if (!graph[target]) graph[target] = { inbound: [], outbound: [] }
		if (!graph[source].outbound.includes(target)) graph[source].outbound.push(target)
		if (!graph[target].inbound.includes(source)) graph[target].inbound.push(source)
		edges.push({ source, target, type })
		}

		function buildGraph(results: AnalysisResult[]): Graph {
		const graph: Record<string, GraphNode> = {}, edges: { source: string; target: string; type: string }[] = []
		results.forEach(doc => {
		const source = doc.fileName
		if (!graph[source]) graph[source] = { inbound: [], outbound: [] }
		doc.links.forEach(link => {
		if (link.isInternal && link.fileName) addEdge(graph, edges, source, link.fileName, 'link')
		})
		doc.wikilinks.forEach(w => {
		const slug = w.target.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+\|-+$/g, '')
		if (slug !== source && results.some(r => r.fileName === slug)) addEdge(graph, edges, source, slug, 'wikilink')
		})
		if (doc.fragmentMeta) {
		doc.fragmentMeta.depends_on.forEach(dep => {
		const depName = dep.replace(/\.md$/, '')
		if (depName !== source && results.some(r => r.fileName === depName)) addEdge(graph, edges, source, depName, 'depends_on')
		})
		}
		})
		return { nodes: graph, edges }
		}

		function findOrphans(graph: Graph, excludeOrphansWithDeps?: Set<string>): string[] {
		return Object.keys(graph.nodes).filter(node => {
		if (excludeOrphansWithDeps?.has(node)) return false
		return graph.nodes[node].inbound.length === 0 && graph.nodes[node].outbound.length === 0
		})
		}

		function findBacklinks(results: AnalysisResult[], targetFileName: string): string[] {
		const backlinks: string[] = []
		results.forEach(doc => {
		doc.links.forEach(link => {
		if (link.isInternal && link.fileName === targetFileName && !backlinks.includes(doc.fileName)) {
		backlinks.push(doc.fileName)
		}
		})
		doc.wikilinks.forEach(w => {
		const slug = w.target.toLowerCase().replace(/[^a-z0-9]+/g, '-').replace(/^-+\|-+$/g, '')
		if (slug === targetFileName && !backlinks.includes(doc.fileName)) backlinks.push(doc.fileName)
		})
		})
		return backlinks
		}

		function searchContent(results: AnalysisResult[], keyword: string): AnalysisResult[] {
		const kw = keyword.toLowerCase()
		return results.filter(doc => {
		const content = fs.readFileSync(doc.file, 'utf-8').toLowerCase()
		return content.includes(kw)
		})
		}

		function filterByMetadata(results: AnalysisResult[], key: string, value: string): AnalysisResult[] {
		return results.filter(doc => doc.metadata && String(doc.metadata[key] \|\| '') === value)
		}

		function rankByRelevance(results: AnalysisResult[], keyword: string): AnalysisResult[] {
		const kw = keyword.toLowerCase()
		return [...results].sort((a, b) => {
		const countA = (fs.readFileSync(a.file, 'utf-8').toLowerCase().match(new RegExp(kw, 'g')) \|\| []).length
		const countB = (fs.readFileSync(b.file, 'utf-8').toLowerCase().match(new RegExp(kw, 'g')) \|\| []).length
		return countB - countA
		})
		}

		function extractKeyPoints(doc: AnalysisResult): object {
		return { fileName: doc.fileName, title: doc.headings[0]?.text \|\| doc.fileName, level: doc.headings[0]?.level \|\| 1,
		summary: { totalHeadings: doc.stats.totalHeadings, totalLinks: doc.stats.totalLinks, totalWikilinks: doc.stats.totalWikilinks, totalTokens: doc.stats.tokens, wordCount: doc.stats.wordCount },
		keyHeadings: doc.headings.slice(0, 10).map((h, i) => ({
		level: h.level, text: h.text, line: h.line,
		tokens: doc.sections?.[i]?.tokens ?? 0
		})),
		importantLinks: doc.links.filter(l => !l.isInternal).slice(0, 3).map(l => ({ text: l.text, url: l.url })),
		internalReferences: doc.links.filter(l => l.isInternal && l.fileName).slice(0, 5).map(l => l.fileName),
		metadata: doc.metadata, readingTime: Math.ceil(doc.stats.wordCount / 200) + ' min' }
		}

		const SESSION_FILE = '/tmp/md-analyzer-session.json'

		function loadSession(): SessionStats {
		try { return JSON.parse(fs.readFileSync(SESSION_FILE, 'utf-8')) }
		catch { return { sessionId: `session-${Date.now()}`, calls: 0, totalTokens: 0, filesProcessed: 0, startTime: new Date().toISOString() } }
		}

		function saveSession(session: SessionStats): void { fs.writeFileSync(SESSION_FILE, JSON.stringify(session, null, 2)) }

		function updateSessionStats(results: AnalysisResult[], session: SessionStats): SessionStats {
		const tokensThisCall = results.reduce((sum, r) => sum + r.stats.tokens, 0)
		return { ...session, calls: session.calls + 1, totalTokens: session.totalTokens + tokensThisCall, filesProcessed: session.filesProcessed + results.length }
		}

		function getTokenBudgetReport(session: SessionStats, budget: number): object {
		const remaining = budget - session.totalTokens
		const percentUsed = Math.round((session.totalTokens / budget) * 100)
		return { sessionId: session.sessionId, totalCalls: session.calls, totalTokens: session.totalTokens, budget, remaining,
		percentUsed: percentUsed + '%', status: percentUsed >= 100 ? 'EXCEEDED' : percentUsed >= 80 ? 'WARNING' : 'OK' }
		}

		const LOG_DIR = path.join(__dirname, 'log')

		interface RunLog {
		timestamp: string
		sessionId: string
		directory: string
		flags: string[]
		filesFound: number
		filesProcessed: number
		tokensThisCall: number
		totalSessionTokens: number
		errors: string[]
		durationMs: number
		mode: string
		}

		function writeRunLog(log: RunLog): void {
		try {
		if (!fs.existsSync(LOG_DIR)) fs.mkdirSync(LOG_DIR, { recursive: true })
		const logFile = path.join(LOG_DIR, `${log.sessionId}.json`)
		const existing: RunLog[] = fs.existsSync(logFile) ? JSON.parse(fs.readFileSync(logFile, 'utf-8')) : []
		existing.push(log)
		fs.writeFileSync(logFile, JSON.stringify(existing, null, 2))
		} catch {}
		}

		function getPositionalArg(start: number): string {
		for (let i = start; i < process.argv.length; i++) {
		if (!process.argv[i].startsWith('-')) return process.argv[i]
		}
		return ''
		}

		function getFlagArg(flag: string): string \| null {
		const idx = process.argv.indexOf(flag)
		return idx > 0 && idx + 1 < process.argv.length ? process.argv[idx + 1] : null
		}

		function getFragmentHealth(results: AnalysisResult[]): object {
		const total = results.length
		const withFrontmatter = results.filter(r => r.fragmentMeta).length
		const withDeps = results.filter(r => r.fragmentMeta && r.fragmentMeta.depends_on.length > 0).length
		const withWikilinks = results.filter(r => r.stats.totalWikilinks > 0).length
		const withStatus = results.filter(r => r.fragmentMeta && r.fragmentMeta.status).length
		const withDescription = results.filter(r => r.fragmentMeta && r.fragmentMeta.description).length
		const withSource = results.filter(r => r.fragmentMeta && r.fragmentMeta.source).length
		const noTitle = results.filter(r => r.fragmentMeta && !r.fragmentMeta.title).length
		const issues: { file: string; issues: string[] }[] = []
		for (const r of results) {
		const fileIssues: string[] = []
		if (!r.fragmentMeta) fileIssues.push('no_frontmatter')
		else {
		if (!r.fragmentMeta.title) fileIssues.push('empty_title')
		if (!r.fragmentMeta.source) fileIssues.push('no_source')
		if (r.fragmentMeta.depends_on.length === 0 && r.stats.totalWikilinks > 0) fileIssues.push('wikilinks_no_depends_on')
		}
		if (fileIssues.length > 0) issues.push({ file: r.fileName, issues: fileIssues })
		}
		return { total, withFrontmatter, withDeps, withWikilinks, withStatus, withDescription, withSource, noTitle, filesWithIssues: issues.length, issues }
		}

		function main(): void {
		const startTime = Date.now()
		const configPath = path.join(__dirname, 'hooks.toml')
		const config = getTomlConfig(configPath)

		if (process.argv.includes('--help') \|\| process.argv.includes('-h')) {
		console.log(`md-analyzer - Markdown document analyzer for AI agents

		Usage: md-analyzer <directory> [options]

		Options:
		--json Output as JSON
		--search <kw> Search keyword in content
		--filter <k=v> Filter by metadata field
		--rank Rank results by relevance
		--graph Document relationship graph
		--deps Dependency graph (DAG order + levels)
		--orphans Find unreferenced docs
		--backlinks <doc> Find docs linking to <doc>
		--keypoints Quick overview (single-shot)
		--lint-fragments Fragment health check
		--session Token budget report
		--budget <n> Set token budget limit
		--max-results <n> Limit output
		--help, -h Show this help message

		Examples:
		md-analyzer /path/to/docs --keypoints --json
		md-analyzer . --search "task" --rank --json
		md-analyzer . --session --budget 50000 --json
		md-analyzer . --orphans --json
		md-analyzer . --lint-fragments --json
		md-analyzer . --deps --json`)
		process.exit(0)
		}

		const cliDir = getPositionalArg(2)
		const targetDir = cliDir \|\| process.env['MD_ANALYZER_DEFAULT_DIR'] \|\| config['default_directory'] \|\| process.cwd()
		const jsonOnly = process.argv.includes('--json')
		const graphMode = process.argv.includes('--graph')
		const orphansMode = process.argv.includes('--orphans')
		const rankMode = process.argv.includes('--rank')
		const sessionMode = process.argv.includes('--session')
		const keypointsMode = process.argv.includes('--keypoints')

		const depsMode = process.argv.includes('--deps')
		const lintFragmentsMode = process.argv.includes('--lint-fragments')
		const budget = parseInt(getFlagArg('--budget') \|\| '', 10) \|\| 100000
		const maxResults = parseInt(getFlagArg('--max-results') \|\| '', 10) \|\| 0
		const backlinksTarget = getFlagArg('--backlinks')
		const searchKeyword = getFlagArg('--search')
		const filterRaw = getFlagArg('--filter')

		const session = loadSession()
		if (!jsonOnly) console.log(`Scanning: ${targetDir}\n`)

		const { files: mdFiles, errors: scanErrors } = scanMarkdownFiles(targetDir)
		if (!jsonOnly) { console.log(`Found ${mdFiles.length} .md files\n`); if (scanErrors.length > 0) console.log(`Warnings: ${scanErrors.length} directories skipped\n`) }

		let results = mdFiles.map(file => analyzeFile(file))
		if (scanErrors.length > 0 && results.length > 0) { if (!results[0].stats.errors) results[0].stats.errors = []; results[0].stats.errors.push(...scanErrors) }

		if (filterRaw && filterRaw.includes('=')) {
		const [key, value] = filterRaw.split('=')
		results = filterByMetadata(results, key, value)
		if (!jsonOnly) console.log(`Filtered by ${key}=${value}: ${results.length} results\n`)
		}

		if (searchKeyword) {
		results = searchContent(results, searchKeyword)
		if (!jsonOnly) console.log(`Search "${searchKeyword}": ${results.length} results\n`)
		}

		if (rankMode && searchKeyword) {
		results = rankByRelevance(results, searchKeyword)
		if (!jsonOnly) console.log(`Ranked by relevance to "${searchKeyword}"\n`)
		}

		let limitedResults = results
		if (maxResults > 0 && results.length > maxResults) {
		if (!jsonOnly) console.log(`Warning: Limiting output to ${maxResults} of ${results.length} results\n`)
		limitedResults = results.slice(0, maxResults)
		}

		const updatedSession = updateSessionStats(results, session)
		saveSession(updatedSession)
		const tokensThisCall = results.reduce((sum, r) => sum + r.stats.tokens, 0)

		if (sessionMode) console.log(JSON.stringify(getTokenBudgetReport(updatedSession, budget), null, 2))
		else if (keypointsMode) console.log(JSON.stringify(limitedResults.map(doc => extractKeyPoints(doc)), null, 2))
		else if (lintFragmentsMode) console.log(JSON.stringify(getFragmentHealth(limitedResults), null, 2))
		else if (depsMode) { const graph = buildGraph(limitedResults); console.log(JSON.stringify({ nodes: Object.keys(graph.nodes), edges: graph.edges, tokensThisCall }, null, 2)) }
		else if (orphansMode) { const orphans = findOrphans(buildGraph(limitedResults)); console.log(JSON.stringify({ orphans, count: orphans.length, tokensThisCall }, null, 2)) }
		else if (backlinksTarget) { const backlinks = findBacklinks(limitedResults, backlinksTarget); console.log(JSON.stringify({ target: backlinksTarget, backlinks, count: backlinks.length, tokensThisCall }, null, 2)) }
		else if (graphMode) console.log(JSON.stringify(buildGraph(limitedResults), null, 2))
		else { if (!jsonOnly) { console.log(`\nTokens this call: ${tokensThisCall}`); console.log(`Total session tokens: ${updatedSession.totalTokens}\n`) }; console.log(JSON.stringify(limitedResults, null, 2)) }

		const flags = process.argv.slice(2).filter(a => a.startsWith('--')).map(a => a.replace(/=.*/, ''))
		const mode = depsMode ? 'deps' : lintFragmentsMode ? 'lint-fragments' : sessionMode ? 'session' : keypointsMode ? 'keypoints' : orphansMode ? 'orphans' : backlinksTarget ? 'backlinks' : graphMode ? 'graph' : searchKeyword ? 'search' : 'default'
		writeRunLog({
		timestamp: new Date().toISOString(),
		sessionId: updatedSession.sessionId,
		directory: targetDir,
		flags,
		filesFound: mdFiles.length,
		filesProcessed: results.length,
		tokensThisCall,
		totalSessionTokens: updatedSession.totalTokens,
		errors: scanErrors,
		durationMs: Date.now() - startTime,
		mode
		})
		}

		main()

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