@mod-computer/cli 0.2.4 → 0.2.5

package/dist/commands/trace.js

@@ -1,1752 +0,0 @@
-/**
- * Trace Command
- * CLI commands for trace management and reporting
- *
- * spec: packages/mod-cli/specs/traces-cli.md
- */
-import fs from 'fs';
-import path from 'path';
-import { execSync } from 'child_process';
-import readline from 'readline';
-import { createModWorkspace } from '@mod/mod-core';
-import { readWorkspaceConnection } from '../lib/storage.js';
-/**
- * Prompt user for confirmation
- */
-async function confirm(message) {
-    const rl = readline.createInterface({
-        input: process.stdin,
-        output: process.stdout,
-    });
-    return new Promise((resolve) => {
-        rl.question(`${message} [y/N]: `, (answer) => {
-            rl.close();
-            resolve(answer.toLowerCase() === 'y' || answer.toLowerCase() === 'yes');
-        });
-    });
-}
-// Track if we've shown the glassware error warning already
-let glasswareErrorShown = false;
-/**
- * Execute a glassware query with grouping and return parsed JSON result
- * Uses --group-mode duplicate so nodes referencing multiple targets appear in all groups
- */
-function runGlasswareGroupedQuery(queryName, groupBy) {
-    try {
-        const cmd = `glassware query ${queryName} --format json --group-by "${groupBy}" --group-mode duplicate`;
-        const output = execSync(cmd, {
-            cwd: process.cwd(),
-            encoding: 'utf-8',
-            stdio: ['pipe', 'pipe', 'pipe'],
-            maxBuffer: 100 * 1024 * 1024, // 100MB buffer for large outputs
-        });
-        return JSON.parse(output);
-    }
-    catch (error) {
-        console.error(`Warning: Grouped query "${queryName}" failed:`, error.message);
-        return { query: queryName, group_by: groupBy, total_count: 0, groups: [] };
-    }
-}
-/**
- * Execute a glassware query and return parsed JSON result
- * Returns empty result on error (glassware may fail on annotation parse errors)
- */
-function runGlasswareQuery(queryName, groupBy) {
-    try {
-        let cmd = `glassware query ${queryName} --format json`;
-        if (groupBy) {
-            cmd += ` --group-by "${groupBy}"`;
-        }
-        const output = execSync(cmd, {
-            cwd: process.cwd(),
-            encoding: 'utf-8',
-            stdio: ['pipe', 'pipe', 'pipe'],
-        });
-        return JSON.parse(output);
-    }
-    catch (error) {
-        // Glassware may fail on annotation parse errors in the codebase
-        // Return empty result rather than failing completely
-        const errMsg = error.stderr?.toString() || error.message || '';
-        if (errMsg.includes('Invalid reference') || errMsg.includes('Parse error')) {
-            // Silently return empty result - annotation errors are common during development
-            glasswareErrorShown = true;
-            return { nodes: [], edges: [] };
-        }
-        throw new Error(`Failed to run glassware query "${queryName}": ${error.message}`);
-    }
-}
-/**
- * Execute glassware show command to get a single node
- */
-function runGlasswareShow(nodeId) {
-    try {
-        const output = execSync(`glassware show ${nodeId}`, {
-            cwd: process.cwd(),
-            encoding: 'utf-8',
-            stdio: ['pipe', 'pipe', 'pipe'],
-        });
-        return JSON.parse(output);
-    }
-    catch {
-        return null;
-    }
-}
-/**
- * Pass through to glassware CLI directly
- */
-function runGlasswareDirect(args) {
-    try {
-        const output = execSync(`glassware ${args.join(' ')}`, {
-            cwd: process.cwd(),
-            encoding: 'utf-8',
-            stdio: ['pipe', 'pipe', 'pipe'],
-        });
-        return output;
-    }
-    catch (error) {
-        if (error.stderr) {
-            return error.stderr.toString();
-        }
-        throw error;
-    }
-}
-function parseListArgs(args) {
-    const result = { json: false, source: 'all' };
-    for (let i = 0; i < args.length; i++) {
-        const arg = args[i];
-        if (arg === '--json') {
-            result.json = true;
-        }
-        else if (arg === '--type' && args[i + 1]) {
-            result.type = args[i + 1];
-            i++;
-        }
-        else if (arg.startsWith('--type=')) {
-            result.type = arg.slice('--type='.length);
-        }
-        else if (arg === '--file' && args[i + 1]) {
-            result.file = args[i + 1];
-            i++;
-        }
-        else if (arg.startsWith('--file=')) {
-            result.file = arg.slice('--file='.length);
-        }
-        else if (arg === '--source' && args[i + 1]) {
-            const src = args[i + 1];
-            if (src === 'mod' || src === 'inline' || src === 'all') {
-                result.source = src;
-            }
-            i++;
-        }
-        else if (arg.startsWith('--source=')) {
-            const src = arg.slice('--source='.length);
-            if (src === 'mod' || src === 'inline' || src === 'all') {
-                result.source = src;
-            }
-        }
-    }
-    return result;
-}
-function parseReportArgs(args) {
-    const result = { json: false };
-    for (let i = 0; i < args.length; i++) {
-        const arg = args[i];
-        if (arg === '--json') {
-            result.json = true;
-        }
-        else if (!arg.startsWith('-') && !result.file) {
-            result.file = arg;
-        }
-    }
-    return result;
-}
-function parseCoverageArgs(args) {
-    return {
-        json: args.includes('--json'),
-    };
-}
-function parseAddArgs(args) {
-    const result = { json: false, allUnmarked: false, link: [], store: 'mod' };
-    for (let i = 0; i < args.length; i++) {
-        const arg = args[i];
-        if (arg === '--json') {
-            result.json = true;
-        }
-        else if (arg === '--all-unmarked') {
-            result.allUnmarked = true;
-        }
-        else if (arg === '--type' && args[i + 1]) {
-            result.type = args[i + 1];
-            i++;
-        }
-        else if (arg.startsWith('--type=')) {
-            result.type = arg.slice('--type='.length);
-        }
-        else if (arg === '--link' && args[i + 1]) {
-            result.link.push(args[i + 1]);
-            i++;
-        }
-        else if (arg.startsWith('--link=')) {
-            result.link.push(arg.slice('--link='.length));
-        }
-        else if (arg === '--store' && args[i + 1]) {
-            const store = args[i + 1];
-            if (store === 'mod' || store === 'inline') {
-                result.store = store;
-            }
-            i++;
-        }
-        else if (arg.startsWith('--store=')) {
-            const store = arg.slice('--store='.length);
-            if (store === 'mod' || store === 'inline') {
-                result.store = store;
-            }
-        }
-        else if (!arg.startsWith('-')) {
-            // Parse file:line format
-            const colonIndex = arg.lastIndexOf(':');
-            if (colonIndex > 0 && !isNaN(parseInt(arg.slice(colonIndex + 1)))) {
-                result.file = arg.slice(0, colonIndex);
-                result.line = parseInt(arg.slice(colonIndex + 1));
-            }
-            else {
-                result.file = arg;
-            }
-        }
-    }
-    return result;
-}
-function parseLinkArgs(args) {
-    const result = { json: false };
-    const nonFlags = args.filter(a => !a.startsWith('-'));
-    if (nonFlags.length >= 1)
-        result.source = nonFlags[0];
-    if (nonFlags.length >= 2)
-        result.target = nonFlags[1];
-    result.json = args.includes('--json');
-    return result;
-}
-function parseDiffArgs(args) {
-    const result = { json: false };
-    for (const arg of args) {
-        if (arg === '--json') {
-            result.json = true;
-        }
-        else if (!arg.startsWith('-') && arg.includes('..')) {
-            result.refRange = arg;
-        }
-    }
-    return result;
-}
-async function requireModWorkspaceConnection(repo) {
-    const cwd = process.cwd();
-    const connection = readWorkspaceConnection(cwd);
-    if (!connection) {
-        throw new Error('Not connected to a workspace. Run "mod connect" first.');
-    }
-    const workspace = createModWorkspace(repo);
-    const opened = await workspace.openWorkspace(connection.workspaceId);
-    return { workspace, opened };
-}
-/**
- * Extract line number from a Trace's location
- */
-function getTraceLineNumber(trace) {
-    if (trace.location && trace.location.type === 'inline' && typeof trace.location.line === 'number') {
-        return trace.location.line;
-    }
-    return 0;
-}
-// =============================================================================
-// Command Handlers (Glassware-based)
-// =============================================================================
-const NODE_TYPES = ['requirement', 'specification', 'implementation', 'test'];
-// glassware[type="implementation", id="impl-trace-list-cmd--cfe82af5", specifications="specification-spec-traces-cli-list--2a13a560,specification-spec-traces-cli-list-type--16dc8808,specification-spec-traces-cli-list-file--33a4a34c,specification-spec-traces-cli-list-all--8ee25150,specification-spec-traces-cli-list-mod--70ded4f0,specification-spec-traces-cli-list-inline--42f73201,specification-spec-traces-cli-list-mod-filehandle--7bd5079f,specification-spec-traces-cli-json-complete--90d4f6fe"]
-async function handleListTraces(args, repo) {
-    const { json, type, file, source } = parseListArgs(args);
-    let allTraces = [];
-    // Get inline traces from glassware
-    if (source === 'inline' || source === 'all') {
-        const typesToQuery = type ? [type] : NODE_TYPES;
-        for (const nodeType of typesToQuery) {
-            const queryName = nodeType === 'specification' ? 'specs'
-                : nodeType === 'implementation' ? 'impls'
-                    : nodeType === 'test' ? 'tests'
-                        : null;
-            if (queryName) {
-                try {
-                    const result = runGlasswareQuery(queryName);
-                    for (const n of result.nodes) {
-                        allTraces.push({
-                            id: n.id,
-                            nodeType: n.type,
-                            file: n.file,
-                            line: n.line,
-                            text: n.text,
-                            source: 'inline',
-                            links: Object.entries(n.attributes || {}).flatMap(([edgeType, targets]) => targets.map(t => ({ edgeType, targetId: t }))),
-                        });
-                    }
-                }
-                catch {
-                    // Query might not exist, skip
-                }
-            }
-        }
-    }
-    // Get Mod storage traces
-    if (source === 'mod' || source === 'all') {
-        try {
-            const { opened } = await requireModWorkspaceConnection(repo);
-            const files = await opened.file.list();
-            for (const fileRef of files) {
-                try {
-                    const handle = await opened.file.getHandle(fileRef.id);
-                    if (!handle)
-                        continue;
-                    const traces = await handle.traces.list();
-                    for (const trace of traces) {
-                        // Filter by type if specified
-                        if (type && trace.nodeType !== type)
-                            continue;
-                        allTraces.push({
-                            id: trace.id,
-                            nodeType: trace.nodeType,
-                            file: fileRef.name,
-                            line: getTraceLineNumber(trace),
-                            text: trace.text,
-                            source: 'mod',
-                            links: trace.links.map(l => ({ edgeType: l.edgeType, targetId: l.targetId })),
-                        });
-                    }
-                }
-                catch {
-                    // Skip files that fail to load
-                }
-            }
-        }
-        catch (error) {
-            if (source === 'mod') {
-                throw error; // Re-throw if mod-only was requested
-            }
-            // For 'all', just continue with inline traces if workspace not connected
-        }
-    }
-    // Filter by file if specified
-    if (file) {
-        allTraces = allTraces.filter(t => t.file.includes(file));
-    }
-    if (json) {
-        console.log(JSON.stringify({
-            traces: allTraces,
-            total: allTraces.length,
-        }, null, 2));
-    }
-    else {
-        // Text output grouped by type
-        const byType = new Map();
-        for (const trace of allTraces) {
-            const list = byType.get(trace.nodeType) || [];
-            list.push(trace);
-            byType.set(trace.nodeType, list);
-        }
-        console.log('Traces');
-        console.log('═'.repeat(70));
-        console.log('');
-        for (const [nodeType, traces] of byType) {
-            console.log(`${nodeType} (${traces.length})`);
-            console.log('─'.repeat(40));
-            for (const trace of traces) {
-                const linkCount = trace.links.length;
-                const linkInfo = linkCount > 0 ? ` (${linkCount} links)` : '';
-                const sourceTag = trace.source === 'mod' ? ' [mod]' : '';
-                console.log(`  ${trace.id}${linkInfo}${sourceTag}`);
-                console.log(`    └─ ${trace.file}:${trace.line}`);
-            }
-            console.log('');
-        }
-        console.log(`Total: ${allTraces.length} traces`);
-    }
-}
-async function handleTraceReport(args) {
-    const { json, file } = parseReportArgs(args);
-    if (!file) {
-        console.error('Usage: mod trace report <file> [--json]');
-        process.exit(1);
-    }
-    // Get all specs from the file
-    let specs = [];
-    try {
-        const result = runGlasswareQuery('specs');
-        specs = result.nodes.filter(n => n.file.includes(file));
-    }
-    catch (error) {
-        console.error('Error querying specs:', error.message);
-        process.exit(1);
-    }
-    // Use glassware's grouping to get implementations grouped by what they implement
-    // This lets glassware resolve the spec references correctly
-    const implsGrouped = runGlasswareGroupedQuery('impls', 'outgoing.implements');
-    const testsGrouped = runGlasswareGroupedQuery('tests', 'outgoing.tests');
-    // Build lookup maps from grouped results (key is the resolved spec/impl node)
-    const implsBySpecId = new Map();
-    for (const group of implsGrouped.groups) {
-        if (group.key?.id) {
-            implsBySpecId.set(group.key.id, group.nodes);
-        }
-    }
-    const testsByImplId = new Map();
-    for (const group of testsGrouped.groups) {
-        if (group.key?.id) {
-            testsByImplId.set(group.key.id, group.nodes);
-        }
-    }
-    // Workaround for glassware edge resolution bug: manually build test->impl mapping
-    // by parsing test attributes and stripping type prefixes
-    try {
-        const testsResult = runGlasswareQuery('tests');
-        for (const test of testsResult.nodes) {
-            const testRefs = test.attributes?.tests || [];
-            for (const ref of testRefs) {
-                // Strip type prefix (e.g., "implementation-impl-foo" -> "impl-foo")
-                let implId = ref;
-                const prefixes = ['implementation-', 'specification-', 'requirement-', 'test-'];
-                for (const prefix of prefixes) {
-                    if (implId.startsWith(prefix)) {
-                        implId = implId.slice(prefix.length);
-                        break;
-                    }
-                }
-                // Add to mapping if not already present
-                if (!testsByImplId.has(implId)) {
-                    testsByImplId.set(implId, []);
-                }
-                const existing = testsByImplId.get(implId);
-                if (!existing.some(t => t.id === test.id)) {
-                    existing.push(test);
-                }
-            }
-        }
-    }
-    catch {
-        // Ignore errors - continue with glassware's grouping
-    }
-    if (json) {
-        console.log(JSON.stringify({
-            file,
-            specs: specs.map(s => ({
-                id: s.id,
-                text: s.text,
-                file: s.file,
-                line: s.line,
-                implementations: implsBySpecId.get(s.id) || [],
-                tests: (implsBySpecId.get(s.id) || []).flatMap(impl => testsByImplId.get(impl.id) || []),
-            })),
-            total: specs.length,
-        }, null, 2));
-    }
-    else {
-        const fileName = file.split('/').pop() || file;
-        console.log(`${fileName} - Trace Report`);
-        console.log('═'.repeat(55));
-        console.log('');
-        let fullyLinked = 0;
-        let partiallyLinked = 0;
-        let unlinked = 0;
-        for (const spec of specs) {
-            // Use glassware-resolved lookups (no prefix needed)
-            const specImpls = implsBySpecId.get(spec.id) || [];
-            const hasImpl = specImpls.length > 0;
-            const hasTests = specImpls.some(impl => (testsByImplId.get(impl.id) || []).length > 0);
-            const statusIcon = hasImpl && hasTests ? '✓' : hasImpl ? '⚠' : '✗';
-            const implStatus = hasImpl ? '✓ Implemented' : '✗ Not implemented';
-            const testStatus = hasImpl ? (hasTests ? '✓ Tested' : '✗ No tests') : '';
-            if (hasImpl && hasTests)
-                fullyLinked++;
-            else if (hasImpl)
-                partiallyLinked++;
-            else
-                unlinked++;
-            const shortId = spec.id.split('--')[0];
-            const title = spec.text.slice(0, 40);
-            console.log(`${statusIcon} ${shortId}: ${title}`);
-            console.log(`   ${implStatus} ${testStatus}`);
-            // glassware[type="implementation", id="impl-trace-report-impl-display--8e040441", specifications="specification-spec-traces-cli-report-impl--44744aac"]
-            for (const impl of specImpls) {
-                console.log(`   └─ impl: ${impl.file}:${impl.line}`);
-                // glassware[type="implementation", id="impl-trace-report-tests-display--9c17e61c", specifications="specification-spec-traces-cli-report-tests--4ec72e90"]
-                const implTests = testsByImplId.get(impl.id) || [];
-                for (const test of implTests) {
-                    console.log(`        └─ test: ${test.file}:${test.line}`);
-                }
-            }
-            console.log('');
-        }
-        // glassware[type="implementation", id="impl-trace-report-summary--0654d7ca", specifications="specification-spec-traces-cli-report-summary--b466878d"]
-        console.log('─'.repeat(55));
-        console.log(`Summary: ${fullyLinked}/${specs.length} fully linked, ` +
-            `${partiallyLinked} partial, ${unlinked} unlinked`);
-    }
-}
-// glassware[type="implementation", id="impl-trace-coverage-cmd--a1f6fa4e", specifications="specification-spec-traces-cli-coverage-reqs--dacbac70,specification-spec-traces-cli-coverage-impl--e5a265c6"]
-async function handleCoverageAnalysis(args) {
-    const { json } = parseCoverageArgs(args);
-    // Get counts from glassware queries
-    let specs = [];
-    let impls = [];
-    let tests = [];
-    let unmetReqs = [];
-    let unimplSpecs = [];
-    let untestedSpecs = [];
-    try {
-        specs = runGlasswareQuery('specs').nodes;
-    }
-    catch { /* query might not exist */ }
-    try {
-        impls = runGlasswareQuery('impls').nodes;
-    }
-    catch { /* query might not exist */ }
-    try {
-        tests = runGlasswareQuery('tests').nodes;
-    }
-    catch { /* query might not exist */ }
-    try {
-        unmetReqs = runGlasswareQuery('unmet-requirements').nodes;
-    }
-    catch { /* query might not exist */ }
-    try {
-        unimplSpecs = runGlasswareQuery('unimplemented-specs').nodes;
-    }
-    catch { /* query might not exist */ }
-    try {
-        untestedSpecs = runGlasswareQuery('untested-specs').nodes;
-    }
-    catch { /* query might not exist */ }
-    const coverage = {
-        specifications: {
-            total: specs.length,
-            implemented: specs.length - unimplSpecs.length,
-            tested: specs.length - untestedSpecs.length,
-        },
-        implementations: {
-            total: impls.length,
-        },
-        tests: {
-            total: tests.length,
-        },
-        unmet: unmetReqs.length,
-    };
-    if (json) {
-        console.log(JSON.stringify({ coverage }, null, 2));
-    }
-    else {
-        console.log('Trace Coverage');
-        console.log('═'.repeat(55));
-        console.log('');
-        // Specifications coverage
-        const specPct = specs.length > 0
-            ? Math.round((coverage.specifications.implemented / specs.length) * 100)
-            : 0;
-        const specBar = '█'.repeat(Math.floor(specPct / 6.25)) + '░'.repeat(16 - Math.floor(specPct / 6.25));
-        console.log(`specification:`);
-        console.log(`  ${specBar}  ${specPct}%  (${coverage.specifications.implemented}/${specs.length} implemented)`);
-        // Test coverage
-        const testPct = specs.length > 0
-            ? Math.round((coverage.specifications.tested / specs.length) * 100)
-            : 0;
-        const testBar = '█'.repeat(Math.floor(testPct / 6.25)) + '░'.repeat(16 - Math.floor(testPct / 6.25));
-        console.log(`tested:`);
-        console.log(`  ${testBar}  ${testPct}%  (${coverage.specifications.tested}/${specs.length} tested)`);
-        console.log('');
-        console.log('─'.repeat(55));
-        console.log(`Total: ${specs.length} specs, ${impls.length} impls, ${tests.length} tests`);
-        if (unmetReqs.length > 0) {
-            console.log(`⚠ Unmet requirements: ${unmetReqs.length}`);
-        }
-        if (unimplSpecs.length > 0) {
-            console.log(`⚠ Unimplemented specs: ${unimplSpecs.length}`);
-        }
-    }
-}
-async function handleUnmetRequirements(args) {
-    const json = args.includes('--json');
-    let unmet = [];
-    try {
-        unmet = runGlasswareQuery('unmet-requirements').nodes;
-    }
-    catch (error) {
-        console.error('Error querying unmet requirements:', error.message);
-        process.exit(1);
-    }
-    if (json) {
-        console.log(JSON.stringify({
-            unmet: unmet.map(n => ({
-                id: n.id,
-                title: n.text,
-                file: n.file,
-                line: n.line,
-            })),
-            total: unmet.length,
-        }, null, 2));
-    }
-    else {
-        if (unmet.length === 0) {
-            console.log('✓ All requirements have implementations');
-            return;
-        }
-        console.log('Unmet Requirements');
-        console.log('═'.repeat(55));
-        console.log('');
-        for (const req of unmet) {
-            const shortId = req.id.split('--')[0];
-            console.log(`✗ ${shortId}`);
-            console.log(`  "${req.text.slice(0, 50)}"`);
-            console.log(`  └─ ${req.file}:${req.line}`);
-            console.log('');
-        }
-        console.log(`Total: ${unmet.length} unmet requirements`);
-    }
-    // Exit non-zero if unmet requirements exist
-    if (unmet.length > 0) {
-        process.exit(1);
-    }
-}
-// glassware[type="implementation", id="impl-trace-diff-cmd--wip", specifications="spec-traces-cli-diff--wip,spec-traces-cli-diff-passthrough--wip,spec-traces-cli-diff-report--wip,spec-traces-cli-diff-suggest--wip,spec-traces-cli-diff-json--wip"]
-async function handleTraceDiff(args) {
-    const { json, refRange } = parseDiffArgs(args);
-    let base;
-    let head;
-    let branchInfo = '';
-    if (refRange && refRange.includes('..')) {
-        // Explicit range provided
-        [base, head] = refRange.split('..');
-    }
-    else {
-        // Auto-detect: find merge-base with main/master
-        try {
-            const currentBranch = execSync('git rev-parse --abbrev-ref HEAD', {
-                encoding: 'utf-8',
-                stdio: ['pipe', 'pipe', 'pipe'],
-            }).trim();
-            // Try main, then master
-            let defaultBranch = 'main';
-            try {
-                execSync('git rev-parse --verify main', { stdio: 'ignore' });
-            }
-            catch {
-                try {
-                    execSync('git rev-parse --verify master', { stdio: 'ignore' });
-                    defaultBranch = 'master';
-                }
-                catch {
-                    console.error('Error: Could not find main or master branch');
-                    process.exit(1);
-                }
-            }
-            // Find where current branch diverged from default
-            const mergeBase = execSync(`git merge-base ${defaultBranch} HEAD`, {
-                encoding: 'utf-8',
-                stdio: ['pipe', 'pipe', 'pipe'],
-            }).trim();
-            base = mergeBase;
-            head = 'HEAD';
-            branchInfo = `Branch: ${currentBranch} (compared to ${defaultBranch})`;
-        }
-        catch (error) {
-            console.error('Error detecting git branch:', error.message);
-            process.exit(1);
-        }
-    }
-    // Get changed files
-    let changedFiles;
-    try {
-        const output = execSync(`git diff --name-only ${base}..${head}`, {
-            encoding: 'utf-8',
-            stdio: ['pipe', 'pipe', 'pipe'],
-        });
-        changedFiles = output.trim().split('\n').filter(Boolean);
-    }
-    catch (error) {
-        console.error('Error getting changed files:', error.message);
-        process.exit(1);
-    }
-    if (changedFiles.length === 0) {
-        if (json) {
-            console.log(JSON.stringify({
-                branch: branchInfo,
-                traced: [],
-                untraced: [],
-                total: 0,
-            }, null, 2));
-        }
-        else {
-            if (branchInfo)
-                console.log(branchInfo);
-            console.log('\nNo files changed.');
-        }
-        return;
-    }
-    // Query all traces to build a file->trace map
-    const fileTraceMap = new Map();
-    // Get inline traces from glassware
-    for (const nodeType of NODE_TYPES) {
-        const queryName = nodeType === 'specification' ? 'specs'
-            : nodeType === 'implementation' ? 'impls'
-                : nodeType === 'test' ? 'tests'
-                    : null;
-        if (queryName) {
-            try {
-                const result = runGlasswareQuery(queryName);
-                for (const n of result.nodes) {
-                    const existing = fileTraceMap.get(n.file) || [];
-                    existing.push({ id: n.id, type: n.type });
-                    fileTraceMap.set(n.file, existing);
-                }
-            }
-            catch {
-                // Query might not exist, skip
-            }
-        }
-    }
-    // Group changed files into traced vs untraced
-    const traced = [];
-    const untraced = [];
-    for (const file of changedFiles) {
-        const traces = fileTraceMap.get(file);
-        if (traces && traces.length > 0) {
-            traced.push({ file, traceId: traces[0].id });
-        }
-        else {
-            // Only flag source files as untraced, skip non-code files
-            const ext = path.extname(file);
-            const codeExtensions = ['.ts', '.tsx', '.js', '.jsx', '.md'];
-            const ignorePaths = ['node_modules', 'dist', '.git', 'package.json', 'package-lock.json', 'pnpm-lock.yaml', '.gitignore', 'tsconfig'];
-            if (codeExtensions.includes(ext) && !ignorePaths.some(p => file.includes(p))) {
-                untraced.push(file);
-            }
-        }
-    }
-    // Output
-    if (json) {
-        console.log(JSON.stringify({
-            branch: branchInfo,
-            traced,
-            untraced,
-            total: changedFiles.length,
-        }, null, 2));
-    }
-    else {
-        if (branchInfo) {
-            console.log(branchInfo);
-            console.log('');
-        }
-        if (traced.length > 0) {
-            console.log('Traced:');
-            for (const t of traced) {
-                const shortId = t.traceId.split('--')[0];
-                console.log(`  ${t.file.padEnd(40)} → ${shortId}`);
-            }
-        }
-        if (untraced.length > 0) {
-            console.log('');
-            console.log('⚠ Untraced:');
-            for (const f of untraced) {
-                console.log(`  ${f}`);
-            }
-            console.log('');
-            console.log('Suggestion: mod trace add <file> --type=utility');
-        }
-        if (traced.length > 0 && untraced.length === 0) {
-            console.log('');
-            console.log('✓ All changed files are traced');
-        }
-    }
-    // Exit non-zero if untraced files exist
-    if (untraced.length > 0) {
-        process.exit(1);
-    }
-}
-// =============================================================================
-// Add/Link Commands (File modification - kept from original)
-// =============================================================================
-// glassware[type="implementation", id="impl-trace-add-cmd--6893858a", specifications="specification-spec-traces-cli-add--daf76036,specification-spec-traces-cli-add-mod-store--522d5263,specification-spec-traces-cli-add-mod-filehandle--9d81aee5,specification-spec-traces-cli-add-store-mod--be78263b,specification-spec-traces-cli-add-store-inline--783bd8a6,specification-spec-traces-cli-add-link--ee46baf2,specification-spec-traces-cli-add-title-from-line--e24dc753,specification-spec-traces-cli-add-insert--d956f641,specification-spec-traces-cli-add-mod-anchor--fb9b7f41"]
-async function handleAddTrace(args, repo) {
-    const { json, type, file, line, link, allUnmarked, store } = parseAddArgs(args);
-    if (!type) {
-        console.error('Usage: mod trace add <file>:<line> --type=<type> [--link=<id>] [--store=mod|inline]');
-        console.error('       mod trace add <file> --type=<type> --all-unmarked [--store=inline]');
-        process.exit(1);
-    }
-    if (!file) {
-        console.error('Error: File path required');
-        process.exit(1);
-    }
-    if (!NODE_TYPES.includes(type)) {
-        console.error(`Error: Invalid node type "${type}". Valid types: ${NODE_TYPES.join(', ')}`);
-        process.exit(1);
-    }
-    // Bulk add only supports inline storage
-    if (allUnmarked) {
-        if (store === 'mod') {
-            console.error('Error: --all-unmarked only supports --store=inline');
-            process.exit(1);
-        }
-        await handleBulkAdd(file, type, json);
-        return;
-    }
-    if (!line) {
-        console.error('Error: Line number required (use file:line format)');
-        process.exit(1);
-    }
-    const fullPath = path.resolve(process.cwd(), file);
-    if (!fs.existsSync(fullPath)) {
-        console.error(`Error: File not found: ${file}`);
-        process.exit(1);
-    }
-    const content = fs.readFileSync(fullPath, 'utf-8');
-    const lines = content.split('\n');
-    if (line < 1 || line > lines.length) {
-        console.error(`Error: Line ${line} out of range (file has ${lines.length} lines)`);
-        process.exit(1);
-    }
-    // Get text at line for title generation
-    const lineText = lines[line - 1].trim();
-    const title = generateTitle(lineText);
-    const id = generateTraceId(title);
-    if (store === 'mod') {
-        // Store in Mod file storage
-        await handleAddTraceMod(repo, file, line, type, id, lineText, link || [], json);
-    }
-    else {
-        // Store as inline annotation
-        await handleAddTraceInline(file, line, type, id, link || [], json, lines);
-    }
-}
-/**
- * Add trace to Mod file storage via FileHandle.traces API
- */
-async function handleAddTraceMod(repo, filePath, line, nodeType, id, text, links, json) {
-    const { opened } = await requireModWorkspaceConnection(repo);
-    // Find the file in workspace
-    const files = await opened.file.list();
-    const fileRef = files.find(f => f.name === filePath || f.name.endsWith(filePath) || filePath.endsWith(f.name));
-    if (!fileRef) {
-        console.error(`Error: File not found in workspace: ${filePath}`);
-        console.error('Available files:');
-        for (const f of files.slice(0, 10)) {
-            console.error(`  ${f.name}`);
-        }
-        process.exit(1);
-    }
-    const handle = await opened.file.getHandle(fileRef.id);
-    if (!handle) {
-        console.error(`Error: Could not get file handle for: ${filePath}`);
-        process.exit(1);
-    }
-    // Create trace anchor with cursor-based positioning
-    // For CLI, we use line-based placeholder cursors since we don't have document cursors
-    const anchor = {
-        fromCursor: `cli:${line}:0`,
-        toCursor: `cli:${line}:${text.length}`,
-        path: ['content'],
-        quotedText: text.slice(0, 100),
-    };
-    // Create trace input with links
-    const traceLinks = links.map(targetId => ({
-        edgeType: getEdgeAttrName(nodeType),
-        targetId,
-    }));
-    const traceId = await handle.traces.create(anchor, {
-        nodeType,
-        createdBy: 'cli',
-        links: traceLinks,
-    });
-    // Flush to persist changes before CLI exits
-    // Need to flush both the file document and the traces document
-    const fileDoc = handle.doc?.() || {};
-    const tracesDocId = fileDoc.tracesDocId;
-    const docsToFlush = [fileRef.id];
-    if (tracesDocId) {
-        docsToFlush.push(tracesDocId);
-    }
-    await flushRepo(repo, docsToFlush);
-    if (json) {
-        console.log(JSON.stringify({
-            created: { id: traceId, type: nodeType, file: filePath, line, links, store: 'mod' },
-        }, null, 2));
-    }
-    else {
-        const linkInfo = links.length > 0 ? `, linked to ${links.join(', ')}` : '';
-        console.log(`Created trace (mod): ${traceId} at ${filePath}:${line}${linkInfo}`);
-    }
-}
-/**
- * Flush repo to persist changes
- */
-async function flushRepo(repo, documentIds) {
-    const flush = repo.flush;
-    if (!flush)
-        return;
-    try {
-        await flush.call(repo, documentIds);
-    }
-    catch (error) {
-        console.error('Warning: Failed to flush changes');
-    }
-}
-/**
- * Add trace as inline annotation in source file
- */
-async function handleAddTraceInline(file, line, type, id, links, json, lines) {
-    // Build annotation
-    const linkAttr = links.length > 0
-        ? `, ${getEdgeAttrName(type)}="${links.join(',')}"`
-        : '';
-    const ext = path.extname(file);
-    const fullPath = path.resolve(process.cwd(), file);
-    if (ext === '.md') {
-        // Note: Split strings to avoid glassware parsing this as an annotation
-        const annotation = ` <glass` + `ware type="${type}" id="${id}"${linkAttr} />`;
-        lines[line - 1] = lines[line - 1] + annotation;
-    }
-    else {
-        const indent = lines[line - 1].match(/^(\s*)/)?.[1] || '';
-        // Note: Split strings to avoid glassware parsing this as an annotation
-        const annotation = `${indent}// glass` + `ware[type="${type}", id="${id}"${linkAttr}]`;
-        lines.splice(line - 1, 0, annotation);
-    }
-    fs.writeFileSync(fullPath, lines.join('\n'));
-    if (json) {
-        console.log(JSON.stringify({
-            created: { id, type, file, line, links, store: 'inline' },
-        }, null, 2));
-    }
-    else {
-        const linkInfo = links.length > 0 ? `, linked to ${links.join(', ')}` : '';
-        console.log(`Created trace (inline): ${id} at ${file}:${line}${linkInfo}`);
-    }
-}
-// glassware[type="implementation", id="impl-trace-link-handler--11d97052", specifications="specification-spec-traces-cli-link-validate--0f83e137,specification-spec-traces-cli-link-mod--e768fb7d,specification-spec-traces-cli-cross-link--60c5d89e,specification-spec-traces-cli-cross-resolve--7153750f"]
-async function handleLinkTraces(args, repo) {
-    const { json, source, target } = parseLinkArgs(args);
-    if (!source || !target) {
-        console.error('Usage: mod trace link <source-id> <target-id>');
-        process.exit(1);
-    }
-    // Try to find source trace in inline storage first, then Mod storage
-    let sourceNode = runGlasswareShow(source);
-    let sourceStorage = 'inline';
-    let sourceModHandle = null;
-    let sourceModTrace = null;
-    let sourceModFile = '';
-    if (!sourceNode && repo) {
-        // Try Mod storage
-        try {
-            const { opened } = await requireModWorkspaceConnection(repo);
-            const files = await opened.file.list();
-            for (const fileRef of files) {
-                const handle = await opened.file.getHandle(fileRef.id);
-                if (!handle)
-                    continue;
-                const traces = await handle.traces.list();
-                const trace = traces.find(t => t.id === source);
-                if (trace) {
-                    sourceModHandle = handle;
-                    sourceModTrace = trace;
-                    sourceModFile = fileRef.name;
-                    sourceStorage = 'mod';
-                    // Create a compatible node structure
-                    sourceNode = {
-                        id: trace.id,
-                        type: trace.nodeType,
-                        file: fileRef.name,
-                        line: getTraceLineNumber(trace),
-                        text: trace.text,
-                        attributes: {},
-                    };
-                    break;
-                }
-            }
-        }
-        catch {
-            // Workspace not connected, continue with inline only
-        }
-    }
-    if (!sourceNode) {
-        console.error(`Error: Source trace not found: ${source}`);
-        process.exit(1);
-    }
-    // Try to find target trace in inline storage first, then Mod storage
-    let targetNode = runGlasswareShow(target);
-    let targetStorage = 'inline';
-    if (!targetNode && repo) {
-        // Try Mod storage
-        try {
-            const { opened } = await requireModWorkspaceConnection(repo);
-            const files = await opened.file.list();
-            for (const fileRef of files) {
-                const handle = await opened.file.getHandle(fileRef.id);
-                if (!handle)
-                    continue;
-                const traces = await handle.traces.list();
-                const trace = traces.find(t => t.id === target);
-                if (trace) {
-                    targetStorage = 'mod';
-                    targetNode = {
-                        id: trace.id,
-                        type: trace.nodeType,
-                        file: fileRef.name,
-                        line: getTraceLineNumber(trace),
-                        text: trace.text,
-                        attributes: {},
-                    };
-                    break;
-                }
-            }
-        }
-        catch {
-            // Workspace not connected, continue with inline only
-        }
-    }
-    if (!targetNode) {
-        console.error(`Error: Target trace not found: ${target}`);
-        process.exit(1);
-    }
-    // Validate edge type constraints
-    const validEdges = {
-        specification: ['requirement'],
-        implementation: ['specification'],
-        test: ['implementation', 'specification'],
-    };
-    const allowedTargets = validEdges[sourceNode.type];
-    if (!allowedTargets || !allowedTargets.includes(targetNode.type)) {
-        console.error(`Error: Cannot link ${sourceNode.type} -> ${targetNode.type}`);
-        console.error(`Valid targets for ${sourceNode.type}: ${allowedTargets?.join(', ') || 'none'}`);
-        process.exit(1);
-    }
-    // Perform the link based on source storage type
-    try {
-        if (sourceStorage === 'mod' && sourceModHandle) {
-            // Link in Mod storage
-            const edgeType = getEdgeAttrName(sourceNode.type);
-            await sourceModHandle.traces.link(source, edgeType, target);
-            if (json) {
-                console.log(JSON.stringify({
-                    linked: {
-                        source,
-                        target,
-                        edgeType,
-                        sourceStorage,
-                        targetStorage,
-                    },
-                }, null, 2));
-            }
-            else {
-                console.log(`Linked ${source} -> ${target} (${edgeType}) [${sourceStorage} -> ${targetStorage}]`);
-            }
-        }
-        else {
-            // Link in inline storage (modify source file)
-            await addLinkToSource(sourceNode, targetNode, json);
-        }
-    }
-    catch (error) {
-        console.error(`Error linking traces: ${error.message}`);
-        process.exit(1);
-    }
-}
-// =============================================================================
-// Glassware Passthrough Commands
-// =============================================================================
-// glassware[type="implementation", id="impl-trace-query-passthrough--3c1755a4", specifications="specification-spec-traces-cli-query--6fa0b9f0"]
-async function handleGlasswareQuery(args) {
-    // Pass through to glassware query
-    const output = runGlasswareDirect(['query', ...args]);
-    console.log(output);
-}
-// glassware[type="implementation", id="impl-trace-glassware-passthrough--1e79ba39", specifications="specification-spec-traces-cli-glassware--9c2ae5eb"]
-async function handleGlasswareDirect(args) {
-    // Pass through to glassware directly
-    const output = runGlasswareDirect(args);
-    console.log(output);
-}
-// =============================================================================
-// Bulk Add Implementation
-// =============================================================================
-// glassware[type="implementation", id="impl-trace-bulk-add--b80f6ac2", specifications="specification-spec-traces-cli-add-bulk--c9537f18"]
-async function handleBulkAdd(file, type, json) {
-    const fullPath = path.resolve(process.cwd(), file);
-    if (!fs.existsSync(fullPath)) {
-        console.error(`Error: File not found: ${file}`);
-        process.exit(1);
-    }
-    const content = fs.readFileSync(fullPath, 'utf-8');
-    const lines = content.split('\n');
-    const ext = path.extname(file);
-    // Find candidate lines based on type and file extension
-    const candidates = findUnmarkedLines(lines, type, ext);
-    if (candidates.length === 0) {
-        if (json) {
-            console.log(JSON.stringify({ created: [], total: 0 }, null, 2));
-        }
-        else {
-            console.log(`No unmarked ${type} lines found in ${file}`);
-        }
-        return;
-    }
-    // Add annotations to candidates (work backwards to preserve line numbers)
-    const created = [];
-    for (let i = candidates.length - 1; i >= 0; i--) {
-        const { lineNum, text } = candidates[i];
-        const title = generateTitle(text);
-        const id = generateTraceId(title);
-        if (ext === '.md') {
-            // Append annotation to end of line
-            lines[lineNum - 1] = lines[lineNum - 1] + ` <glass` + `ware type="${type}" id="${id}" />`;
-        }
-        else {
-            // Insert annotation above the line
-            const indent = lines[lineNum - 1].match(/^(\s*)/)?.[1] || '';
-            const annotation = `${indent}// glass` + `ware[type="${type}", id="${id}"]`;
-            lines.splice(lineNum - 1, 0, annotation);
-        }
-        created.unshift({ id, type, file, line: lineNum });
-    }
-    fs.writeFileSync(fullPath, lines.join('\n'));
-    if (json) {
-        console.log(JSON.stringify({ created, total: created.length }, null, 2));
-    }
-    else {
-        console.log(`Created ${created.length} traces:`);
-        for (const trace of created) {
-            console.log(`  ${trace.id} at ${trace.file}:${trace.line}`);
-        }
-    }
-}
-/**
- * Find lines that match the type pattern and don't already have glassware annotations
- */
-function findUnmarkedLines(lines, type, ext) {
-    const candidates = [];
-    for (let i = 0; i < lines.length; i++) {
-        const line = lines[i];
-        const lineNum = i + 1;
-        // Skip if already has glassware annotation
-        if (line.includes('glassware') || line.includes('<glassware')) {
-            continue;
-        }
-        // Check if line matches pattern for the type
-        if (matchesTypePattern(line, type, ext, lines, i)) {
-            candidates.push({ lineNum, text: line.trim() });
-        }
-    }
-    return candidates;
-}
-/**
- * Determine if a line matches the pattern for a given trace type
- */
-function matchesTypePattern(line, type, ext, lines, idx) {
-    const trimmed = line.trim();
-    // Skip empty lines, comments-only, and code blocks
-    if (!trimmed || trimmed.startsWith('```') || trimmed.startsWith('<!--')) {
-        return false;
-    }
-    if (ext === '.md') {
-        // Markdown patterns
-        switch (type) {
-            case 'requirement':
-                // Requirements often in lists with "must", "should", "shall"
-                return (/^[-*]\s+.*(must|should|shall|can|will)/i.test(trimmed) ||
-                    /^[-*]\s+User\s+(can|must|should)/i.test(trimmed) ||
-                    /^[-*]\s+The\s+system\s+(must|should|shall)/i.test(trimmed));
-            case 'specification':
-                // Specs start with description and often contain technical details
-                return (/^[-*]\s+.*(must|should|shall)/i.test(trimmed) &&
-                    !trimmed.toLowerCase().includes('user'));
-            default:
-                return false;
-        }
-    }
-    else {
-        // Code file patterns
-        switch (type) {
-            case 'implementation':
-                // Functions, classes, exports
-                return (/^(export\s+)?(async\s+)?function\s+\w+/.test(trimmed) ||
-                    /^(export\s+)?class\s+\w+/.test(trimmed) ||
-                    /^(export\s+)?const\s+\w+\s*=\s*(async\s+)?\(/.test(trimmed) ||
-                    /^(export\s+)?const\s+\w+\s*=\s*(async\s+)?function/.test(trimmed));
-            case 'test':
-                // Test functions
-                return (/^(it|test|describe)\s*\(/.test(trimmed) ||
-                    /^(export\s+)?const\s+\w+Test\s*=/.test(trimmed));
-            default:
-                return false;
-        }
-    }
-}
-// =============================================================================
-// Link Command Implementation
-// =============================================================================
-/**
- * Add a link from source trace to target trace by modifying the source file
- */
-// glassware[type="implementation", id="impl-trace-link-cmd--c78fb60b", specifications="specification-spec-traces-cli-link--e92da014,specification-spec-traces-cli-link-update--0b94d120"]
-async function addLinkToSource(sourceNode, targetNode, json) {
-    const fullPath = path.resolve(process.cwd(), sourceNode.file);
-    if (!fs.existsSync(fullPath)) {
-        throw new Error(`Source file not found: ${sourceNode.file}`);
-    }
-    const content = fs.readFileSync(fullPath, 'utf-8');
-    const lines = content.split('\n');
-    const ext = path.extname(sourceNode.file);
-    // Determine the edge type based on source node type
-    const edgeAttr = getEdgeAttrName(sourceNode.type);
-    // Find the annotation line
-    let annotationLine = -1;
-    let originalAnnotation = '';
-    for (let i = Math.max(0, sourceNode.line - 3); i < Math.min(lines.length, sourceNode.line + 1); i++) {
-        const line = lines[i];
-        if (line.includes(sourceNode.id)) {
-            annotationLine = i;
-            originalAnnotation = line;
-            break;
-        }
-    }
-    if (annotationLine === -1) {
-        throw new Error(`Could not find annotation for ${sourceNode.id} near line ${sourceNode.line}`);
-    }
-    // Parse and update the annotation
-    let updatedLine;
-    if (ext === '.md') {
-        // Markdown format: annotation tag with type, id, and attributes
-        if (originalAnnotation.includes(`${edgeAttr}="`)) {
-            // Add to existing attribute
-            updatedLine = originalAnnotation.replace(new RegExp(`(${edgeAttr}=")([^"]*)("`), `$1$2,${targetNode.id}$3`);
-        }
-        else {
-            // Add new attribute before />
-            updatedLine = originalAnnotation.replace(/\s*\/>/, ` ${edgeAttr}="${targetNode.id}" />`);
-        }
-    }
-    else {
-        // Code format: annotation with type, id, and attributes
-        if (originalAnnotation.includes(`${edgeAttr}="`)) {
-            // Add to existing attribute
-            updatedLine = originalAnnotation.replace(new RegExp(`(${edgeAttr}=")([^"]*)("`), `$1$2,${targetNode.id}$3`);
-        }
-        else {
-            // Add new attribute before ]
-            updatedLine = originalAnnotation.replace(/\]$/, `, ${edgeAttr}="${targetNode.id}"]`);
-        }
-    }
-    lines[annotationLine] = updatedLine;
-    fs.writeFileSync(fullPath, lines.join('\n'));
-    // Determine edge type name for output
-    const edgeTypeName = getEdgeTypeName(sourceNode.type, targetNode.type);
-    if (json) {
-        console.log(JSON.stringify({
-            linked: {
-                source: sourceNode.id,
-                target: targetNode.id,
-                edgeType: edgeTypeName,
-                file: sourceNode.file,
-                line: annotationLine + 1,
-            },
-        }, null, 2));
-    }
-    else {
-        console.log(`Linked ${sourceNode.id} -> ${targetNode.id} (${edgeTypeName})`);
-    }
-}
-/**
- * Get the edge type name based on source and target node types
- */
-function getEdgeTypeName(sourceType, targetType) {
-    if (sourceType === 'specification' && targetType === 'requirement')
-        return 'specifies';
-    if (sourceType === 'implementation' && targetType === 'specification')
-        return 'implements';
-    if (sourceType === 'test' && targetType === 'implementation')
-        return 'tests';
-    if (sourceType === 'test' && targetType === 'specification')
-        return 'tests';
-    return 'links';
-}
-function parseGetArgs(args) {
-    const result = { json: false };
-    const nonFlags = args.filter(a => !a.startsWith('-'));
-    if (nonFlags.length >= 1)
-        result.id = nonFlags[0];
-    result.json = args.includes('--json');
-    return result;
-}
-function parseDeleteArgs(args) {
-    const result = { json: false, force: false };
-    const nonFlags = args.filter(a => !a.startsWith('-'));
-    if (nonFlags.length >= 1)
-        result.id = nonFlags[0];
-    result.json = args.includes('--json');
-    result.force = args.includes('--force') || args.includes('-f');
-    return result;
-}
-function parseUnlinkArgs(args) {
-    const result = { json: false };
-    for (let i = 0; i < args.length; i++) {
-        const arg = args[i];
-        if (arg === '--json') {
-            result.json = true;
-        }
-        else if (arg === '--edge-type' && args[i + 1]) {
-            result.edgeType = args[i + 1];
-            i++;
-        }
-        else if (arg.startsWith('--edge-type=')) {
-            result.edgeType = arg.slice('--edge-type='.length);
-        }
-        else if (!arg.startsWith('-')) {
-            if (!result.source) {
-                result.source = arg;
-            }
-            else if (!result.target) {
-                result.target = arg;
-            }
-        }
-    }
-    return result;
-}
-/**
- * Get trace details from Mod storage
- */
-// glassware[type="implementation", id="impl-trace-get--ca299267", specifications="specification-spec-traces-cli-get--55d212ec,specification-spec-traces-cli-get-details--a42429ba,specification-spec-traces-cli-get-json--b662053f"]
-async function handleGetTrace(args, repo) {
-    const { json, id } = parseGetArgs(args);
-    if (!id) {
-        console.error('Usage: mod trace get <trace-id> [--json]');
-        process.exit(1);
-    }
-    const { opened } = await requireModWorkspaceConnection(repo);
-    const files = await opened.file.list();
-    // Search for trace across all files
-    for (const fileRef of files) {
-        try {
-            const handle = await opened.file.getHandle(fileRef.id);
-            if (!handle)
-                continue;
-            const traces = await handle.traces.list();
-            const trace = traces.find(t => t.id === id);
-            if (trace) {
-                const lineNum = getTraceLineNumber(trace);
-                const locationInfo = trace.location?.type === 'inline'
-                    ? `line ${lineNum}`
-                    : trace.location?.quotedText
-                        ? `"${trace.location.quotedText.slice(0, 30)}..."`
-                        : 'cursor-based';
-                if (json) {
-                    console.log(JSON.stringify({
-                        trace: {
-                            id: trace.id,
-                            nodeType: trace.nodeType,
-                            file: fileRef.name,
-                            line: lineNum,
-                            text: trace.text,
-                            links: trace.links,
-                            location: trace.location,
-                        },
-                    }, null, 2));
-                }
-                else {
-                    console.log(`Trace: ${trace.id}`);
-                    console.log('═'.repeat(55));
-                    console.log(`Type:     ${trace.nodeType}`);
-                    console.log(`File:     ${fileRef.name}`);
-                    console.log(`Location: ${locationInfo}`);
-                    console.log(`Text:     ${trace.text}`);
-                    if (trace.links.length > 0) {
-                        console.log(`Links:`);
-                        for (const link of trace.links) {
-                            console.log(`  → ${link.targetId} (${link.edgeType})`);
-                        }
-                    }
-                }
-                return;
-            }
-        }
-        catch {
-            // Skip files that fail to load
-        }
-    }
-    console.error(`Trace not found: ${id}`);
-    process.exit(1);
-}
-/**
- * Delete a trace from Mod storage
- */
-// glassware[type="implementation", id="impl-trace-delete--20f630b7", specifications="specification-spec-traces-cli-delete--f27d3f33,specification-spec-traces-cli-delete-confirm--a8fbd99d"]
-async function handleDeleteTrace(args, repo) {
-    const { json, id, force } = parseDeleteArgs(args);
-    if (!id) {
-        console.error('Usage: mod trace delete <trace-id> [--force] [--json]');
-        process.exit(1);
-    }
-    const { opened } = await requireModWorkspaceConnection(repo);
-    const files = await opened.file.list();
-    // Search for trace across all files
-    for (const fileRef of files) {
-        try {
-            const handle = await opened.file.getHandle(fileRef.id);
-            if (!handle)
-                continue;
-            const traces = await handle.traces.list();
-            const trace = traces.find(t => t.id === id);
-            if (trace) {
-                // Require confirmation unless --force is provided
-                if (!force && !json) {
-                    const confirmed = await confirm(`Delete trace "${id}" from ${fileRef.name}?`);
-                    if (!confirmed) {
-                        console.log('Deletion cancelled.');
-                        process.exit(0);
-                    }
-                }
-                await handle.traces.delete(id);
-                if (json) {
-                    console.log(JSON.stringify({
-                        deleted: { id, file: fileRef.name },
-                    }, null, 2));
-                }
-                else {
-                    console.log(`Deleted trace: ${id} from ${fileRef.name}`);
-                }
-                return;
-            }
-        }
-        catch {
-            // Skip files that fail to load
-        }
-    }
-    console.error(`Trace not found: ${id}`);
-    process.exit(1);
-}
-/**
- * Remove a link between traces in Mod storage
- */
-// glassware[type="implementation", id="impl-trace-unlink--09745920", specifications="specification-spec-traces-cli-unlink--ff5cb1d8"]
-async function handleUnlinkTrace(args, repo) {
-    const { json, source, target, edgeType } = parseUnlinkArgs(args);
-    if (!source || !target) {
-        console.error('Usage: mod trace unlink <source-id> <target-id> [--edge-type=<type>] [--json]');
-        process.exit(1);
-    }
-    const { opened } = await requireModWorkspaceConnection(repo);
-    const files = await opened.file.list();
-    // Find source trace
-    for (const fileRef of files) {
-        try {
-            const handle = await opened.file.getHandle(fileRef.id);
-            if (!handle)
-                continue;
-            const traces = await handle.traces.list();
-            const trace = traces.find(t => t.id === source);
-            if (trace) {
-                // Find matching link
-                const linkIndex = trace.links.findIndex(l => l.targetId === target && (!edgeType || l.edgeType === edgeType));
-                if (linkIndex === -1) {
-                    console.error(`Link not found: ${source} -> ${target}`);
-                    process.exit(1);
-                }
-                const removedLink = trace.links[linkIndex];
-                await handle.traces.unlink(source, removedLink.edgeType, target);
-                if (json) {
-                    console.log(JSON.stringify({
-                        unlinked: {
-                            source,
-                            target,
-                            edgeType: removedLink.edgeType,
-                            file: fileRef.name,
-                        },
-                    }, null, 2));
-                }
-                else {
-                    console.log(`Unlinked: ${source} -> ${target} (${removedLink.edgeType})`);
-                }
-                return;
-            }
-        }
-        catch {
-            // Skip files that fail to load
-        }
-    }
-    console.error(`Source trace not found: ${source}`);
-    process.exit(1);
-}
-// =============================================================================
-// Utility Functions
-// =============================================================================
-function generateTitle(lineText) {
-    let text = lineText
-        .replace(/^#+\s*/, '')
-        .replace(/^[-*]\s*/, '')
-        .replace(/\*\*|__/g, '')
-        .replace(/\*|_/g, '')
-        .replace(/`/g, '')
-        .replace(/<[^>]+>/g, '')
-        .replace(/\/\/.*$/, '')
-        .trim();
-    if (text.length > 40) {
-        text = text.slice(0, 37) + '...';
-    }
-    return text || 'trace';
-}
-function generateTraceId(title) {
-    const slug = title
-        .toLowerCase()
-        .replace(/[^a-z0-9]+/g, '-')
-        .replace(/^-+|-+$/g, '')
-        .slice(0, 30);
-    return `${slug}--wip`;
-}
-function getEdgeAttrName(nodeType) {
-    switch (nodeType) {
-        case 'specification': return 'requirements';
-        case 'implementation': return 'specifications';
-        case 'test': return 'specifications';
-        default: return 'links';
-    }
-}
-// =============================================================================
-// Help
-// =============================================================================
-function showHelp() {
-    console.log(`
-mod trace - Manage requirement traces (powered by glassware)
-
-Usage:
-  mod trace list [--source=all|mod|inline] [--type=<type>] [--file=<path>] [--json]
-  mod trace report <file> [--json]
-  mod trace coverage [--json]
-  mod trace unmet [--json]
-  mod trace diff [<base>..<head>] [--json]
-  mod trace add <file>:<line> --type=<type> [--store=mod|inline] [--link=<id>] [--json]
-  mod trace get <trace-id> [--json]
-  mod trace delete <trace-id> [--json]
-  mod trace link <source-id> <target-id> [--json]
-  mod trace unlink <source-id> <target-id> [--edge-type=<type>] [--json]
-  mod trace query <name> [--format=json]
-  mod trace glassware <args>
-
-Commands:
-  list      List all traces with optional filters (default: --source=all)
-  report    Show trace report for a specific file
-  coverage  Show workspace-wide trace coverage
-  unmet     List requirements without implementations (exits non-zero if gaps)
-  diff      Find untraced files on branch (exits non-zero if untraced)
-  add       Add a trace (default: --store=mod for Mod file storage)
-  get       Get trace details from Mod storage
-  delete    Delete a trace from Mod storage
-  link      Create a link between two traces (inline annotations)
-  unlink    Remove a link between traces (Mod storage)
-  query     Pass through to glassware query
-  glassware Pass through to glassware CLI
-
-Storage Options:
-  --source  For list: where to read traces from (all|mod|inline, default: all)
-  --store   For add: where to store trace (mod|inline, default: mod)
-            - mod: Store in Mod file storage (FileHandle.traces API)
-            - inline: Store as glassware annotation in source file
-
-Options:
-  --json      Output in JSON format for agent consumption
-  --type      Filter by node type (requirement, specification, implementation, test)
-  --file      Filter by file path
-  --link      Link new trace to existing trace (for add command)
-  --edge-type Specify edge type for unlink command
-
-Diff Command:
-  mod trace diff                    # Auto-detect: compare current branch to main
-  mod trace diff main..HEAD         # Explicit range
-  mod trace diff main..feat/auth    # Compare branches
-  mod trace diff --json             # JSON output
-
-Examples:
-  mod trace list                              # List from all sources
-  mod trace list --source=mod                 # List only from Mod storage
-  mod trace list --source=inline --type=spec  # List inline specs only
-  mod trace add spec.md:10 --type=spec        # Add to Mod storage (default)
-  mod trace add src/foo.ts:20 --type=impl --store=inline  # Add inline
-  mod trace get my-trace-id--wip              # Get trace details
-  mod trace delete my-trace-id--wip           # Delete from Mod storage
-  mod trace unlink src-id tgt-id              # Remove link
-  mod trace report specs/auth.md
-  mod trace coverage --json
-
-Pre-merge validation:
-  mod trace diff && mod trace unmet && git push
-`);
-}
-// =============================================================================
-// Main Command
-// =============================================================================
-export async function traceCommand(args, repo) {
-    const [subcommand, ...rest] = args;
-    try {
-        switch (subcommand) {
-            case 'list':
-                await handleListTraces(rest, repo);
-                break;
-            case 'report':
-                await handleTraceReport(rest);
-                break;
-            case 'coverage':
-                await handleCoverageAnalysis(rest);
-                break;
-            case 'unmet':
-                await handleUnmetRequirements(rest);
-                break;
-            case 'diff':
-                await handleTraceDiff(rest);
-                break;
-            case 'add':
-                await handleAddTrace(rest, repo);
-                break;
-            case 'get':
-                await handleGetTrace(rest, repo);
-                break;
-            case 'delete':
-                await handleDeleteTrace(rest, repo);
-                break;
-            case 'link':
-                await handleLinkTraces(rest, repo);
-                break;
-            case 'unlink':
-                await handleUnlinkTrace(rest, repo);
-                break;
-            case 'query':
-                await handleGlasswareQuery(rest);
-                break;
-            case 'glassware':
-                await handleGlasswareDirect(rest);
-                break;
-            case 'help':
-            case '--help':
-            case '-h':
-                showHelp();
-                break;
-            default:
-                if (!subcommand) {
-                    showHelp();
-                }
-                else {
-                    console.error(`Unknown subcommand: ${subcommand}`);
-                    console.error('Run "mod trace help" for usage');
-                    process.exit(1);
-                }
-        }
-    }
-    catch (error) {
-        console.error('Error:', error.message);
-        process.exit(1);
-    }
-    process.exit(0);
-}
-// =============================================================================
-// COMMENTED OUT: Original mod-core TraceService approach
-// This works but duplicates glassware's file parsing. Kept for reference.
-// =============================================================================
-/*
-import {
-  TraceService,
-  createTraceService,
-  InlineAdapter,
-  createInlineAdapter,
-  DefaultAdapterRegistry,
-} from '@mod/mod-core';
-import type {
-  Trace,
-  TraceSchema,
-  TraceFilter,
-  TraceReport,
-  CoverageReport,
-  InlineAdapterConfig,
-} from '@mod/mod-core';
-import {
-  formatTracesTable,
-  formatTracesJson,
-  formatTraceReport,
-  formatTraceReportJson,
-  formatCoverageReport,
-  formatCoverageJson,
-  formatUnmetRequirements,
-  formatUnmetJson,
-} from '../lib/trace-formatters.js';
-
-const DEFAULT_SCHEMA: TraceSchema = {
-  nodeTypes: ['requirement', 'specification', 'implementation', 'test'],
-  edgeTypes: {
-    specifies: { attribute: 'specifies', from: 'specification', to: 'requirement' },
-    implements: { attribute: 'requirements', from: 'implementation', to: 'specification' },
-    tests: { attribute: 'tests', from: 'test', to: 'implementation' },
-  },
-};
-
-function createTraceServiceWithAdapter(): TraceService {
-  const workspaceRoot = process.cwd();
-  const registry = new DefaultAdapterRegistry();
-
-  const config: InlineAdapterConfig = {
-    paths: ['**\/*.ts', '**\/*.js', '**\/*.md', '**\/*.tsx', '**\/*.jsx'],
-    rootDir: workspaceRoot,
-    watchEnabled: false,
-  };
-
-  const adapter = createInlineAdapter(config, DEFAULT_SCHEMA);
-  registry.register(adapter);
-
-  scanFilesForTraces(adapter, workspaceRoot);
-
-  return createTraceService(workspaceRoot, registry);
-}
-
-function scanFilesForTraces(adapter: InlineAdapter, rootDir: string): void {
-  const patterns = ['**\/*.ts', '**\/*.js', '**\/*.md', '**\/*.tsx', '**\/*.jsx'];
-  const ignorePatterns = ['node_modules', 'dist', '.git', 'coverage', '.next', 'build'];
-
-  function walkDir(dir: string): void {
-    try {
-      const entries = fs.readdirSync(dir, { withFileTypes: true });
-
-      for (const entry of entries) {
-        const fullPath = path.join(dir, entry.name);
-        const relativePath = path.relative(rootDir, fullPath);
-
-        if (ignorePatterns.some(p => relativePath.includes(p))) {
-          continue;
-        }
-
-        if (entry.isDirectory()) {
-          walkDir(fullPath);
-        } else if (entry.isFile()) {
-          const ext = path.extname(entry.name);
-          if (['.ts', '.js', '.md', '.tsx', '.jsx'].includes(ext)) {
-            try {
-              const content = fs.readFileSync(fullPath, 'utf-8');
-              adapter.parseFileContent(relativePath, content);
-            } catch {
-              // Skip files that can't be read
-            }
-          }
-        }
-      }
-    } catch {
-      // Skip directories that can't be read
-    }
-  }
-
-  walkDir(rootDir);
-}
-
-// Original handlers used formatters from trace-formatters.ts
-// and the TraceService from mod-core. See trace-formatters.ts
-// for the formatting logic which is still valid if you want
-// to use the mod-core approach.
-*/