@codeyam/codeyam-cli 0.1.21 → 0.1.23

package/codeyam-cli/src/commands/editor.js

@@ -357,7 +357,7 @@ function printExtractionPlanInstructions() {
  */
 function printComponentCaptureInstructions() {
     checkbox('Create isolation route dirs: `codeyam editor isolate ComponentA ComponentB ...`');
-    console.log(chalk.dim('    This creates app/codeyam-isolate/layout.tsx (with production notFound() guard) and'));
+    console.log(chalk.dim('    This creates app/isolated-components/layout.tsx (with production notFound() guard) and'));
     console.log(chalk.dim('    a directory per component. List ALL components that need isolation routes.'));
     checkbox('For each visual component:');
     console.log(chalk.dim('    1. Read the source AND find where it is used in the app to understand:'));
@@ -369,8 +369,8 @@ function printComponentCaptureInstructions() {
     console.log(chalk.dim('       — Different visual states: loading, error, disabled, selected, hover'));
     console.log(chalk.dim('       — Boundary values: single item vs many, min/max ratings, very long names'));
     console.log(chalk.dim('    3. Create ONE isolation route per component with a scenarios map and ?s= query param:'));
-    console.log(chalk.dim('       Remix:   app/routes/codeyam-isolate.ComponentName.tsx → /codeyam-isolate/ComponentName'));
-    console.log(chalk.dim('       Next.js: app/codeyam-isolate/ComponentName/page.tsx → /codeyam-isolate/ComponentName'));
+    console.log(chalk.dim('       Remix:   app/routes/isolated-components.ComponentName.tsx → /isolated-components/ComponentName'));
+    console.log(chalk.dim('       Next.js: app/isolated-components/ComponentName/page.tsx → /isolated-components/ComponentName'));
     console.log(chalk.dim('       The route defines a `scenarios` object mapping scenario names to props,'));
     console.log(chalk.dim('       reads `?s=ScenarioName` from the URL, and renders the component with those props.'));
     console.log(chalk.dim('       Wrap the component in a capture container with id="codeyam-capture":'));
@@ -383,9 +383,9 @@ function printComponentCaptureInstructions() {
     console.log(chalk.dim('    4. Wait 2 seconds for HMR, then register + capture each scenario:'));
     console.log(chalk.dim(`       codeyam editor register '{"name":"ComponentName - Scenario",`));
     console.log(chalk.dim(`         "componentName":"ComponentName","componentPath":"path/to/file.tsx",`));
-    console.log(chalk.dim(`         "url":"/codeyam-isolate/ComponentName?s=Scenario",`));
+    console.log(chalk.dim(`         "url":"/isolated-components/ComponentName?s=Scenario",`));
     console.log(chalk.dim(`         "mockData":{"routes":{"/api/...":{"body":[...]}}}}'`));
-    console.log(chalk.yellow('       IMPORTANT: url MUST be an isolation route (/codeyam-isolate/... or /isolated-components/...).'));
+    console.log(chalk.yellow('       IMPORTANT: url MUST be an isolation route (/isolated-components/...).'));
     console.log(chalk.yellow('       Do NOT use real page URLs (like /library) for component scenarios.'));
     console.log(chalk.dim('       mockData.routes provides data for API calls the component makes internally'));
     console.log(chalk.dim('       (omit mockData if the component has no internal API calls)'));
@@ -395,7 +395,7 @@ function printComponentCaptureInstructions() {
     console.log(chalk.dim('    Isolation routes are committed to git — the layout guard blocks them in production'));
     console.log();
     console.log(chalk.bold('  Bulk registration: write all component scenarios to a temp file as an array:'));
-    console.log(chalk.dim('    [{"name":"Comp - Default","componentName":"Comp","componentPath":"...","url":"/codeyam-isolate/Comp?s=Default"}, ...]'));
+    console.log(chalk.dim('    [{"name":"Comp - Default","componentName":"Comp","componentPath":"...","url":"/isolated-components/Comp?s=Default"}, ...]'));
     console.log(chalk.dim('    codeyam editor register @.codeyam/tmp/scenarios.json'));
 }
 /**
@@ -448,7 +448,9 @@ function stopGate(current, opts) {
     // Skip step 1 (no feature name yet — task starts at step 2)
     if (current >= 2) {
         console.log(chalk.bold.cyan('━━━ TASK ━━━'));
-        console.log(chalk.cyan('Mark your current task (if any) as complete.'));
+        console.log(chalk.cyan('Before creating the task below, delete ALL existing tasks:'));
+        console.log(chalk.cyan('  1. Run TaskList to find all tasks'));
+        console.log(chalk.cyan('  2. Run TaskUpdate with status "deleted" for EACH task returned'));
         console.log(chalk.cyan('Then create a new task with this EXACT title (copy verbatim):'));
         console.log();
         let taskTitle;
@@ -1361,6 +1363,9 @@ function printStep9(root, feature) {
     console.log(chalk.dim('    If the audit reports issues (including pre-existing ones), fix ALL of them — do not skip.'));
     console.log(chalk.dim('    Re-run `codeyam editor audit` until all checks pass. Do NOT run `codeyam editor analyze-imports`'));
     console.log(chalk.dim('    — the audit runs targeted analysis automatically and is much faster.'));
+    console.log(chalk.dim('    If the audit reports "MANUAL ANALYSIS REQUIRED" for any entities,'));
+    console.log(chalk.dim('    follow the manual analysis steps in the audit output.'));
+    console.log(chalk.dim('    Do NOT re-run analyze-imports for those entities — it will fail again.'));
     console.log();
     stopGate(9);
 }
@@ -1962,7 +1967,7 @@ function printMigrateStep8(root) {
     console.log(chalk.bold.red('Re-register App Scenarios (REQUIRED):'));
     console.log(chalk.yellow(`  You MUST re-register application scenarios for "${page.route}" to get fresh screenshots.`));
     checkbox('Fetch existing scenarios: `codeyam editor scenarios`');
-    checkbox('Find all scenarios that use the real page route (not /codeyam-isolate/ paths)');
+    checkbox('Find all scenarios that use the real page route (not /isolated-components/ paths)');
     checkbox('Re-register each one with the SAME name to update its screenshot');
     console.log(chalk.dim(`    Example: codeyam editor register '{"name":"${pageName} - Full Data","type":"application","url":"${page.route}",...}'`));
     checkbox('After each registration, check the response for `clientErrors`');
@@ -1973,7 +1978,7 @@ function printMigrateStep8(root) {
     printComponentCaptureInstructions();
     console.log();
     console.log(chalk.bold('Verify:'));
-    checkbox('Run `codeyam editor analyze-imports` to populate import graph');
+    checkbox('Run `codeyam editor analyze-imports` to populate import graph (or `codeyam editor analyze-imports path/to/file.tsx ...` for specific files)');
     checkbox('Run library function tests: `npx jest --testPathPattern="<relevant>" --maxWorkers=2`');
     checkbox('Run `codeyam editor audit` to check completeness');
     checkbox('Check for client errors: `codeyam editor client-errors`');
@@ -2351,10 +2356,14 @@ async function handleAnalyzeImports(options = {}) {
         glossaryEntries = sanitizeGlossaryEntries(parsed);
     }
     catch {
+        if (options.silent)
+            return;
         console.error(chalk.red('Error: Could not parse .codeyam/glossary.json.'));
         process.exit(1);
     }
     if (glossaryEntries.length === 0) {
+        if (options.silent)
+            return;
         console.error(chalk.red('Error: glossary.json is empty.'));
         process.exit(1);
     }
@@ -2423,6 +2432,15 @@ async function handleAnalyzeImports(options = {}) {
     catch {
         // Non-fatal — fall back to analyzing all files
     }
+    // If specific file paths were requested, scope analysis to only those files.
+    // The full filePaths set is still used for the import graph below.
+    if (options.filePaths && options.filePaths.length > 0) {
+        const requested = new Set(options.filePaths);
+        targetFilePaths = targetFilePaths.filter((fp) => requested.has(fp));
+        if (targetFilePaths.length === 0 && !options.silent) {
+            console.log(chalk.dim('Requested file(s) already analyzed or not in glossary — skipping analysis.'));
+        }
+    }
     // Run data-structure-only analysis for entities that need it.
     // Don't pass entityNames — entities may not exist yet (fresh clone).
     // The analyzer will discover and create them from file paths.
@@ -2439,11 +2457,93 @@ async function handleAnalyzeImports(options = {}) {
         catch (err) {
             progress.fail('Analysis failed');
             const msg = err instanceof Error ? err.message : String(err);
+            if (options.silent) {
+                // Internal caller — don't kill the process, let the caller handle it
+                return;
+            }
             console.error(chalk.red(`Error: ${msg}`));
             process.exit(1);
         }
         progress.succeed('Analysis complete');
     }
+    // Surface analysis errors if any occurred
+    const errorReportPath = path.join(root, '.codeyam', 'analysis-errors.txt');
+    if (fs.existsSync(errorReportPath)) {
+        if (!options.silent) {
+            console.log(chalk.yellow('\nSome entity analyses failed. Full details in .codeyam/analysis-errors.txt'));
+            console.log(chalk.yellow('Send this file to the CodeYam team for diagnosis.'));
+            console.log(chalk.dim('Affected entities will be missing from the import graph.'));
+        }
+        // Write structured analysis-failures.json for the audit to detect.
+        // Parse the error report to find which entities failed, and cross-reference
+        // with the files we tried to analyze.
+        try {
+            const { readAnalysisFailures, writeAnalysisFailures } = await import('../utils/manualEntityAnalysis.js');
+            const errorContent = fs.readFileSync(errorReportPath, 'utf8');
+            const existingFailures = readAnalysisFailures(root);
+            // Parse error messages to identify failed file paths.
+            // Error format: "Error on step <StepName> for entity <Name> (<filePath>)"
+            // or more generic "CodeYam Error: <message>"
+            const entityErrorRegex = /(?:Error on step \w+ for entity (\w+))|(?:entity[: ]+["']?(\w+)["']?)/gi;
+            const failedEntityNames = new Set();
+            let match;
+            while ((match = entityErrorRegex.exec(errorContent)) !== null) {
+                const name = match[1] || match[2];
+                if (name)
+                    failedEntityNames.add(name);
+            }
+            // Map failed entity names back to file paths from targetFilePaths
+            const glossaryPath = path.join(root, '.codeyam', 'glossary.json');
+            let glossary = [];
+            try {
+                glossary = sanitizeGlossaryEntries(JSON.parse(fs.readFileSync(glossaryPath, 'utf8')));
+            }
+            catch {
+                // Non-fatal
+            }
+            // Also: any targetFilePaths that didn't produce entities are failures
+            const now = new Date().toISOString();
+            const updatedFailures = { ...existingFailures };
+            if (failedEntityNames.size > 0) {
+                for (const name of failedEntityNames) {
+                    const entry = glossary.find((e) => e.name === name);
+                    if (entry) {
+                        updatedFailures[entry.filePath] = {
+                            entityName: name,
+                            error: `Automated analysis failed — see .codeyam/analysis-errors.txt`,
+                            failedAt: now,
+                        };
+                    }
+                }
+            }
+            else if (targetFilePaths.length > 0) {
+                // Couldn't parse specific entity names — mark all target files
+                // that we attempted to analyze as potentially failed
+                for (const fp of targetFilePaths) {
+                    const entry = glossary.find((e) => e.filePath === fp);
+                    updatedFailures[fp] = {
+                        entityName: entry?.name || path.basename(fp, path.extname(fp)),
+                        error: `Automated analysis failed — see .codeyam/analysis-errors.txt`,
+                        failedAt: now,
+                    };
+                }
+            }
+            writeAnalysisFailures(root, updatedFailures);
+        }
+        catch {
+            // Non-fatal — failure tracking is best-effort
+        }
+    }
+    else {
+        // No errors — clear any stale failure tracking
+        try {
+            const { writeAnalysisFailures } = await import('../utils/manualEntityAnalysis.js');
+            writeAnalysisFailures(root, {});
+        }
+        catch {
+            // Non-fatal
+        }
+    }
     // Load entities WITH metadata from database
     progress.start('Loading entity metadata...');
     await initializeEnvironment();
@@ -2905,7 +3005,7 @@ async function handleRegister(jsonArg) {
     }
     // Detect duplicate screenshots in the batch
     if (isBatch && screenshotEntries.length > 1) {
-        const { computeScreenshotHash, findDuplicateScreenshots } = await import('../utils/screenshotHash');
+        const { computeScreenshotHash, findDuplicateScreenshots } = await import('../utils/screenshotHash.js');
         const hashEntries = screenshotEntries
             .map((e) => {
             const hash = computeScreenshotHash(e.screenshotAbsPath);
@@ -3235,10 +3335,11 @@ function handleChange(feature) {
  * Fetch the audit result from the server.
  * Returns null if the server is unreachable.
  */
-async function fetchAuditResult() {
+async function fetchAuditResult(options) {
     const port = getServerPort();
+    const params = options?.skipTests ? '?skipTests=true' : '';
     try {
-        const res = await fetch(`http://localhost:${port}/api/editor-audit`);
+        const res = await fetch(`http://localhost:${port}/api/editor-audit${params}`);
         if (!res.ok)
             return null;
         return await res.json();
@@ -3287,8 +3388,8 @@ async function checkAuditGate() {
         catch {
             // Fall through
         }
-        // Re-check after backfill
-        const retry = await fetchAuditResult();
+        // Re-check after backfill — skip re-running tests (backfill is DB-only)
+        const retry = await fetchAuditResult({ skipTests: true });
         if (retry?.summary?.allPassing === true)
             return true;
     }
@@ -3349,6 +3450,10 @@ function printAuditGateFailures(data) {
         const runnerErrors = (data.functions || []).filter((f) => f.status === 'runner_error');
         for (const f of runnerErrors) {
             issues.push(`    → ${f.name}${f.testFile ? ` (${f.testFile})` : ''}`);
+            if (f.hint)
+                issues.push(`      ${f.hint}`);
+            else if (f.errorMessage)
+                issues.push(`      Error: ${f.errorMessage}`);
         }
     }
     if (s.functionsNameMismatch > 0) {
@@ -3356,13 +3461,44 @@ function printAuditGateFailures(data) {
         const mismatch = (data.functions || []).filter((f) => f.status === 'name_mismatch');
         for (const f of mismatch) {
             issues.push(`    → ${f.name}${f.testFile ? ` (${f.testFile})` : ''}`);
+            if (f.hint)
+                issues.push(`      Fix: ${f.hint}`);
         }
     }
-    if (s.missingFromGlossary > 0)
+    if (s.missingFromGlossary > 0) {
         issues.push(`${s.missingFromGlossary} file(s) with scenarios not in glossary`);
+        const missingGlossary = data.missingFromGlossary || [];
+        for (const m of missingGlossary) {
+            issues.push(`    → ${m.name} (${m.filePath})`);
+        }
+        const missingPaths = missingGlossary
+            .map((m) => m.filePath)
+            .filter(Boolean);
+        if (missingPaths.length > 0) {
+            issues.push(`      Fix: Run \`codeyam editor analyze-imports ${missingPaths.join(' ')}\``);
+        }
+        else {
+            issues.push(`      Fix: Run \`codeyam editor analyze-imports\` to add these files to the glossary`);
+        }
+    }
     if (s.incompleteEntities > 0) {
+        // Check for persistent analysis failures
+        let analysisFailures = {};
+        try {
+            const failuresPath = path.join(getProjectRoot(), '.codeyam', 'analysis-failures.json');
+            if (fs.existsSync(failuresPath)) {
+                analysisFailures = JSON.parse(fs.readFileSync(failuresPath, 'utf8'));
+            }
+        }
+        catch {
+            // Non-fatal
+        }
         const preCount = s.preExistingIncompleteEntities || 0;
-        if (preCount > 0 && preCount === s.incompleteEntities) {
+        const hasFailures = Object.keys(analysisFailures).length > 0;
+        if (hasFailures) {
+            issues.push(`${s.incompleteEntities} entity/entities — automated analysis failed, manual analysis required`);
+        }
+        else if (preCount > 0 && preCount === s.incompleteEntities) {
             issues.push(`${s.incompleteEntities} entity/entities need import analysis (pre-existing — not caused by your current changes, but must be fixed before proceeding)`);
         }
         else if (preCount > 0) {
@@ -3371,18 +3507,52 @@ function printAuditGateFailures(data) {
         else {
             issues.push(`${s.incompleteEntities} entity/entities need import analysis`);
         }
+        const incomplete = data.incompleteEntities || [];
+        for (const e of incomplete) {
+            const failureEntry = Object.values(analysisFailures).find((f) => f.entityName === e.name);
+            if (failureEntry) {
+                issues.push(`    → ${e.name} — MANUAL ANALYSIS REQUIRED (automated analysis failed)`);
+                issues.push(`      Run \`codeyam editor audit\` for step-by-step manual analysis instructions`);
+            }
+            else {
+                issues.push(`    → ${e.name} (${e.scenarioCount} scenario${e.scenarioCount !== 1 ? 's' : ''})${e.preExisting ? ' [pre-existing]' : ''}`);
+            }
+        }
+        if (!hasFailures) {
+            issues.push(`      Fix: Run \`codeyam editor analyze-imports\` to build import graphs`);
+        }
     }
     if (s.unassociatedScenarios > 0) {
-        issues.push(`${s.unassociatedScenarios} component(s) have scenarios with no entity link — run \`codeyam editor analyze-imports\` then re-run audit`);
         const unassociated = data.unassociatedScenarios || [];
+        const unassocPaths = unassociated
+            .map((u) => u.filePath)
+            .filter(Boolean);
+        if (unassocPaths.length > 0) {
+            issues.push(`${s.unassociatedScenarios} component(s) have scenarios with no entity link — run \`codeyam editor analyze-imports ${unassocPaths.join(' ')}\` then re-run audit`);
+        }
+        else {
+            issues.push(`${s.unassociatedScenarios} component(s) have scenarios with no entity link — run \`codeyam editor analyze-imports\` then re-run audit`);
+        }
         for (const u of unassociated) {
             issues.push(`    → ${u.name} (${u.filePath}) — ${u.scenarioCount} scenario${u.scenarioCount !== 1 ? 's' : ''}`);
         }
     }
-    if (s.miscategorizedScenarios > 0)
+    if (s.miscategorizedScenarios > 0) {
         issues.push(`${s.miscategorizedScenarios} component(s) using page URLs instead of isolation routes`);
-    if (s.scenariosNeedingRecapture > 0)
+        const miscategorized = data.miscategorizedScenarios || [];
+        for (const m of miscategorized) {
+            issues.push(`    → ${m.componentName} at ${m.url} (${m.scenarioNames.length} scenario${m.scenarioNames.length !== 1 ? 's' : ''})`);
+        }
+        issues.push(`      Fix: Re-register these as app-level scenarios (with pageFilePath, no componentName) or use isolation routes`);
+    }
+    if (s.scenariosNeedingRecapture > 0) {
         issues.push(`${s.scenariosNeedingRecapture} scenario(s) need recapture (dependency tree changed)`);
+        const recapture = data.scenariosNeedingRecapture || [];
+        for (const r of recapture) {
+            issues.push(`    → "${r.scenarioName}" (entity: ${r.entityName}, ${r.status?.status || 'changed'})`);
+        }
+        issues.push(`      Fix: Re-capture affected scenarios to update screenshots after code changes`);
+    }
     if (issues.length > 0) {
         console.error(chalk.yellow('\nAudit failures:'));
         for (const issue of issues) {
@@ -3417,16 +3587,16 @@ function printAuditGateFailures(data) {
  * which glossary components have registered scenarios and which functions
  * have test files. Exits with code 1 if anything is missing.
  */
-async function handleAudit() {
+async function handleAudit(options) {
     let data = await fetchAuditResult();
     if (!data) {
         console.error(chalk.red('Error: Could not reach the CodeYam server. Is it running?'));
         process.exit(1);
     }
-    // Lightweight auto-fix: backfill entity_sha on scenarios that were
-    // registered before entity records existed. This is fast (DB-only).
-    // We do NOT run handleAnalyzeImports here — it scans all files and takes
-    // minutes on large projects. Users should run it separately if needed.
+    // Two-phase auto-fix for entity associations:
+    // Phase 1: DB-only backfill — fast, matches existing entities to scenarios.
+    // Phase 2: If backfill fails, targeted analyze-imports for only the
+    // specific unresolved files (1-3 files, not the full glossary scan).
     const incompleteBeforeFix = data.incompleteEntities || [];
     const unassociatedBeforeFix = data.unassociatedScenarios || [];
     let autoRemediationFailed = false;
@@ -3451,20 +3621,65 @@ async function handleAudit() {
         catch {
             // Fall through — re-fetch will show remaining issues
         }
-        // Re-fetch audit results after the backfill
-        data = await fetchAuditResult();
+        // Re-fetch audit results after the backfill — skip re-running tests
+        // since they haven't changed (backfill is DB-only).
+        data = await fetchAuditResult({ skipTests: true });
         if (!data) {
             console.error(chalk.red('Error: Could not reach the CodeYam server after backfill.'));
             process.exit(1);
         }
-        // If issues persist after backfill, flag it so we show clear guidance
+        // If issues persist after DB-only backfill, run targeted analyze-imports
+        // for ONLY the specific files that need entities. This is fast (1-3 files)
+        // unlike full analyze-imports which scans all glossary entries.
+        const incompleteAfterBackfill = data.incompleteEntities || [];
+        const unassociatedAfterBackfill = data.unassociatedScenarios || [];
+        if (incompleteAfterBackfill.length > 0 ||
+            unassociatedAfterBackfill.length > 0) {
+            const { determineTargetedAnalysisPaths } = await import('../utils/editorAudit.js');
+            const targetPaths = determineTargetedAnalysisPaths({
+                unassociatedScenarios: unassociatedAfterBackfill,
+                incompleteEntities: incompleteAfterBackfill,
+            });
+            if (targetPaths.length > 0) {
+                console.log(chalk.dim(`Running targeted analysis for ${targetPaths.length} file${targetPaths.length !== 1 ? 's' : ''}...`));
+                try {
+                    await handleAnalyzeImports({
+                        silent: true,
+                        filePaths: targetPaths,
+                    });
+                    // Retry backfill after analysis created entities
+                    const entities = await loadEntities({});
+                    if (entities && entities.length > 0) {
+                        const { getDatabase: getDb } = await import('../../../packages/database/index.js');
+                        const freshDb = getDb();
+                        await backfillEntityShaOnScenarios(freshDb, entities.map((e) => ({
+                            sha: e.sha,
+                            name: e.name,
+                            filePath: e.filePath || '',
+                            isDefaultExport: e.metadata?.notExported === false &&
+                                e.metadata?.namedExport === false,
+                        })));
+                    }
+                    // Re-fetch audit results after targeted analysis
+                    data = await fetchAuditResult({ skipTests: true });
+                    if (!data) {
+                        console.error(chalk.red('Error: Could not reach the CodeYam server after analysis.'));
+                        process.exit(1);
+                    }
+                }
+                catch {
+                    // Targeted analysis failed — fall through to show remaining issues
+                }
+            }
+        }
+        // Check if issues persist after all remediation attempts
         const incompleteAfterFix = data.incompleteEntities || [];
         const unassociatedAfterFix = data.unassociatedScenarios || [];
         if (incompleteAfterFix.length > 0 || unassociatedAfterFix.length > 0) {
             autoRemediationFailed = true;
         }
     }
-    const { components, functions, summary } = data;
+    let { components, functions, summary } = data;
     console.log();
     console.log(chalk.bold.cyan('━━━ Editor Audit ━━━'));
     console.log();
@@ -3563,51 +3778,53 @@ async function handleAudit() {
         for (const m of missingFromGlossary) {
             console.log(`  ${chalk.red('✗')} ${m.name} ${chalk.dim(`(${m.filePath})`)} — ${m.scenarioCount} scenario${m.scenarioCount !== 1 ? 's' : ''} but not in glossary`);
         }
-        console.log(chalk.yellow('    Add these to .codeyam/glossary.json and run `codeyam editor analyze-imports`'));
-        console.log();
-    }
-    // Incomplete entities (scenarios without analyses) — auto-fix by running
-    // targeted analysis on just the affected files (fast: 2 files vs 117+).
-    let incompleteEntities = data.incompleteEntities || [];
-    if (incompleteEntities.length > 0) {
-        const { getIncompleteEntityFilePaths } = await import('../utils/editorAudit.js');
-        try {
-            const { getDatabase } = await import('../../../packages/database/index.js');
-            const db = getDatabase();
-            const filePaths = await getIncompleteEntityFilePaths(db, incompleteEntities);
-            if (filePaths.length > 0) {
-                console.log(chalk.dim(`Running targeted import analysis for ${filePaths.length} incomplete entit${filePaths.length !== 1 ? 'ies' : 'y'}...`));
-                const root = getProjectRoot();
-                try {
-                    const { runAnalysisForEntities } = await import('../utils/analysisRunner.js');
-                    await runAnalysisForEntities({
-                        projectRoot: root,
-                        filePaths,
-                        progress: new ProgressReporter(),
-                        onlyDataStructure: true,
-                    });
-                    // Re-fetch audit results after targeted fix
-                    const refreshed = await fetchAuditResult();
-                    if (refreshed) {
-                        data = refreshed;
-                        incompleteEntities = data.incompleteEntities || [];
-                    }
-                }
-                catch {
-                    // Fall through — report remaining incomplete entities below
-                }
-            }
+        const mgPaths = missingFromGlossary
+            .map((m) => m.filePath)
+            .filter(Boolean);
+        if (mgPaths.length > 0) {
+            console.log(chalk.yellow(`    Add these to .codeyam/glossary.json and run \`codeyam editor analyze-imports ${mgPaths.join(' ')}\``));
         }
-        catch {
-            // DB not available — fall through to reporting
+        else {
+            console.log(chalk.yellow('    Add these to .codeyam/glossary.json and run `codeyam editor analyze-imports`'));
         }
+        console.log();
     }
+    // Incomplete entities (scenarios without analyses) — report with guidance.
+    // We intentionally do NOT run analysis here: it starts the analyzer
+    // template which is slow even for a few files. Users should run
+    // `codeyam editor analyze-imports` separately if needed.
+    const incompleteEntities = data.incompleteEntities || [];
     if (incompleteEntities.length > 0) {
-        const { formatIncompleteEntityGuidance } = await import('../utils/editorAudit.js');
+        const { formatIncompleteEntityGuidance, formatManualAnalysisGuidance } = await import('../utils/editorAudit.js');
+        const { readAnalysisFailures } = await import('../utils/manualEntityAnalysis.js');
+        // Check for persistent analysis failures
+        const analysisFailures = readAnalysisFailures(getProjectRoot());
         console.log(chalk.bold('Incomplete entities (need import analysis):'));
         for (const e of incompleteEntities) {
-            const guidance = formatIncompleteEntityGuidance(e);
-            console.log(`  ${chalk.red('✗')} ${guidance}`);
+            // Check if this entity has a persistent failure
+            const failureEntry = Object.values(analysisFailures).find((f) => f.entityName === e.name);
+            if (failureEntry) {
+                // Show manual analysis instructions instead of "run analyze-imports"
+                const filePath = Object.entries(analysisFailures).find(([, f]) => f.entityName === e.name)?.[0];
+                const guidance = formatManualAnalysisGuidance({
+                    name: e.name,
+                    filePath: filePath || '',
+                    scenarioCount: e.scenarioCount,
+                    error: failureEntry.error,
+                });
+                // Print each line with proper indentation
+                for (const line of guidance.split('\n')) {
+                    console.log(`  ${chalk.red('✗')} ${line}`);
+                }
+            }
+            else {
+                const guidance = formatIncompleteEntityGuidance(e);
+                console.log(`  ${chalk.red('✗')} ${guidance}`);
+            }
+        }
+        const incompleteErrorReportPath = path.join(getProjectRoot(), '.codeyam', 'analysis-errors.txt');
+        if (fs.existsSync(incompleteErrorReportPath)) {
+            console.log(chalk.dim('    See .codeyam/analysis-errors.txt for error details.'));
         }
         console.log();
     }
@@ -3624,12 +3841,22 @@ async function handleAudit() {
                 console.log(chalk.dim(`      … and ${u.scenarioNames.length - 3} more`));
             }
         }
+        const uaPaths = unassociatedScenarios
+            .map((u) => u.filePath)
+            .filter(Boolean);
+        const uaCmd = uaPaths.length > 0
+            ? `codeyam editor analyze-imports ${uaPaths.join(' ')}`
+            : 'codeyam editor analyze-imports';
         if (autoRemediationFailed) {
             console.log(chalk.yellow('    analyze-imports ran automatically but could not resolve these.'));
-            console.log(chalk.yellow('    Run `codeyam editor analyze-imports` to see the full error output.'));
+            console.log(chalk.yellow(`    Run \`${uaCmd}\` to see the full error output.`));
         }
         else {
-            console.log(chalk.yellow('    Run `codeyam editor analyze-imports` to create entity records, then re-run audit to backfill.'));
+            console.log(chalk.yellow(`    Run \`${uaCmd}\` to create entity records, then re-run audit to backfill.`));
+        }
+        const unassocErrorReportPath = path.join(getProjectRoot(), '.codeyam', 'analysis-errors.txt');
+        if (fs.existsSync(unassocErrorReportPath)) {
+            console.log(chalk.dim('    See .codeyam/analysis-errors.txt for error details.'));
         }
         console.log();
     }
@@ -3658,7 +3885,26 @@ async function handleAudit() {
                 : `${s.status.status}`;
             console.log(`  ${chalk.red('✗')} ${s.scenarioName} ${chalk.dim(`(${s.entityName} — ${reason})`)}`);
         }
-        console.log(chalk.yellow('    Run: codeyam editor recapture-stale'));
+        if (options?.fix) {
+            // --fix: auto-recapture stale scenarios instead of just reporting them
+            const { shouldAutoRecapture } = await import('../utils/editorAudit.js');
+            if (shouldAutoRecapture({ fix: true, scenariosNeedingRecapture })) {
+                console.log(chalk.cyan('    --fix: auto-recapturing stale scenarios...'));
+                console.log();
+                await handleRecaptureStale();
+                // Re-fetch audit results so the summary and exit code reflect
+                // the post-fix state, not the pre-fix state.
+                const refreshed = await fetchAuditResult({ skipTests: true });
+                if (refreshed) {
+                    data = refreshed;
+                    ({ components, functions, summary } = data);
+                }
+            }
+        }
+        else {
+            console.log(chalk.yellow('    Run: codeyam editor recapture-stale'));
+            console.log(chalk.dim('    Or: codeyam editor audit --fix (to auto-recapture)'));
+        }
         console.log();
     }
     // Duplicate glossary names (warning, not a failure)
@@ -3721,17 +3967,6 @@ async function handleAudit() {
     if (!allOk) {
         process.exit(1);
     }
-    // Auto-run analyze-imports when audit passes — this builds the import graph
-    // so the App tab can show component/function dependencies for each page.
-    // Previously this was a manual step that Claude had to remember to run.
-    console.log(chalk.dim('Building import graph...'));
-    try {
-        await handleAnalyzeImports({ silent: true });
-    }
-    catch {
-        // Non-fatal — audit passed, import graph is a bonus
-        console.log(chalk.yellow('Warning: Could not build import graph. Run `codeyam editor analyze-imports` manually.'));
-    }
 }
 // ─── Recapture-stale subcommand ────────────────────────────────────────
 /**
@@ -3938,14 +4173,14 @@ async function handleScenarioCoverage() {
     // Safety net: heal any scenarios with null entity_sha before checking coverage
     try {
         const { getDatabase } = await import('../../../packages/database/index.js');
-        const { countScenariosNeedingEntityBackfill } = await import('../utils/editorScenarios');
+        const { countScenariosNeedingEntityBackfill } = await import('../utils/editorScenarios.js');
         const db = getDatabase();
         const backfillCount = await countScenariosNeedingEntityBackfill(db);
         if (backfillCount > 0) {
             console.log(chalk.dim(`  Healing ${backfillCount} scenario(s) with unlinked entities...`));
             await handleAnalyzeImports({ silent: true });
             // Run backfill after analysis
-            const { backfillEntityShaOnScenarios } = await import('../utils/editorScenarios');
+            const { backfillEntityShaOnScenarios } = await import('../utils/editorScenarios.js');
             const entities = await loadEntities({});
             if (entities && entities.length > 0) {
                 await backfillEntityShaOnScenarios(db, entities.map((e) => ({
@@ -4442,14 +4677,205 @@ function handleEditorDebug(args) {
     console.log(chalk.dim('  Open index.md for the full list of scenario outputs.'));
     console.log();
 }
+// ─── Manual entity analysis ───────────────────────────────────────────
+/**
+ * `codeyam editor manual-entity <JSON|@file>`
+ *
+ * Creates entity and analysis records from Claude-provided metadata when
+ * automated analyze-imports fails. This unblocks the audit gate without
+ * needing the analyzer template to parse the source file.
+ */
+async function handleManualEntity(jsonArg) {
+    const root = getProjectRoot();
+    // Parse JSON input (supports @file.json convention)
+    const parsed = parseRegisterArg(jsonArg);
+    if (parsed.error || !parsed.body) {
+        console.error(chalk.red(`Error: ${parsed.error || 'Invalid input'}`));
+        console.error(chalk.dim('  Usage: codeyam editor manual-entity \'{"name":"Header","filePath":"src/components/Header.tsx","entityType":"visual",...}\''));
+        console.error(chalk.dim('  Or: codeyam editor manual-entity @.codeyam/tmp/manual-entity.json'));
+        process.exit(1);
+    }
+    const input = parsed.body;
+    // Validate input
+    const { validateManualEntityInput, convertTypeInfoToDataForMocks, readAnalysisFailures, clearFailureForPath, writeAnalysisFailures, } = await import('../utils/manualEntityAnalysis.js');
+    // Read glossary for validation
+    const glossaryPath = path.join(root, '.codeyam', 'glossary.json');
+    let glossaryEntries = [];
+    try {
+        glossaryEntries = sanitizeGlossaryEntries(JSON.parse(fs.readFileSync(glossaryPath, 'utf8')));
+    }
+    catch {
+        // Empty glossary — validation will still check file existence
+    }
+    const errors = validateManualEntityInput(input, glossaryEntries, {
+        fileExists: (p) => fs.existsSync(path.join(root, p)),
+    });
+    if (errors.length > 0) {
+        console.error(chalk.red('Validation errors:'));
+        for (const err of errors) {
+            console.error(chalk.red(`  • ${err}`));
+        }
+        process.exit(1);
+    }
+    // Read source file and compute SHA
+    const sourceContent = fs.readFileSync(path.join(root, input.filePath), 'utf8');
+    const { generateSha } = await import('../../../packages/database/index.js');
+    const entitySha = generateSha(input.filePath, input.name, sourceContent);
+    // Get project and branch
+    await initializeEnvironment();
+    const configPath = path.join(root, '.codeyam', 'config.json');
+    let projectSlug;
+    try {
+        const config = JSON.parse(fs.readFileSync(configPath, 'utf8'));
+        projectSlug = config.projectSlug;
+    }
+    catch {
+        console.error(chalk.red('Error: .codeyam/config.json not found or invalid.'));
+        process.exit(1);
+    }
+    const { project, branch } = await requireBranchAndProject(projectSlug);
+    const { getDatabase } = await import('../../../packages/database/index.js');
+    const db = getDatabase();
+    // Convert type info to dataForMocks format
+    const dataForMocks = convertTypeInfoToDataForMocks(input.typeInfo);
+    // Create entity record
+    const entityMetadata = {
+        importedExports: (input.importedExports || []).map((ie) => ({
+            name: ie.name,
+            filePath: ie.filePath,
+        })),
+        manuallyAnalyzed: true,
+    };
+    // Check if entity already exists
+    const existingEntity = await db
+        .selectFrom('entities')
+        .select('sha')
+        .where('sha', '=', entitySha)
+        .executeTakeFirst();
+    if (!existingEntity) {
+        await db
+            .insertInto('entities')
+            .values({
+            sha: entitySha,
+            project_id: project.id,
+            name: input.name,
+            entity_type: input.entityType,
+            file_path: input.filePath,
+            metadata: JSON.stringify(entityMetadata),
+        })
+            .onConflict((oc) => oc.column('sha').doNothing())
+            .execute();
+        console.log(chalk.dim(`Created entity record: ${input.name} (${entitySha.slice(0, 8)}...)`));
+    }
+    else {
+        // Update metadata on existing entity
+        await db
+            .updateTable('entities')
+            .set({
+            metadata: JSON.stringify(entityMetadata),
+        })
+            .where('sha', '=', entitySha)
+            .execute();
+        console.log(chalk.dim(`Updated existing entity: ${input.name} (${entitySha.slice(0, 8)}...)`));
+    }
+    // Create entity_branch record
+    await db
+        .insertInto('entity_branches')
+        .values({
+        entity_sha: entitySha,
+        branch_id: branch.id,
+        active: true,
+    })
+        .onConflict((oc) => oc.columns(['entity_sha', 'branch_id']).doUpdateSet({ active: true }))
+        .execute();
+    // Create analysis record
+    const { randomUUID } = await import('crypto');
+    const analysisId = randomUUID();
+    const now = new Date().toISOString();
+    const analysisMetadata = {
+        scenariosDataStructure: {
+            dataForMocks: Object.keys(dataForMocks).length > 0 ? dataForMocks : null,
+        },
+        mergedDataStructure: {
+            dependencySchemas: null,
+        },
+        manuallyAnalyzed: true,
+    };
+    const analysisStatus = {
+        startedAt: now,
+        finishedAt: now,
+        steps: [],
+        errors: [],
+    };
+    // Check if analysis already exists for this entity
+    const existingAnalysis = await db
+        .selectFrom('analyses')
+        .select('id')
+        .where('entity_sha', '=', entitySha)
+        .executeTakeFirst();
+    if (!existingAnalysis) {
+        await db
+            .insertInto('analyses')
+            .values({
+            id: analysisId,
+            project_id: project.id,
+            entity_sha: entitySha,
+            entity_name: input.name,
+            entity_type: input.entityType,
+            file_path: input.filePath,
+            status: JSON.stringify(analysisStatus),
+            metadata: JSON.stringify(analysisMetadata),
+        })
+            .execute();
+        console.log(chalk.dim(`Created analysis record: ${analysisId.slice(0, 8)}...`));
+    }
+    else {
+        // Update existing analysis with manual metadata
+        await db
+            .updateTable('analyses')
+            .set({
+            metadata: JSON.stringify(analysisMetadata),
+            status: JSON.stringify(analysisStatus),
+        })
+            .where('entity_sha', '=', entitySha)
+            .execute();
+        console.log(chalk.dim(`Updated existing analysis for ${input.name}`));
+    }
+    // Backfill entity_sha on scenarios
+    const backfillResult = await backfillEntityShaOnScenarios(db, [
+        {
+            sha: entitySha,
+            name: input.name,
+            filePath: input.filePath,
+            isDefaultExport: false,
+        },
+    ]);
+    if (backfillResult.updated > 0) {
+        console.log(chalk.dim(`Linked ${backfillResult.updated} scenario(s) to entity`));
+    }
+    // Clear from analysis failures tracker
+    const failures = readAnalysisFailures(root);
+    if (failures[input.filePath]) {
+        const updated = clearFailureForPath(failures, input.filePath);
+        writeAnalysisFailures(root, updated);
+        console.log(chalk.dim(`Cleared analysis failure for ${input.filePath}`));
+    }
+    console.log();
+    console.log(chalk.green.bold(`✓ Manual entity analysis complete: ${input.name}`));
+    console.log(chalk.dim(`  Entity SHA: ${entitySha.slice(0, 12)}...`));
+    console.log(chalk.dim(`  Imports: ${(input.importedExports || []).length} glossary entities`));
+    console.log(chalk.dim(`  Type info: ${Object.keys(dataForMocks).length} fields`));
+    console.log();
+    console.log(chalk.dim('Re-run `codeyam editor audit` to verify.'));
+}
 // ─── Command definition ───────────────────────────────────────────────
 const editorCommand = {
     command: 'editor [step] [json]',
     describe: 'Editor mode guided workflow',
     builder: (yargs) => {
         const stepDescription = IS_INTERNAL_BUILD
-            ? 'Step number (1-18) or subcommand (template, register, isolate, analyze-imports, dependents, audit, scenarios, scenario-coverage, recapture-stale, change, sync, debug, preview, show-results, hide-results, commit, journal, journal-list, journal-update, dev-server, client-errors, task-ontrack)'
-            : 'Step number (1-18) or subcommand (template, register, isolate, analyze-imports, dependents, audit, scenarios, scenario-coverage, recapture-stale, change, sync, preview, show-results, hide-results, commit, journal, journal-list, journal-update, dev-server, client-errors, task-ontrack)';
+            ? 'Step number (1-18) or subcommand (template, register, isolate, analyze-imports, manual-entity, dependents, audit, scenarios, scenario-coverage, recapture-stale, change, sync, debug, preview, show-results, hide-results, commit, journal, journal-list, journal-update, dev-server, client-errors, task-ontrack)'
+            : 'Step number (1-18) or subcommand (template, register, isolate, analyze-imports, manual-entity, dependents, audit, scenarios, scenario-coverage, recapture-stale, change, sync, preview, show-results, hide-results, commit, journal, journal-list, journal-update, dev-server, client-errors, task-ontrack)';
         let builder = yargs
             .positional('step', {
             type: 'string',
@@ -4480,6 +4906,11 @@ const editorCommand = {
             alias: 'p',
             describe: 'Port to run the web server on',
             default: 3111,
+        })
+            .option('fix', {
+            type: 'boolean',
+            describe: 'For audit: also recapture stale scenarios after displaying results',
+            default: false,
         });
         if (IS_INTERNAL_BUILD) {
             builder = builder
@@ -4591,7 +5022,9 @@ const editorCommand = {
                     'Ask user what to build next and restart codeyam editor workflow';
             }
             console.log(chalk.bold.cyan('━━━ TASK ━━━'));
-            console.log(chalk.cyan('Mark your current task (if any) as complete.'));
+            console.log(chalk.cyan('Before creating the task below, delete ALL existing tasks:'));
+            console.log(chalk.cyan('  1. Run TaskList to find all tasks'));
+            console.log(chalk.cyan('  2. Run TaskUpdate with status "deleted" for EACH task returned'));
             console.log(chalk.cyan('Then create a new task with this EXACT title (copy verbatim):'));
             console.log();
             console.log(chalk.bold.cyan(`EXACT_TASK_TITLE: ${taskTitle}`));
@@ -4605,9 +5038,16 @@ const editorCommand = {
             fs.writeFileSync(trackingPath, JSON.stringify({ step: state.step, taskCreated: true }, null, 2), 'utf8');
             return;
         }
-        // Subcommand: codeyam editor analyze-imports
+        // Subcommand: codeyam editor analyze-imports [file1.tsx file2.tsx ...]
         if (argv.step === 'analyze-imports') {
-            await handleAnalyzeImports();
+            const { parseAnalyzeImportsArgs } = await import('./editorAnalyzeImportsArgs.js');
+            const requestedPaths = parseAnalyzeImportsArgs(argv.json, argv._);
+            await handleAnalyzeImports(requestedPaths.length > 0 ? { filePaths: requestedPaths } : {});
+            return;
+        }
+        // Subcommand: codeyam editor manual-entity <JSON|@file>
+        if (argv.step === 'manual-entity') {
+            await handleManualEntity(argv.json || '');
             return;
         }
         // Subcommand: codeyam editor dependents <EntityName>
@@ -4615,9 +5055,9 @@ const editorCommand = {
             await handleDependents(argv.json || '');
             return;
         }
-        // Subcommand: codeyam editor audit
+        // Subcommand: codeyam editor audit [--fix]
         if (argv.step === 'audit') {
-            await handleAudit();
+            await handleAudit({ fix: argv.fix || false });
             return;
         }
         // Subcommand: codeyam editor scenarios
@@ -4850,13 +5290,24 @@ const editorCommand = {
                     try {
                         const { getDatabase: getDb } = await import('../../../packages/database/index.js');
                         const seedDb = getDb();
-                        const appScenario = await seedDb
+                        // Prefer the home page scenario (url "/") since the App tab
+                        // sorts "Home" first — fall back to any application scenario.
+                        const homeScenario = await seedDb
                             .selectFrom('editor_scenarios')
                             .select(['id', 'name', 'type'])
                             .where('project_id', '=', project.id)
-                            .where('type', '=', 'application')
+                            .where('url', '=', '/')
+                            .where('component_name', 'is', null)
                             .orderBy('created_at', 'asc')
                             .executeTakeFirst();
+                        const appScenario = homeScenario ||
+                            (await seedDb
+                                .selectFrom('editor_scenarios')
+                                .select(['id', 'name', 'type'])
+                                .where('project_id', '=', project.id)
+                                .where('type', '=', 'application')
+                                .orderBy('created_at', 'asc')
+                                .executeTakeFirst());
                         if (appScenario) {
                             const seedFile = path.join(projectRoot, '.codeyam', 'editor-scenarios', `${appScenario.id}.seed.json`);
                             if (fs.existsSync(seedFile)) {
@@ -4999,7 +5450,7 @@ const editorCommand = {
                         if (!needsAnalysis) {
                             try {
                                 const { getDatabase } = await import('../../../packages/database/index.js');
-                                const { countScenariosNeedingEntityBackfill } = await import('../utils/editorScenarios');
+                                const { countScenariosNeedingEntityBackfill } = await import('../utils/editorScenarios.js');
                                 const db = getDatabase();
                                 const backfillCount = await countScenariosNeedingEntityBackfill(db);
                                 if (backfillCount > 0) {
@@ -5038,7 +5489,7 @@ const editorCommand = {
                         .execute();
                     if (unresolved.length > 0) {
                         const { scanPageFilePaths: scanPfp } = await import('../utils/entityChangeStatus.server.js');
-                        const { matchUrlToPageFile } = await import('../utils/routePatternMatching');
+                        const { matchUrlToPageFile } = await import('../utils/routePatternMatching.js');
                         const { allFiles: pfpFiles } = scanPfp(projectRoot);
                         let pfpResolved = 0;
                         for (const row of unresolved) {