container-superposition 0.1.7 → 0.1.8

package/dist/tool/cli/run.js

@@ -0,0 +1,318 @@
+import * as fs from 'fs';
+import * as path from 'path';
+import chalk from 'chalk';
+import boxen from 'boxen';
+import ora from 'ora';
+import { composeDevContainer, generateManifestOnly } from '../questionnaire/composer.js';
+import { loadManifest } from '../schema/manifest-migrations.js';
+import { printSummary } from '../utils/summary.js';
+import { buildAnswersFromManifest, buildAnswersFromProjectConfig, buildProjectConfigSelectionFromAnswers, findManifestFile, findDefaultRegenManifest, findProjectConfig, loadProjectConfig, writeProjectConfig, writeProjectConfigCustomizations, } from '../schema/project-config.js';
+import { isInsideGitRepo, createBackup, ensureBackupPatternsInGitignore } from '../utils/backup.js';
+import { buildAnswersFromCliArgs, mergeAnswers } from '../questionnaire/answers.js';
+import { applyPresetSelections } from '../questionnaire/presets.js';
+import { runQuestionnaire, loadOverlaysConfigWrapper, PRESETS_DIR, } from '../questionnaire/questionnaire.js';
+import { parseCliArgs } from './args.js';
+export async function main() {
+    try {
+        const cliArgs = await parseCliArgs();
+        const initialCwd = process.cwd();
+        if (cliArgs?.projectRoot) {
+            const resolvedProjectRoot = path.resolve(initialCwd, cliArgs.projectRoot);
+            if (!fs.existsSync(resolvedProjectRoot)) {
+                console.error(chalk.red(`✗ Project root not found: ${resolvedProjectRoot}`));
+                process.exit(1);
+            }
+            if (!fs.statSync(resolvedProjectRoot).isDirectory()) {
+                console.error(chalk.red(`✗ Project root is not a directory: ${resolvedProjectRoot}`));
+                process.exit(1);
+            }
+            process.chdir(resolvedProjectRoot);
+        }
+        let projectFileOutputPath;
+        let existingProjectFileDetected = false;
+        if (cliArgs?.commandName === 'init' || cliArgs?.commandName === undefined) {
+            const discoveredProjectFiles = findProjectConfig(process.cwd());
+            if (discoveredProjectFiles.length > 1) {
+                console.error(chalk.red('✗ Found both .superposition.yml and superposition.yml in the repository root. Keep only one.'));
+                console.error(chalk.gray('  Recommended: keep .superposition.yml (dotfile) to keep the root tidy; delete superposition.yml.'));
+                process.exit(1);
+            }
+            if (discoveredProjectFiles.length === 1) {
+                existingProjectFileDetected = true;
+            }
+            projectFileOutputPath =
+                discoveredProjectFiles[0]?.path ?? path.join(process.cwd(), '.superposition.yml');
+        }
+        let projectConfig = undefined;
+        let projectConfigAnswers;
+        if (!cliArgs?.manifestPath) {
+            const overlaysConfigForProject = loadOverlaysConfigWrapper();
+            projectConfig = loadProjectConfig(overlaysConfigForProject, process.cwd()) ?? undefined;
+            if (projectConfig) {
+                projectConfigAnswers = await applyPresetSelections(buildAnswersFromProjectConfig(projectConfig.selection, overlaysConfigForProject), overlaysConfigForProject, PRESETS_DIR);
+            }
+        }
+        let manifest;
+        let manifestDir;
+        let backupDir;
+        let useManifestOnly = false;
+        let useProjectOnly = false;
+        if (cliArgs?.commandName === 'regen' && !cliArgs.manifestPath && !cliArgs.fromProject) {
+            if (projectConfigAnswers) {
+                useProjectOnly = true;
+            }
+            else {
+                const discoveredManifestPath = findDefaultRegenManifest(cliArgs?.config?.outputPath || './.devcontainer');
+                if (discoveredManifestPath) {
+                    console.error(chalk.red('✗ Error: No project file found'));
+                    console.error(chalk.cyan('  Found superposition.json but no superposition.yml project file.'));
+                    console.error(chalk.gray('  Run `cs migrate` to create a project file from your existing manifest, then run `regen` again.'));
+                }
+                else {
+                    console.error(chalk.red('✗ Error: No project file found'));
+                    console.error(chalk.gray('  Create .superposition.yml or superposition.yml in your repository root.'));
+                    console.error(chalk.dim('  Or run `cs init` to create a new configuration interactively.'));
+                }
+                process.exit(1);
+            }
+        }
+        if (cliArgs?.commandName === 'regen' && cliArgs?.manifestPath) {
+            console.warn(chalk.yellow('⚠️  --from-manifest is deprecated for regen. Run `cs migrate` to create a project file, then use `regen` without this flag.'));
+        }
+        if (cliArgs?.manifestPath) {
+            const manifestPath = findManifestFile(cliArgs.manifestPath);
+            if (!manifestPath) {
+                console.error(chalk.red('✗ Could not find manifest file'));
+                console.error(chalk.red(`  Searched for: ${cliArgs.manifestPath}`));
+                process.exit(1);
+            }
+            manifestDir = path.dirname(manifestPath);
+            const loadedManifest = loadManifest(manifestPath);
+            if (!loadedManifest) {
+                process.exit(1);
+            }
+            manifest = loadedManifest;
+            if (cliArgs.backupDir) {
+                backupDir = cliArgs.backupDir;
+            }
+            if (cliArgs.noInteractive) {
+                useManifestOnly = true;
+            }
+        }
+        if (cliArgs?.fromProject) {
+            if (!projectConfigAnswers || !projectConfig) {
+                console.error(chalk.red('✗ Could not find project file'));
+                console.error(chalk.red('  Searched for: .superposition.yml, superposition.yml'));
+                process.exit(1);
+            }
+            useProjectOnly = cliArgs.noInteractive || cliArgs.commandName === 'regen';
+        }
+        if (cliArgs?.noInteractive && !cliArgs?.manifestPath && !projectConfigAnswers) {
+            console.error(chalk.red('✗ Error: --no-interactive requires persisted input'));
+            console.error(chalk.dim('  Use --from-project or run from a repository with .superposition.yml or superposition.yml'));
+            process.exit(1);
+        }
+        const resolvedOutputPath = cliArgs?.config?.outputPath ||
+            projectConfigAnswers?.outputPath ||
+            manifestDir ||
+            './.devcontainer';
+        const backupCheckPath = path.resolve(resolvedOutputPath);
+        const inGitRepo = isInsideGitRepo(backupCheckPath);
+        let shouldBackup;
+        if (cliArgs?.backupOverride === true) {
+            shouldBackup = true;
+        }
+        else if (cliArgs?.backupOverride === false) {
+            shouldBackup = false;
+        }
+        else {
+            shouldBackup = !inGitRepo;
+            if (!shouldBackup) {
+                console.log(chalk.dim('ℹ  Skipping backup — git repo detected (use --backup to force one)\n'));
+            }
+        }
+        const isReplayMode = cliArgs?.commandName === 'regen' || useManifestOnly || useProjectOnly;
+        let actualBackupPath;
+        if (shouldBackup && isReplayMode) {
+            const outputPath = resolvedOutputPath;
+            const backupPath = await createBackup(outputPath, backupDir);
+            if (backupPath) {
+                actualBackupPath = backupPath;
+                console.log(chalk.green(`✓ Backup created: ${backupPath}\n`));
+                ensureBackupPatternsInGitignore(outputPath);
+            }
+        }
+        const mainOverlaysConfig = loadOverlaysConfigWrapper();
+        let answers;
+        const hasCliOverrides = cliArgs &&
+            Object.keys(cliArgs.config).some((key) => key !== 'outputPath' &&
+                key !== 'preset' &&
+                key !== 'presetChoices' &&
+                !(key === 'target' && cliArgs.config.target === 'local') &&
+                !(key === 'editor' && cliArgs.config.editor === 'vscode') &&
+                cliArgs.config[key] !== undefined);
+        const hasAnyCliConfig = cliArgs &&
+            Object.entries(cliArgs.config).some(([key, value]) => value !== undefined &&
+                !(key === 'target' && value === 'local') &&
+                !(key === 'editor' && value === 'vscode'));
+        if (useManifestOnly && manifest && !hasCliOverrides) {
+            const manifestAnswers = buildAnswersFromManifest(manifest, mainOverlaysConfig, manifestDir);
+            answers = mergeAnswers(manifestAnswers);
+            console.log('\n' +
+                boxen(chalk.bold.cyan('Regenerating from Manifest (No Interactive)\n\n') +
+                    chalk.white('Configuration:\n') +
+                    chalk.gray(`  Template: ${manifest.baseTemplate}\n`) +
+                    chalk.gray(`  Base Image: ${manifest.baseImage}\n`) +
+                    (manifest.containerName
+                        ? chalk.gray(`  Container: ${manifest.containerName}\n`)
+                        : '') +
+                    chalk.gray(`  Overlays: ${manifest.overlays.join(', ')}\n`) +
+                    (manifest.preset ? chalk.gray(`  Preset: ${manifest.preset}\n`) : '') +
+                    (manifest.portOffset
+                        ? chalk.gray(`  Port offset: ${manifest.portOffset}\n`)
+                        : '') +
+                    chalk.gray(`  Output: ${answers.outputPath}`), { padding: 1, borderColor: 'cyan', borderStyle: 'round', margin: 1 }));
+        }
+        else if (useProjectOnly && projectConfigAnswers && !hasCliOverrides) {
+            const projectFileName = projectConfig?.file.fileName ?? '.superposition.yml';
+            answers = mergeAnswers(projectConfigAnswers, {
+                outputPath: cliArgs?.config?.outputPath ||
+                    projectConfigAnswers.outputPath ||
+                    './.devcontainer',
+                minimal: cliArgs?.config?.minimal,
+                editor: cliArgs?.config?.editor,
+            });
+            console.log('\n' +
+                boxen(chalk.bold.cyan('Regenerating from Project File (No Interactive)\n\n') +
+                    chalk.white('Configuration:\n') +
+                    chalk.gray(`  Project file: ${projectFileName}\n`) +
+                    chalk.gray(`  Output: ${answers.outputPath}`), {
+                    padding: 1,
+                    borderColor: 'cyan',
+                    borderStyle: 'round',
+                    margin: 1,
+                }));
+        }
+        else if ((cliArgs && (cliArgs.config.stack || hasCliOverrides)) ||
+            (projectConfigAnswers && (cliArgs?.noInteractive || hasAnyCliConfig))) {
+            const cliAnswers = buildAnswersFromCliArgs(cliArgs.config);
+            const manifestAnswers = manifest
+                ? buildAnswersFromManifest(manifest, mainOverlaysConfig, manifestDir)
+                : undefined;
+            answers = mergeAnswers(projectConfigAnswers, manifestAnswers, cliAnswers, {
+                outputPath: cliAnswers.outputPath || projectConfigAnswers?.outputPath || './.devcontainer',
+            });
+            const modeLabel = useManifestOnly && hasCliOverrides
+                ? 'Regenerating from Manifest with Overrides'
+                : useProjectOnly && projectConfigAnswers
+                    ? 'Regenerating from Project File with Overrides'
+                    : projectConfigAnswers && !manifest
+                        ? 'Running from Project Config'
+                        : 'Running in CLI mode';
+            console.log('\n' +
+                boxen(chalk.bold(modeLabel), {
+                    padding: 0.5,
+                    borderColor: 'blue',
+                    borderStyle: 'round',
+                }));
+            if ((useManifestOnly || useProjectOnly) && hasCliOverrides) {
+                const overrides = [];
+                if (cliAnswers.minimal)
+                    overrides.push('minimal mode');
+                if (cliAnswers.editor)
+                    overrides.push(`editor: ${cliAnswers.editor}`);
+                if (overrides.length > 0) {
+                    console.log(chalk.dim(`   Overrides: ${overrides.join(', ')}`));
+                }
+            }
+        }
+        else {
+            const interactiveAnswers = await runQuestionnaire(manifest, manifestDir, cliArgs?.config.preset || projectConfigAnswers?.preset, cliArgs?.config.presetChoices || projectConfigAnswers?.presetChoices, projectConfigAnswers);
+            answers = mergeAnswers(projectConfigAnswers, interactiveAnswers);
+        }
+        if (!manifest && projectConfig?.selection.customizations) {
+            const materializedOutputPath = path.resolve(answers.outputPath);
+            if (!fs.existsSync(materializedOutputPath)) {
+                fs.mkdirSync(materializedOutputPath, { recursive: true });
+            }
+            writeProjectConfigCustomizations(materializedOutputPath, projectConfig.selection.customizations);
+        }
+        const summaryLines = [
+            chalk.bold.white('Configuration Summary\n'),
+            chalk.cyan('Base:            ') + chalk.white(answers.stack),
+        ];
+        if (answers.language && answers.language.length > 0) {
+            summaryLines.push(chalk.cyan('Languages:       ') + chalk.white(answers.language.join(', ')));
+        }
+        if (answers.database && answers.database.length > 0) {
+            summaryLines.push(chalk.cyan('Database:        ') + chalk.white(answers.database.join(', ')));
+        }
+        summaryLines.push(chalk.cyan('Playwright:      ') + chalk.white(answers.playwright ? 'Yes' : 'No'));
+        if (answers.observability && answers.observability.length > 0) {
+            summaryLines.push(chalk.cyan('Observability:   ') + chalk.white(answers.observability.join(', ')));
+        }
+        if (answers.cloudTools && answers.cloudTools.length > 0) {
+            summaryLines.push(chalk.cyan('Cloud tools:     ') + chalk.white(answers.cloudTools.join(', ')));
+        }
+        if (projectConfig?.file && !manifest) {
+            summaryLines.push(chalk.cyan('Project config:  ') + chalk.white(projectConfig.file.fileName));
+        }
+        summaryLines.push(chalk.cyan('Output:          ') + chalk.white(answers.outputPath));
+        console.log('\n' +
+            boxen(summaryLines.join('\n'), {
+                padding: 1,
+                borderColor: 'green',
+                borderStyle: 'round',
+                margin: { top: 0, bottom: 1 },
+            }));
+        if (existingProjectFileDetected && projectFileOutputPath) {
+            const relPath = path.relative(process.cwd(), projectFileOutputPath);
+            console.log(chalk.yellow(`⚠ Existing project file will be updated: ${relPath}\n  Run \`cs regen\` instead to replay the existing configuration without changes.`));
+        }
+        if (projectFileOutputPath) {
+            try {
+                const projectSelection = buildProjectConfigSelectionFromAnswers(answers);
+                writeProjectConfig(projectFileOutputPath, projectSelection);
+                console.log(chalk.green(`✓ Project config written: ${path.relative(process.cwd(), projectFileOutputPath)}`));
+            }
+            catch (projectFileError) {
+                console.error(chalk.yellow(`⚠ Failed to write project config: ${projectFileError instanceof Error ? projectFileError.message : String(projectFileError)}`));
+            }
+        }
+        const isManifestOnly = cliArgs?.writeManifestOnly === true || cliArgs?.noScaffold === true;
+        const spinner = ora({
+            text: isManifestOnly
+                ? chalk.cyan('Generating manifest file...')
+                : chalk.cyan('Generating devcontainer configuration...'),
+            color: 'cyan',
+        }).start();
+        try {
+            let summary;
+            if (isManifestOnly) {
+                summary = await generateManifestOnly(answers, undefined, {
+                    isRegen: isReplayMode,
+                });
+                spinner.succeed(chalk.green('Manifest created successfully!'));
+            }
+            else {
+                summary = await composeDevContainer(answers, undefined, { isRegen: isReplayMode });
+                spinner.succeed(chalk.green('DevContainer created successfully!'));
+            }
+            if (actualBackupPath) {
+                summary.backupPath = actualBackupPath;
+            }
+            printSummary(summary);
+        }
+        catch (error) {
+            spinner.fail(chalk.red(isManifestOnly ? 'Failed to create manifest' : 'Failed to create devcontainer'));
+            throw error;
+        }
+    }
+    catch (error) {
+        console.error('\n' +
+            boxen(chalk.bold.red('Error\n\n') +
+                chalk.white(error instanceof Error ? error.message : String(error)), { padding: 1, borderColor: 'red', borderStyle: 'round' }));
+        process.exit(1);
+    }
+}
+//# sourceMappingURL=run.js.map

package/dist/tool/cli/run.js.map

@@ -0,0 +1 @@
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package/dist/tool/commands/doctor.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../../tool/commands/doctor.ts"],"names":[],"mappings":"AAAA;;GAEG;AAQH,OAAO,KAAK,EACR,cAAc,EAmBjB,MAAM,oBAAoB,CAAC;AAc5B,UAAU,aAAa;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,IAAI,CAAC,EAAE,OAAO,CAAC;CAClB;AAwxDD;;GAEG;AACH,wBAAsB,aAAa,CAC/B,cAAc,EAAE,cAAc,EAC9B,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,aAAa,GACvB,OAAO,CAAC,IAAI,CAAC,CA0Jf"}
+{"version":3,"file":"doctor.d.ts","sourceRoot":"","sources":["../../../tool/commands/doctor.ts"],"names":[],"mappings":"AAAA;;GAEG;AAQH,OAAO,KAAK,EACR,cAAc,EAmBjB,MAAM,oBAAoB,CAAC;AAe5B,UAAU,aAAa;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,GAAG,CAAC,EAAE,OAAO,CAAC;IACd,IAAI,CAAC,EAAE,OAAO,CAAC;CAClB;AAq7DD;;GAEG;AACH,wBAAsB,aAAa,CAC/B,cAAc,EAAE,cAAc,EAC9B,WAAW,EAAE,MAAM,EACnB,OAAO,EAAE,aAAa,GACvB,OAAO,CAAC,IAAI,CAAC,CA6Jf"}

package/dist/tool/commands/doctor.js

@@ -12,6 +12,7 @@ import { detectManifestVersion, isVersionSupported, needsMigration, migrateManif
 import { MERGE_STRATEGY } from '../utils/merge.js';
 import { extractPorts } from '../utils/port-utils.js';
 import { composeDevContainer } from '../questionnaire/composer.js';
+import { mergeAnswers } from '../questionnaire/answers.js';
 import { loadProjectConfig } from '../schema/project-config.js';
 // ─── Remediation registry ─────────────────────────────────────────────────
 const REMEDIATION_REGISTRY = new Map([
@@ -418,6 +419,52 @@ function validateOverlayManifest(overlayDir, overlayId) {
             };
         }
     }
+    // Validate compose_imports if present
+    if (manifest.compose_imports && manifest.compose_imports.length > 0) {
+        const overlaysDir = path.dirname(overlayDir);
+        const sharedBase = path.resolve(overlaysDir, '.shared');
+        const missingImports = [];
+        const invalidImports = [];
+        const traversalImports = [];
+        for (const importPath of manifest.compose_imports) {
+            if (!importPath.startsWith('.shared/')) {
+                traversalImports.push(`${importPath} (must begin with '.shared/')`);
+                continue;
+            }
+            const resolved = path.resolve(overlaysDir, importPath);
+            if (!resolved.startsWith(sharedBase + path.sep) && resolved !== sharedBase) {
+                traversalImports.push(`${importPath} (resolves outside '.shared/' directory)`);
+                continue;
+            }
+            const fullImportPath = path.join(overlaysDir, importPath);
+            if (!fs.existsSync(fullImportPath)) {
+                missingImports.push(importPath);
+                continue;
+            }
+            const ext = path.extname(importPath).toLowerCase();
+            if (!['.yaml', '.yml'].includes(ext)) {
+                invalidImports.push(`${importPath} (must be .yml or .yaml for compose_imports)`);
+            }
+        }
+        if (traversalImports.length > 0 || missingImports.length > 0 || invalidImports.length > 0) {
+            const details = [];
+            if (traversalImports.length > 0) {
+                details.push(`Path traversal rejected: ${traversalImports.join(', ')}`);
+            }
+            if (missingImports.length > 0) {
+                details.push(`Missing compose_imports: ${missingImports.join(', ')}`);
+            }
+            if (invalidImports.length > 0) {
+                details.push(`Invalid compose_imports: ${invalidImports.join(', ')}`);
+            }
+            return {
+                name: `Overlay: ${overlayId}`,
+                status: 'warn',
+                message: 'compose_import validation issues',
+                details,
+            };
+        }
+    }
     return {
         name: `Overlay: ${overlayId}`,
         status: 'pass',
@@ -817,15 +864,84 @@ function checkMergeStrategy(outputPath) {
     return results;
 }
 /**
- * Generate doctor report
+ * Check for drift between the project config file and the last generated manifest.
+ * Reports a warning when the overlay lists differ so users know to run `regen`.
  */
-function generateReport(environmentChecks, overlayChecks, manifestChecks, mergeChecks, portChecks) {
+function checkProjectFileDrift(overlaysConfig, workingDir, manifestPath) {
+    // Load project config — skip silently if not present
+    let projectConfig;
+    try {
+        projectConfig = loadProjectConfig(overlaysConfig, workingDir);
+    }
+    catch {
+        return [];
+    }
+    if (!projectConfig) {
+        return [];
+    }
+    // Load manifest — if not present while the project file exists, report it informatively
+    if (!fs.existsSync(manifestPath)) {
+        return [
+            {
+                name: 'Project file drift',
+                status: 'warn',
+                message: 'Project file found but no generated manifest — run `cs regen` to generate',
+                fixEligibility: 'not-applicable',
+            },
+        ];
+    }
+    let manifest;
+    try {
+        const raw = JSON.parse(fs.readFileSync(manifestPath, 'utf8'));
+        manifest = needsMigration(raw) ? migrateManifest(raw) : raw;
+    }
+    catch {
+        return [];
+    }
+    // Compare overlay sets (order-independent).
+    // Exclude auto-resolved dependencies from the manifest side — the project file only
+    // stores user-selected overlays; auto-resolved ones are re-calculated at generation time.
+    const autoResolvedAdded = new Set(manifest.autoResolved?.added ?? []);
+    const projectOverlays = new Set(projectConfig.selection.overlays ?? []);
+    const manifestBaseOverlays = new Set((manifest.overlays ?? []).filter((o) => !autoResolvedAdded.has(o)));
+    const inProjectNotManifest = [...projectOverlays].filter((o) => !manifestBaseOverlays.has(o));
+    const inManifestNotProject = [...manifestBaseOverlays].filter((o) => !projectOverlays.has(o));
+    if (inProjectNotManifest.length === 0 && inManifestNotProject.length === 0) {
+        return [
+            {
+                name: 'Project file drift',
+                status: 'pass',
+                message: 'Project file and generated manifest are consistent',
+                fixEligibility: 'not-applicable',
+            },
+        ];
+    }
+    const details = [];
+    if (inProjectNotManifest.length > 0) {
+        details.push(`In project file but not in manifest: ${inProjectNotManifest.join(', ')}`);
+    }
+    if (inManifestNotProject.length > 0) {
+        details.push(`In manifest but not in project file: ${inManifestNotProject.join(', ')}`);
+    }
+    details.push('Run "cs regen" to regenerate with the current project file configuration');
+    return [
+        {
+            name: 'Project file drift',
+            status: 'warn',
+            message: 'Project file and generated manifest have diverged',
+            details,
+            fixEligibility: 'manual-only',
+        },
+    ];
+}
+function generateReport(environmentChecks, overlayChecks, manifestChecks, mergeChecks, portChecks, driftChecks = []) {
     const allChecks = [
         ...environmentChecks,
         ...overlayChecks,
         ...manifestChecks,
         ...mergeChecks,
         ...portChecks,
+        ...driftChecks,
     ];
     const passed = allChecks.filter((c) => c.status === 'pass').length;
     const warnings = allChecks.filter((c) => c.status === 'warn').length;
@@ -837,6 +953,7 @@ function generateReport(environmentChecks, overlayChecks, manifestChecks, mergeC
         manifest: manifestChecks,
         merge: mergeChecks,
         ports: portChecks,
+        drift: driftChecks,
         summary: {
             passed,
             warnings,
@@ -913,6 +1030,20 @@ function formatAsText(report) {
             lines.push(formatCheckResult(check));
         }
     }
+    // Drift section
+    if (report.drift.length > 0) {
+        const failedDrift = report.drift.filter((c) => c.status !== 'pass');
+        if (failedDrift.length > 0) {
+            lines.push(chalk.bold('\nProject File:'));
+            for (const check of failedDrift) {
+                lines.push(formatCheckResult(check));
+            }
+        }
+        else {
+            lines.push(chalk.bold('\nProject File:'));
+            lines.push(`  ${chalk.green('✓')} ${chalk.white('Project file and manifest are consistent')}`);
+        }
+    }
     // Summary
     lines.push(chalk.bold('\nSummary:'));
     lines.push(`  ${chalk.green('✓')} ${report.summary.passed} passed`);
@@ -960,6 +1091,7 @@ function reportToFindings(report) {
         ...checksToFindings(report.manifest, 'manifest', 'manifest'),
         ...checksToFindings(report.merge, 'merge', 'devcontainer'),
         ...checksToFindings(report.ports, 'ports', 'environment'),
+        ...checksToFindings(report.drift, 'manifest', 'manifest'),
     ];
 }
 /**
@@ -1202,7 +1334,7 @@ async function executeRegeneration(outputPath, overlaysConfig, overlaysDir, sile
             rechecked: false,
         };
     }
-    const answers = buildAnswersFromManifest(manifest, outputPath, overlaysConfig);
+    const answers = mergeAnswers(buildAnswersFromManifest(manifest, outputPath, overlaysConfig));
     // Suppress console output during regeneration when in JSON mode
     const originalLog = console.log;
     if (silent) {
@@ -1439,7 +1571,7 @@ function determineExitDisposition(summary, finalFindings) {
 /**
  * Run the full fix flow: diagnose → narrate → remediate → re-check → summarise.
  */
-async function executeFixRun(report, outputPath, overlaysConfig, overlaysDir, requestedJson, explicitManifestPath) {
+async function executeFixRun(report, outputPath, overlaysConfig, overlaysDir, requestedJson, explicitManifestPath, workingDir = process.cwd()) {
     const initialFindings = reportToFindings(report);
     // Separate automatic and manual-only fixable findings
     const autoFixable = initialFindings.filter((f) => f.fixEligibility === 'automatic' && f.status !== 'pass');
@@ -1500,12 +1632,14 @@ async function executeFixRun(report, outputPath, overlaysConfig, overlaysDir, re
     const overlayChecks = checkOverlays(overlaysDir);
     const finalManifestPath = explicitManifestPath ?? path.join(outputPath, 'superposition.json');
     const portChecks = checkPorts(overlaysConfig, finalManifestPath);
+    const finalDriftChecks = checkProjectFileDrift(overlaysConfig, workingDir, finalManifestPath);
     const finalFindings = [
         ...checksToFindings(envChecks, 'environment', 'environment'),
         ...checksToFindings(manifestChecks, 'manifest', 'manifest'),
         ...checksToFindings(mergeChecks, 'merge', 'devcontainer'),
         ...checksToFindings(overlayChecks, 'overlay', 'full'),
         ...checksToFindings(portChecks, 'ports', 'environment'),
+        ...checksToFindings(finalDriftChecks, 'manifest', 'manifest'),
     ];
     const summary = buildOutcomeSummary(executions);
     const exitDisposition = determineExitDisposition(summary, finalFindings);
@@ -1678,15 +1812,16 @@ export async function doctorCommand(overlaysConfig, overlaysDir, options) {
     const mergeChecks = checkMergeStrategy(outputPath);
     const manifestPath = explicitManifestPath ?? path.join(outputPath, 'superposition.json');
     const portChecks = checkPorts(overlaysConfig, manifestPath);
+    const driftChecks = checkProjectFileDrift(overlaysConfig, workingDir, manifestPath);
     // Generate report
-    const report = generateReport(environmentChecks, overlayChecks, manifestChecks, mergeChecks, portChecks);
+    const report = generateReport(environmentChecks, overlayChecks, manifestChecks, mergeChecks, portChecks, driftChecks);
     if (options.fix) {
         // ── Fix flow ──────────────────────────────────────────────────────────
         if (!options.json) {
             // Print diagnostic findings first (as normal)
             console.log(formatAsText(report));
         }
-        const fixRun = await executeFixRun(report, outputPath, overlaysConfig, overlaysDir, options.json ?? false, explicitManifestPath);
+        const fixRun = await executeFixRun(report, outputPath, overlaysConfig, overlaysDir, options.json ?? false, explicitManifestPath, workingDir);
         if (options.json) {
             console.log(JSON.stringify(fixRun, null, 2));
         }