@gefyra/diffyr6-cli 1.0.0 → 1.0.2

package/src/upgrade-sushi.js

@@ -1,553 +1,553 @@
-import fsp from 'fs/promises';
-import path from 'path';
-import os from 'os';
-import { createAnimator, spawnProcess } from './utils/process.js';
-import { fileExists, pathExists } from './utils/fs.js';
-import { parseSushiLog } from './utils/sushi-log.js';
-
-const SOURCE_VERSION = '4.0.1';
-const TARGET_VERSION = '6.0.0-ballot3';
-const MAX_ITERATIONS = 25;
-const SNOMED_CT_ERROR_TEXT = 'Resolved value "SNOMED_CT" is not a valid URI';
-
-/**
- * Upgrades a SUSHI project to FHIR R6
- */
-export async function upgradeSushiToR6(sourceDir, sushiExecutable = 'sushi -s') {
-  await ensureDirectory(sourceDir);
-  const workingDir = await createR6Workspace(sourceDir);
-
-  const configs = await findSushiConfigs(workingDir);
-  if (configs.length === 0) {
-    throw new Error(`No sushi-config.yaml found in ${workingDir}`);
-  }
-
-  await Promise.all(
-    configs.map(async (configPath) => {
-      const updated = await updateFhirVersion(configPath, SOURCE_VERSION, TARGET_VERSION);
-      if (updated) {
-        console.log(`  Updated ${path.basename(configPath)} to ${TARGET_VERSION}`);
-      }
-    })
-  );
-
-  await renameProfilesWithSuffix(workingDir);
-  await runSushiUntilSuccess(workingDir, sushiExecutable);
-  
-  return workingDir;
-}
-
-async function ensureDirectory(dir) {
-  const stat = await fsp.stat(dir).catch(() => null);
-  if (!stat || !stat.isDirectory()) {
-    throw new Error(`Path is not a directory: ${dir}`);
-  }
-}
-
-async function createR6Workspace(sourceDir) {
-  const targetDir = deriveR6Path(sourceDir);
-  const exists = await pathExists(targetDir);
-  if (exists) {
-    throw new Error(`Target directory already exists: ${targetDir}`);
-  }
-  console.log(`  Copying ${sourceDir} to ${targetDir}...`);
-  await fsp.cp(sourceDir, targetDir, { recursive: true });
-  return targetDir;
-}
-
-function deriveR6Path(sourceDir) {
-  const parent = path.dirname(sourceDir);
-  const base = path.basename(sourceDir);
-  const hasR4Suffix = base.toLowerCase().endsWith('r4');
-  const trimmed = hasR4Suffix ? base.slice(0, -2) : base;
-  return path.join(parent, `${trimmed}R6`);
-}
-
-async function findSushiConfigs(rootDir) {
-  const entries = await fsp.readdir(rootDir, { withFileTypes: true });
-  const targets = [];
-  for (const entry of entries) {
-    if (!entry.isFile()) {
-      continue;
-    }
-    const lower = entry.name.toLowerCase();
-    if (lower === 'sushi-config.yaml' || lower === 'sushi-config.yml') {
-      targets.push(path.join(rootDir, entry.name));
-    }
-  }
-  return targets;
-}
-
-async function updateFhirVersion(filePath, fromVersion, toVersion) {
-  const original = await fsp.readFile(filePath, 'utf8');
-  const updated = replaceFhirVersion(original, fromVersion, toVersion);
-  if (updated === original) {
-    return false;
-  }
-  await fsp.writeFile(filePath, updated, 'utf8');
-  return true;
-}
-
-function replaceFhirVersion(content, fromVersion, toVersion) {
-  const regex = new RegExp(
-    `(fhirVersion\\s*:\\s*)(["']?)${escapeRegExp(fromVersion)}\\2`,
-    'i'
-  );
-  return content.replace(regex, (_, prefix, quote) => {
-    const q = quote || '';
-    return `${prefix}${q}${toVersion}${q}`;
-  });
-}
-
-function escapeRegExp(value) {
-  return value.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
-}
-
-async function renameProfilesWithSuffix(rootDir) {
-  const fshFiles = await collectFshFiles(rootDir);
-  if (fshFiles.length === 0) {
-    console.warn('  No FSH files found, skipping profile renaming');
-    return;
-  }
-  const renameMap = await buildProfileRenameMap(fshFiles);
-  if (renameMap.size === 0) {
-    console.log('  No profiles without R6 suffix found');
-    return;
-  }
-  const changedFiles = await applyProfileRenames(fshFiles, renameMap);
-  console.log(`  Renamed ${renameMap.size} profile(s) in ${changedFiles} file(s)`);
-}
-
-async function collectFshFiles(dir) {
-  const files = [];
-  async function walk(current) {
-    const entries = await fsp.readdir(current, { withFileTypes: true }).catch(() => []);
-    for (const entry of entries) {
-      const entryPath = path.join(current, entry.name);
-      if (entry.isDirectory()) {
-        await walk(entryPath);
-      } else if (entry.isFile() && entry.name.toLowerCase().endsWith('.fsh')) {
-        files.push(entryPath);
-      }
-    }
-  }
-  await walk(dir);
-  return files;
-}
-
-async function buildProfileRenameMap(files) {
-  const renameMap = new Map();
-  const profileRegex = /^Profile:\s*(\S+)/;
-  for (const file of files) {
-    const content = await fsp.readFile(file, 'utf8');
-    const lines = content.split(/\r?\n/);
-    for (const line of lines) {
-      const match = line.match(profileRegex);
-      if (!match) {
-        continue;
-      }
-      const name = match[1];
-      if (name.endsWith('R6') || renameMap.has(name)) {
-        continue;
-      }
-      renameMap.set(name, `${name}R6`);
-    }
-  }
-  return renameMap;
-}
-
-async function applyProfileRenames(files, renameMap) {
-  if (renameMap.size === 0) {
-    return 0;
-  }
-  const patterns = [...renameMap.entries()].map(([oldName, newName]) => ({
-    newName,
-    regex: createProfileNameRegex(oldName),
-  }));
-
-  let changedFiles = 0;
-  for (const file of files) {
-    const original = await fsp.readFile(file, 'utf8');
-    let updated = original;
-    
-    for (const { newName, regex } of patterns) {
-      updated = updated.replace(regex, (_, prefix = '') => `${prefix || ''}${newName}`);
-    }
-    
-    for (const [oldName, newName] of renameMap.entries()) {
-      const oldIdPart = camelCaseToKebabCase(oldName);
-      const newIdPart = camelCaseToKebabCase(newName);
-      
-      const urlPattern = new RegExp(
-        `(\\^url\\s*=\\s*["\'])([^"']*\\/)${escapeRegExp(oldIdPart)}(["\'])`,
-        'g'
-      );
-      updated = updated.replace(urlPattern, (_, prefix, urlPrefix, suffix) => {
-        return `${prefix}${urlPrefix}${newIdPart}${suffix}`;
-      });
-      
-      const idPattern = new RegExp(
-        `(\\^id\\s*=\\s*["\'])${escapeRegExp(oldIdPart)}(["\'])`,
-        'g'
-      );
-      updated = updated.replace(idPattern, (_, prefix, suffix) => {
-        return `${prefix}${newIdPart}${suffix}`;
-      });
-    }
-    
-    if (updated !== original) {
-      await fsp.writeFile(file, updated, 'utf8');
-      changedFiles += 1;
-    }
-  }
-  return changedFiles;
-}
-
-function camelCaseToKebabCase(str) {
-  return str
-    .replace(/([a-z])([A-Z])/g, '$1-$2')
-    .toLowerCase();
-}
-
-function createProfileNameRegex(name) {
-  const prefix = '(^|[^A-Za-z0-9._-])';
-  const suffix = '(?=[^A-Za-z0-9._-]|$)';
-  const pattern = `${prefix}(${escapeRegExp(name)})${suffix}`;
-  return new RegExp(pattern, 'gm');
-}
-
-async function runSushiUntilSuccess(targetDir, sushiExecutable) {
-  let iteration = 0;
-  while (iteration < MAX_ITERATIONS) {
-    iteration += 1;
-    console.log(`  SUSHI iteration ${iteration}...`);
-    const { stdout, stderr, exitCode } = await runSushi(sushiExecutable, targetDir);
-    const combinedLog = [stdout, stderr].filter(Boolean).join('\n');
-    const logPath = path.join(targetDir, `sushi-upgrade-${iteration}.log`);
-    await fsp.writeFile(logPath, combinedLog, 'utf8');
-    if (exitCode === 0) {
-      console.log(`  SUSHI completed successfully (iteration ${iteration})`);
-      return;
-    }
-    console.warn(`  SUSHI exited with code ${exitCode}, analyzing errors...`);
-
-    const errors = parseSushiLog(combinedLog);
-    const snomedFix = await fixSnomedCtIssues(errors, targetDir);
-    if (snomedFix) {
-      console.log('  Applied SNOMED_CT fix, re-running...');
-      continue;
-    }
-    const cardinalityFix = await fixMinCardinalityInstanceErrors(errors, targetDir);
-    if (cardinalityFix) {
-      console.log(`  Disabled ${cardinalityFix} instance file(s), re-running...`);
-      continue;
-    }
-    const modifications = await commentErrorLines(errors, targetDir);
-    if (modifications === 0) {
-      throw new Error('SUSHI failed but no lines could be commented out');
-    }
-    console.log(`  Commented out lines in ${modifications} file(s)`);
-  }
-  throw new Error(`SUSHI failed after ${MAX_ITERATIONS} attempts`);
-}
-
-async function runSushi(executable, targetDir) {
-  const animator = createAnimator('SUSHI working...');
-  animator.start();
-  try {
-    const parts = executable.trim().split(/\s+/);
-    const command = parts[0];
-    const args = [...parts.slice(1), targetDir];
-    
-    return await spawnProcess(command, args, process.cwd());
-  } finally {
-    animator.stop();
-  }
-}
-
-async function commentErrorLines(logEntries, workingDir) {
-  const grouped = new Map();
-
-  for (const entry of logEntries) {
-    const normalizedPath = normalizeLogPath(entry.file, workingDir);
-    if (!normalizedPath || typeof entry.line !== 'number') {
-      continue;
-    }
-    if (!grouped.has(normalizedPath)) {
-      grouped.set(normalizedPath, new Set());
-    }
-    const startLine = entry.line;
-    const endLine = entry.endLine || entry.line;
-    for (let ln = startLine; ln <= endLine; ln++) {
-      grouped.get(normalizedPath).add(ln);
-    }
-  }
-
-  let modifiedFiles = 0;
-  for (const [filePath, lines] of grouped.entries()) {
-    const updated = await commentLinesInFile(filePath, [...lines]);
-    if (updated) {
-      modifiedFiles += 1;
-    }
-  }
-  return modifiedFiles;
-}
-
-function normalizeLogPath(filePath, workingDir) {
-  if (!filePath) {
-    return null;
-  }
-  let candidate = filePath.trim();
-  if (!candidate) {
-    return null;
-  }
-
-  if (/^[A-Za-z]:[\\/]/.test(candidate)) {
-    if (process.platform === 'win32') {
-      candidate = candidate.replace(/\//g, '\\');
-    } else {
-      const drive = candidate[0].toLowerCase();
-      const rest = candidate.slice(2).replace(/\\/g, '/').replace(/^\/+/, '');
-      candidate = `/mnt/${drive}/${rest}`;
-    }
-  } else if (process.platform === 'win32') {
-    candidate = candidate.replace(/\//g, '\\');
-  } else {
-    candidate = candidate.replace(/\\/g, '/');
-  }
-
-  if (!path.isAbsolute(candidate)) {
-    candidate = path.join(workingDir, candidate);
-  }
-
-  return candidate;
-}
-
-async function commentLinesInFile(filePath, lineNumbers) {
-  const stat = await fsp.stat(filePath).catch(() => null);
-  if (!stat || !stat.isFile()) {
-    console.warn(`Could not find file: ${filePath}`);
-    return false;
-  }
-
-  const original = await fsp.readFile(filePath, 'utf8');
-  const newline = original.includes('\r\n') ? '\r\n' : '\n';
-  const lines = original.split(/\r?\n/);
-  let changed = false;
-
-  const expandedLines = expandContainsBlockLines(lines, lineNumbers);
-
-  expandedLines
-    .filter((n) => Number.isInteger(n) && n > 0 && n <= lines.length)
-    .sort((a, b) => a - b)
-    .forEach((lineNumber) => {
-      const idx = lineNumber - 1;
-      const current = lines[idx];
-      if (current.trim().startsWith('// AUTO-DISABLED (SUSHI R6):')) {
-        return;
-      }
-      const indent = current.match(/^\s*/)[0] || '';
-      const content = current.trimStart();
-      lines[idx] = `${indent}// AUTO-DISABLED (SUSHI R6): ${content}`;
-      changed = true;
-    });
-
-  if (changed) {
-    const updated = lines.join(newline);
-    await fsp.writeFile(filePath, updated, 'utf8');
-  }
-
-  return changed;
-}
-
-function expandContainsBlockLines(lines, lineNumbers) {
-  const expanded = new Set(lineNumbers);
-
-  for (const lineNumber of lineNumbers) {
-    const idx = lineNumber - 1;
-    if (idx < 0 || idx >= lines.length) {
-      continue;
-    }
-
-    const currentLine = lines[idx].trim();
-    
-    if (currentLine.includes(' contains') || currentLine.endsWith(' and')) {
-      let nextIdx = idx + 1;
-      while (nextIdx < lines.length) {
-        const nextLine = lines[nextIdx].trim();
-        if (nextLine.startsWith('// AUTO-DISABLED (SUSHI R6):')) {
-          nextIdx++;
-          continue;
-        }
-        if (nextLine === '') {
-          nextIdx++;
-          continue;
-        }
-        const isIndentedContinuation = lines[nextIdx].match(/^\s+/) && 
-          (nextLine.match(/^\w+\s+\d/) || nextLine.endsWith(' and') || nextLine.endsWith('MS') || nextLine.endsWith('MS and'));
-        const isSliceDefinition = nextLine.match(/^\w+\s+\d+\.\.(\d+|\*)\s*(MS)?\s*(and)?\s*$/);
-        
-        if (isIndentedContinuation || isSliceDefinition) {
-          expanded.add(nextIdx + 1);
-          nextIdx++;
-        } else {
-          break;
-        }
-      }
-    }
-
-    const softIndexMatch = currentLine.match(/^\*\s*(\S+)\[(\d+|\+)\]\./);
-    if (softIndexMatch) {
-      const elementPath = softIndexMatch[1];
-      let nextIdx = idx + 1;
-      while (nextIdx < lines.length) {
-        const nextLine = lines[nextIdx].trim();
-        if (nextLine.startsWith('// AUTO-DISABLED (SUSHI R6):')) {
-          nextIdx++;
-          continue;
-        }
-        if (nextLine === '') {
-          nextIdx++;
-          continue;
-        }
-        const eqPattern = new RegExp(`^\\*\\s*${escapeRegExp(elementPath)}\\[=\\]\\.`);
-        if (eqPattern.test(nextLine)) {
-          expanded.add(nextIdx + 1);
-          nextIdx++;
-        } else if (nextLine.match(new RegExp(`^\\*\\s*${escapeRegExp(elementPath)}\\[(\\d+|\\+)\\]\\.`))) {
-          break;
-        } else {
-          break;
-        }
-      }
-    }
-  }
-
-  return [...expanded];
-}
-
-async function fixSnomedCtIssues(logEntries, workingDir) {
-  const hasSnomedError = logEntries.some(
-    (entry) => typeof entry.message === 'string' && entry.message.includes(SNOMED_CT_ERROR_TEXT)
-  );
-  if (!hasSnomedError) {
-    return false;
-  }
-  const replacements = await replacePlainSnomedReferences(workingDir);
-  const aliasAdded = await ensureSnomedAliasDefinition(workingDir);
-  if (replacements > 0 || aliasAdded) {
-    console.log(`  Fixed SNOMED_CT in ${replacements} file(s)${aliasAdded ? ' and added alias' : ''}`);
-    return true;
-  }
-  return false;
-}
-
-async function replacePlainSnomedReferences(rootDir) {
-  const files = await collectFshFiles(rootDir);
-  let changedFiles = 0;
-  const pattern = /(^|[^$A-Za-z0-9_])SNOMED_CT\b/gm;
-  for (const file of files) {
-    const original = await fsp.readFile(file, 'utf8');
-    const updated = original.replace(pattern, (_, prefix) => `${prefix}$SNOMED_CT`);
-    if (updated !== original) {
-      await fsp.writeFile(file, updated, 'utf8');
-      changedFiles += 1;
-    }
-  }
-  return changedFiles;
-}
-
-async function ensureSnomedAliasDefinition(rootDir) {
-  const { filePath, exists } = await resolveAliasFilePath(rootDir);
-  let content = '';
-  if (exists) {
-    content = await fsp.readFile(filePath, 'utf8');
-    if (/^\s*Alias:\s*\$SNOMED_CT\b/m.test(content)) {
-      return false;
-    }
-  }
-  await fsp.mkdir(path.dirname(filePath), { recursive: true });
-  const aliasLine = 'Alias: $SNOMED_CT = http://snomed.info/sct';
-  if (!exists || content.length === 0) {
-    const newline = os.EOL || '\n';
-    await fsp.writeFile(filePath, `${aliasLine}${newline}`, 'utf8');
-    return true;
-  }
-  const newline = content.includes('\r\n') ? '\r\n' : '\n';
-  const needsNewline = content.endsWith('\r') || content.endsWith('\n');
-  const suffix = needsNewline ? '' : newline;
-  const updated = `${content}${suffix}${aliasLine}${newline}`;
-  await fsp.writeFile(filePath, updated, 'utf8');
-  return true;
-}
-
-async function fixMinCardinalityInstanceErrors(logEntries, workingDir) {
-  const candidates = logEntries.filter(
-    (entry) =>
-      entry &&
-      typeof entry.message === 'string' &&
-      entry.message.includes('minimum cardinality 1 but occurs 0 time(s).') &&
-      typeof entry.file === 'string'
-  );
-  if (candidates.length === 0) {
-    return 0;
-  }
-
-  let disabled = 0;
-  for (const entry of candidates) {
-    const sourcePath = normalizeLogPath(entry.file, workingDir);
-    if (
-      !sourcePath ||
-      !sourcePath.endsWith('.fsh') ||
-      !sourcePath.includes(`${path.sep}instances${path.sep}`)
-    ) {
-      continue;
-    }
-    const targetPath = sourcePath.slice(0, -4);
-    const renamed = await disableInstanceFile(sourcePath, targetPath);
-    if (renamed) {
-      disabled += 1;
-    }
-  }
-  return disabled;
-}
-
-async function disableInstanceFile(sourcePath, targetPath) {
-  const stat = await fsp.stat(sourcePath).catch(() => null);
-  if (!stat || !stat.isFile()) {
-    return false;
-  }
-  const original = await fsp.readFile(sourcePath, 'utf8');
-  const newline = original.includes('\r\n') ? '\r\n' : '\n';
-  const lines = original.split(/\r?\n/);
-  let renamedInstance = false;
-  for (let i = 0; i < lines.length; i += 1) {
-    const match = lines[i].match(/^(\s*Instance:\s*)(\S+)(.*)$/);
-    if (match) {
-      lines[i] = `${match[1]}${match[2]}-disabled${match[3] || ''}`;
-      renamedInstance = true;
-      break;
-    }
-  }
-  if (renamedInstance) {
-    const updated = lines.join(newline);
-    await fsp.writeFile(sourcePath, updated, 'utf8');
-  }
-  await fsp.rename(sourcePath, targetPath).catch(() => null);
-  return true;
-}
-
-async function resolveAliasFilePath(rootDir) {
-  const candidates = [
-    path.join(rootDir, 'input', 'fsh', 'aliases.fsh'),
-    path.join(rootDir, 'input', 'fsh', 'alias.fsh'),
-    path.join(rootDir, 'aliases.fsh'),
-    path.join(rootDir, 'alias.fsh'),
-  ];
-  for (const candidate of candidates) {
-    if (await fileExists(candidate)) {
-      return { filePath: candidate, exists: true };
-    }
-  }
-  return { filePath: candidates[0], exists: false };
-}
+import fsp from 'fs/promises';
+import path from 'path';
+import os from 'os';
+import { createAnimator, spawnProcess } from './utils/process.js';
+import { fileExists, pathExists } from './utils/fs.js';
+import { parseSushiLog } from './utils/sushi-log.js';
+
+const SOURCE_VERSION = '4.0.1';
+const TARGET_VERSION = '6.0.0-ballot3';
+const MAX_ITERATIONS = 25;
+const SNOMED_CT_ERROR_TEXT = 'Resolved value "SNOMED_CT" is not a valid URI';
+
+/**
+ * Upgrades a SUSHI project to FHIR R6
+ */
+export async function upgradeSushiToR6(sourceDir, sushiExecutable = 'sushi -s') {
+  await ensureDirectory(sourceDir);
+  const workingDir = await createR6Workspace(sourceDir);
+
+  const configs = await findSushiConfigs(workingDir);
+  if (configs.length === 0) {
+    throw new Error(`No sushi-config.yaml found in ${workingDir}`);
+  }
+
+  await Promise.all(
+    configs.map(async (configPath) => {
+      const updated = await updateFhirVersion(configPath, SOURCE_VERSION, TARGET_VERSION);
+      if (updated) {
+        console.log(`  Updated ${path.basename(configPath)} to ${TARGET_VERSION}`);
+      }
+    })
+  );
+
+  await renameProfilesWithSuffix(workingDir);
+  await runSushiUntilSuccess(workingDir, sushiExecutable);
+  
+  return workingDir;
+}
+
+async function ensureDirectory(dir) {
+  const stat = await fsp.stat(dir).catch(() => null);
+  if (!stat || !stat.isDirectory()) {
+    throw new Error(`Path is not a directory: ${dir}`);
+  }
+}
+
+async function createR6Workspace(sourceDir) {
+  const targetDir = deriveR6Path(sourceDir);
+  const exists = await pathExists(targetDir);
+  if (exists) {
+    throw new Error(`Target directory already exists: ${targetDir}`);
+  }
+  console.log(`  Copying ${sourceDir} to ${targetDir}...`);
+  await fsp.cp(sourceDir, targetDir, { recursive: true });
+  return targetDir;
+}
+
+function deriveR6Path(sourceDir) {
+  const parent = path.dirname(sourceDir);
+  const base = path.basename(sourceDir);
+  const hasR4Suffix = base.toLowerCase().endsWith('r4');
+  const trimmed = hasR4Suffix ? base.slice(0, -2) : base;
+  return path.join(parent, `${trimmed}R6`);
+}
+
+async function findSushiConfigs(rootDir) {
+  const entries = await fsp.readdir(rootDir, { withFileTypes: true });
+  const targets = [];
+  for (const entry of entries) {
+    if (!entry.isFile()) {
+      continue;
+    }
+    const lower = entry.name.toLowerCase();
+    if (lower === 'sushi-config.yaml' || lower === 'sushi-config.yml') {
+      targets.push(path.join(rootDir, entry.name));
+    }
+  }
+  return targets;
+}
+
+async function updateFhirVersion(filePath, fromVersion, toVersion) {
+  const original = await fsp.readFile(filePath, 'utf8');
+  const updated = replaceFhirVersion(original, fromVersion, toVersion);
+  if (updated === original) {
+    return false;
+  }
+  await fsp.writeFile(filePath, updated, 'utf8');
+  return true;
+}
+
+function replaceFhirVersion(content, fromVersion, toVersion) {
+  const regex = new RegExp(
+    `(fhirVersion\\s*:\\s*)(["']?)${escapeRegExp(fromVersion)}\\2`,
+    'i'
+  );
+  return content.replace(regex, (_, prefix, quote) => {
+    const q = quote || '';
+    return `${prefix}${q}${toVersion}${q}`;
+  });
+}
+
+function escapeRegExp(value) {
+  return value.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
+}
+
+async function renameProfilesWithSuffix(rootDir) {
+  const fshFiles = await collectFshFiles(rootDir);
+  if (fshFiles.length === 0) {
+    console.warn('  No FSH files found, skipping profile renaming');
+    return;
+  }
+  const renameMap = await buildProfileRenameMap(fshFiles);
+  if (renameMap.size === 0) {
+    console.log('  No profiles without R6 suffix found');
+    return;
+  }
+  const changedFiles = await applyProfileRenames(fshFiles, renameMap);
+  console.log(`  Renamed ${renameMap.size} profile(s) in ${changedFiles} file(s)`);
+}
+
+async function collectFshFiles(dir) {
+  const files = [];
+  async function walk(current) {
+    const entries = await fsp.readdir(current, { withFileTypes: true }).catch(() => []);
+    for (const entry of entries) {
+      const entryPath = path.join(current, entry.name);
+      if (entry.isDirectory()) {
+        await walk(entryPath);
+      } else if (entry.isFile() && entry.name.toLowerCase().endsWith('.fsh')) {
+        files.push(entryPath);
+      }
+    }
+  }
+  await walk(dir);
+  return files;
+}
+
+async function buildProfileRenameMap(files) {
+  const renameMap = new Map();
+  const profileRegex = /^Profile:\s*(\S+)/;
+  for (const file of files) {
+    const content = await fsp.readFile(file, 'utf8');
+    const lines = content.split(/\r?\n/);
+    for (const line of lines) {
+      const match = line.match(profileRegex);
+      if (!match) {
+        continue;
+      }
+      const name = match[1];
+      if (name.endsWith('R6') || renameMap.has(name)) {
+        continue;
+      }
+      renameMap.set(name, `${name}R6`);
+    }
+  }
+  return renameMap;
+}
+
+async function applyProfileRenames(files, renameMap) {
+  if (renameMap.size === 0) {
+    return 0;
+  }
+  const patterns = [...renameMap.entries()].map(([oldName, newName]) => ({
+    newName,
+    regex: createProfileNameRegex(oldName),
+  }));
+
+  let changedFiles = 0;
+  for (const file of files) {
+    const original = await fsp.readFile(file, 'utf8');
+    let updated = original;
+    
+    for (const { newName, regex } of patterns) {
+      updated = updated.replace(regex, (_, prefix = '') => `${prefix || ''}${newName}`);
+    }
+    
+    for (const [oldName, newName] of renameMap.entries()) {
+      const oldIdPart = camelCaseToKebabCase(oldName);
+      const newIdPart = camelCaseToKebabCase(newName);
+      
+      const urlPattern = new RegExp(
+        `(\\^url\\s*=\\s*["\'])([^"']*\\/)${escapeRegExp(oldIdPart)}(["\'])`,
+        'g'
+      );
+      updated = updated.replace(urlPattern, (_, prefix, urlPrefix, suffix) => {
+        return `${prefix}${urlPrefix}${newIdPart}${suffix}`;
+      });
+      
+      const idPattern = new RegExp(
+        `(\\^id\\s*=\\s*["\'])${escapeRegExp(oldIdPart)}(["\'])`,
+        'g'
+      );
+      updated = updated.replace(idPattern, (_, prefix, suffix) => {
+        return `${prefix}${newIdPart}${suffix}`;
+      });
+    }
+    
+    if (updated !== original) {
+      await fsp.writeFile(file, updated, 'utf8');
+      changedFiles += 1;
+    }
+  }
+  return changedFiles;
+}
+
+function camelCaseToKebabCase(str) {
+  return str
+    .replace(/([a-z])([A-Z])/g, '$1-$2')
+    .toLowerCase();
+}
+
+function createProfileNameRegex(name) {
+  const prefix = '(^|[^A-Za-z0-9._-])';
+  const suffix = '(?=[^A-Za-z0-9._-]|$)';
+  const pattern = `${prefix}(${escapeRegExp(name)})${suffix}`;
+  return new RegExp(pattern, 'gm');
+}
+
+async function runSushiUntilSuccess(targetDir, sushiExecutable) {
+  let iteration = 0;
+  while (iteration < MAX_ITERATIONS) {
+    iteration += 1;
+    console.log(`  SUSHI iteration ${iteration}...`);
+    const { stdout, stderr, exitCode } = await runSushi(sushiExecutable, targetDir);
+    const combinedLog = [stdout, stderr].filter(Boolean).join('\n');
+    const logPath = path.join(targetDir, `sushi-upgrade-${iteration}.log`);
+    await fsp.writeFile(logPath, combinedLog, 'utf8');
+    if (exitCode === 0) {
+      console.log(`  SUSHI completed successfully (iteration ${iteration})`);
+      return;
+    }
+    console.warn(`  SUSHI exited with code ${exitCode}, analyzing errors...`);
+
+    const errors = parseSushiLog(combinedLog);
+    const snomedFix = await fixSnomedCtIssues(errors, targetDir);
+    if (snomedFix) {
+      console.log('  Applied SNOMED_CT fix, re-running...');
+      continue;
+    }
+    const cardinalityFix = await fixMinCardinalityInstanceErrors(errors, targetDir);
+    if (cardinalityFix) {
+      console.log(`  Disabled ${cardinalityFix} instance file(s), re-running...`);
+      continue;
+    }
+    const modifications = await commentErrorLines(errors, targetDir);
+    if (modifications === 0) {
+      throw new Error('SUSHI failed but no lines could be commented out');
+    }
+    console.log(`  Commented out lines in ${modifications} file(s)`);
+  }
+  throw new Error(`SUSHI failed after ${MAX_ITERATIONS} attempts`);
+}
+
+async function runSushi(executable, targetDir) {
+  const animator = createAnimator('SUSHI working...');
+  animator.start();
+  try {
+    const parts = executable.trim().split(/\s+/);
+    const command = parts[0];
+    const args = [...parts.slice(1), targetDir];
+    
+    return await spawnProcess(command, args, process.cwd());
+  } finally {
+    animator.stop();
+  }
+}
+
+async function commentErrorLines(logEntries, workingDir) {
+  const grouped = new Map();
+
+  for (const entry of logEntries) {
+    const normalizedPath = normalizeLogPath(entry.file, workingDir);
+    if (!normalizedPath || typeof entry.line !== 'number') {
+      continue;
+    }
+    if (!grouped.has(normalizedPath)) {
+      grouped.set(normalizedPath, new Set());
+    }
+    const startLine = entry.line;
+    const endLine = entry.endLine || entry.line;
+    for (let ln = startLine; ln <= endLine; ln++) {
+      grouped.get(normalizedPath).add(ln);
+    }
+  }
+
+  let modifiedFiles = 0;
+  for (const [filePath, lines] of grouped.entries()) {
+    const updated = await commentLinesInFile(filePath, [...lines]);
+    if (updated) {
+      modifiedFiles += 1;
+    }
+  }
+  return modifiedFiles;
+}
+
+function normalizeLogPath(filePath, workingDir) {
+  if (!filePath) {
+    return null;
+  }
+  let candidate = filePath.trim();
+  if (!candidate) {
+    return null;
+  }
+
+  if (/^[A-Za-z]:[\\/]/.test(candidate)) {
+    if (process.platform === 'win32') {
+      candidate = candidate.replace(/\//g, '\\');
+    } else {
+      const drive = candidate[0].toLowerCase();
+      const rest = candidate.slice(2).replace(/\\/g, '/').replace(/^\/+/, '');
+      candidate = `/mnt/${drive}/${rest}`;
+    }
+  } else if (process.platform === 'win32') {
+    candidate = candidate.replace(/\//g, '\\');
+  } else {
+    candidate = candidate.replace(/\\/g, '/');
+  }
+
+  if (!path.isAbsolute(candidate)) {
+    candidate = path.join(workingDir, candidate);
+  }
+
+  return candidate;
+}
+
+async function commentLinesInFile(filePath, lineNumbers) {
+  const stat = await fsp.stat(filePath).catch(() => null);
+  if (!stat || !stat.isFile()) {
+    console.warn(`Could not find file: ${filePath}`);
+    return false;
+  }
+
+  const original = await fsp.readFile(filePath, 'utf8');
+  const newline = original.includes('\r\n') ? '\r\n' : '\n';
+  const lines = original.split(/\r?\n/);
+  let changed = false;
+
+  const expandedLines = expandContainsBlockLines(lines, lineNumbers);
+
+  expandedLines
+    .filter((n) => Number.isInteger(n) && n > 0 && n <= lines.length)
+    .sort((a, b) => a - b)
+    .forEach((lineNumber) => {
+      const idx = lineNumber - 1;
+      const current = lines[idx];
+      if (current.trim().startsWith('// AUTO-DISABLED (SUSHI R6):')) {
+        return;
+      }
+      const indent = current.match(/^\s*/)[0] || '';
+      const content = current.trimStart();
+      lines[idx] = `${indent}// AUTO-DISABLED (SUSHI R6): ${content}`;
+      changed = true;
+    });
+
+  if (changed) {
+    const updated = lines.join(newline);
+    await fsp.writeFile(filePath, updated, 'utf8');
+  }
+
+  return changed;
+}
+
+function expandContainsBlockLines(lines, lineNumbers) {
+  const expanded = new Set(lineNumbers);
+
+  for (const lineNumber of lineNumbers) {
+    const idx = lineNumber - 1;
+    if (idx < 0 || idx >= lines.length) {
+      continue;
+    }
+
+    const currentLine = lines[idx].trim();
+    
+    if (currentLine.includes(' contains') || currentLine.endsWith(' and')) {
+      let nextIdx = idx + 1;
+      while (nextIdx < lines.length) {
+        const nextLine = lines[nextIdx].trim();
+        if (nextLine.startsWith('// AUTO-DISABLED (SUSHI R6):')) {
+          nextIdx++;
+          continue;
+        }
+        if (nextLine === '') {
+          nextIdx++;
+          continue;
+        }
+        const isIndentedContinuation = lines[nextIdx].match(/^\s+/) && 
+          (nextLine.match(/^\w+\s+\d/) || nextLine.endsWith(' and') || nextLine.endsWith('MS') || nextLine.endsWith('MS and'));
+        const isSliceDefinition = nextLine.match(/^\w+\s+\d+\.\.(\d+|\*)\s*(MS)?\s*(and)?\s*$/);
+        
+        if (isIndentedContinuation || isSliceDefinition) {
+          expanded.add(nextIdx + 1);
+          nextIdx++;
+        } else {
+          break;
+        }
+      }
+    }
+
+    const softIndexMatch = currentLine.match(/^\*\s*(\S+)\[(\d+|\+)\]\./);
+    if (softIndexMatch) {
+      const elementPath = softIndexMatch[1];
+      let nextIdx = idx + 1;
+      while (nextIdx < lines.length) {
+        const nextLine = lines[nextIdx].trim();
+        if (nextLine.startsWith('// AUTO-DISABLED (SUSHI R6):')) {
+          nextIdx++;
+          continue;
+        }
+        if (nextLine === '') {
+          nextIdx++;
+          continue;
+        }
+        const eqPattern = new RegExp(`^\\*\\s*${escapeRegExp(elementPath)}\\[=\\]\\.`);
+        if (eqPattern.test(nextLine)) {
+          expanded.add(nextIdx + 1);
+          nextIdx++;
+        } else if (nextLine.match(new RegExp(`^\\*\\s*${escapeRegExp(elementPath)}\\[(\\d+|\\+)\\]\\.`))) {
+          break;
+        } else {
+          break;
+        }
+      }
+    }
+  }
+
+  return [...expanded];
+}
+
+async function fixSnomedCtIssues(logEntries, workingDir) {
+  const hasSnomedError = logEntries.some(
+    (entry) => typeof entry.message === 'string' && entry.message.includes(SNOMED_CT_ERROR_TEXT)
+  );
+  if (!hasSnomedError) {
+    return false;
+  }
+  const replacements = await replacePlainSnomedReferences(workingDir);
+  const aliasAdded = await ensureSnomedAliasDefinition(workingDir);
+  if (replacements > 0 || aliasAdded) {
+    console.log(`  Fixed SNOMED_CT in ${replacements} file(s)${aliasAdded ? ' and added alias' : ''}`);
+    return true;
+  }
+  return false;
+}
+
+async function replacePlainSnomedReferences(rootDir) {
+  const files = await collectFshFiles(rootDir);
+  let changedFiles = 0;
+  const pattern = /(^|[^$A-Za-z0-9_])SNOMED_CT\b/gm;
+  for (const file of files) {
+    const original = await fsp.readFile(file, 'utf8');
+    const updated = original.replace(pattern, (_, prefix) => `${prefix}$SNOMED_CT`);
+    if (updated !== original) {
+      await fsp.writeFile(file, updated, 'utf8');
+      changedFiles += 1;
+    }
+  }
+  return changedFiles;
+}
+
+async function ensureSnomedAliasDefinition(rootDir) {
+  const { filePath, exists } = await resolveAliasFilePath(rootDir);
+  let content = '';
+  if (exists) {
+    content = await fsp.readFile(filePath, 'utf8');
+    if (/^\s*Alias:\s*\$SNOMED_CT\b/m.test(content)) {
+      return false;
+    }
+  }
+  await fsp.mkdir(path.dirname(filePath), { recursive: true });
+  const aliasLine = 'Alias: $SNOMED_CT = http://snomed.info/sct';
+  if (!exists || content.length === 0) {
+    const newline = os.EOL || '\n';
+    await fsp.writeFile(filePath, `${aliasLine}${newline}`, 'utf8');
+    return true;
+  }
+  const newline = content.includes('\r\n') ? '\r\n' : '\n';
+  const needsNewline = content.endsWith('\r') || content.endsWith('\n');
+  const suffix = needsNewline ? '' : newline;
+  const updated = `${content}${suffix}${aliasLine}${newline}`;
+  await fsp.writeFile(filePath, updated, 'utf8');
+  return true;
+}
+
+async function fixMinCardinalityInstanceErrors(logEntries, workingDir) {
+  const candidates = logEntries.filter(
+    (entry) =>
+      entry &&
+      typeof entry.message === 'string' &&
+      entry.message.includes('minimum cardinality 1 but occurs 0 time(s).') &&
+      typeof entry.file === 'string'
+  );
+  if (candidates.length === 0) {
+    return 0;
+  }
+
+  let disabled = 0;
+  for (const entry of candidates) {
+    const sourcePath = normalizeLogPath(entry.file, workingDir);
+    if (
+      !sourcePath ||
+      !sourcePath.endsWith('.fsh') ||
+      !sourcePath.includes(`${path.sep}instances${path.sep}`)
+    ) {
+      continue;
+    }
+    const targetPath = sourcePath.slice(0, -4);
+    const renamed = await disableInstanceFile(sourcePath, targetPath);
+    if (renamed) {
+      disabled += 1;
+    }
+  }
+  return disabled;
+}
+
+async function disableInstanceFile(sourcePath, targetPath) {
+  const stat = await fsp.stat(sourcePath).catch(() => null);
+  if (!stat || !stat.isFile()) {
+    return false;
+  }
+  const original = await fsp.readFile(sourcePath, 'utf8');
+  const newline = original.includes('\r\n') ? '\r\n' : '\n';
+  const lines = original.split(/\r?\n/);
+  let renamedInstance = false;
+  for (let i = 0; i < lines.length; i += 1) {
+    const match = lines[i].match(/^(\s*Instance:\s*)(\S+)(.*)$/);
+    if (match) {
+      lines[i] = `${match[1]}${match[2]}-disabled${match[3] || ''}`;
+      renamedInstance = true;
+      break;
+    }
+  }
+  if (renamedInstance) {
+    const updated = lines.join(newline);
+    await fsp.writeFile(sourcePath, updated, 'utf8');
+  }
+  await fsp.rename(sourcePath, targetPath).catch(() => null);
+  return true;
+}
+
+async function resolveAliasFilePath(rootDir) {
+  const candidates = [
+    path.join(rootDir, 'input', 'fsh', 'aliases.fsh'),
+    path.join(rootDir, 'input', 'fsh', 'alias.fsh'),
+    path.join(rootDir, 'aliases.fsh'),
+    path.join(rootDir, 'alias.fsh'),
+  ];
+  for (const candidate of candidates) {
+    if (await fileExists(candidate)) {
+      return { filePath: candidate, exists: true };
+    }
+  }
+  return { filePath: candidates[0], exists: false };
+}