Update md-compiler MDX-to-Markdown pipeline and tests

Cargo.toml

@@ -9,7 +9,7 @@ members = [
 ]
 
 [workspace.package]
-version = "2026.10329.110"
+version = "2026.10330.108"
 edition = "2024"
 license = "AGPL-3.0-only"
 authors = ["TrueNine"]

cli/npm/darwin-arm64/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@truenine/memory-sync-cli-darwin-arm64",
-  "version": "2026.10329.110",
+  "version": "2026.10330.108",
   "os": [
     "darwin"
   ],

cli/npm/darwin-x64/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@truenine/memory-sync-cli-darwin-x64",
-  "version": "2026.10329.110",
+  "version": "2026.10330.108",
   "os": [
     "darwin"
   ],

cli/npm/linux-arm64-gnu/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@truenine/memory-sync-cli-linux-arm64-gnu",
-  "version": "2026.10329.110",
+  "version": "2026.10330.108",
   "os": [
     "linux"
   ],

cli/npm/linux-x64-gnu/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@truenine/memory-sync-cli-linux-x64-gnu",
-  "version": "2026.10329.110",
+  "version": "2026.10330.108",
   "os": [
     "linux"
   ],

cli/npm/win32-x64-msvc/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@truenine/memory-sync-cli-win32-x64-msvc",
-  "version": "2026.10329.110",
+  "version": "2026.10330.108",
   "os": [
     "win32"
   ],

cli/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@truenine/memory-sync-cli",
   "type": "module",
-  "version": "2026.10329.110",
+  "version": "2026.10330.108",
   "description": "TrueNine Memory Synchronization CLI",
   "author": "TrueNine",
   "license": "AGPL-3.0-only",

cli/scripts/benchmark-cleanup.ts

@@ -10,7 +10,6 @@ delete process.env['VITEST']
 delete process.env['VITEST_WORKER_ID']
 
 const cleanupModule = await import('../src/commands/CleanupUtils')
-const fallbackModule = await import('../src/commands/CleanupUtils.fallback')
 const pluginCore = await import('../src/plugins/plugin-core')
 
 function createMockLogger(): ILogger {
@@ -136,15 +135,9 @@ async function main(): Promise<void> {
     const iterations = 25
 
     process.stdout.write(`cleanup benchmark iterations=${iterations}\n`)
-    const fallbackAvg = await measure('fallback-plan', iterations, async () => {
-      await fallbackModule.collectDeletionTargets([plugin], cleanCtx)
-    })
-    const nativeAvg = await measure('native-plan', iterations, async () => {
+    await measure('native-plan', iterations, async () => {
       await cleanupModule.collectDeletionTargets([plugin], cleanCtx)
     })
-
-    const delta = nativeAvg - fallbackAvg
-    process.stdout.write(`delta=${delta.toFixed(2)}ms (${((delta / fallbackAvg) * 100).toFixed(2)}%)\n`)
   }
   finally {
     fs.rmSync(tempDir, {recursive: true, force: true})

cli/scripts/cleanup-native-smoke.ts

@@ -9,7 +9,6 @@ delete process.env['VITEST']
 delete process.env['VITEST_WORKER_ID']
 
 const cleanupModule = await import('../src/commands/CleanupUtils')
-const fallbackModule = await import('../src/commands/CleanupUtils.fallback')
 const pluginCore = await import('../src/plugins/plugin-core')
 
 function createMockLogger(): ILogger {
@@ -106,21 +105,18 @@ async function main(): Promise<void> {
     const cleanCtx = createCleanContext(workspaceDir)
 
     const nativePlan = await cleanupModule.collectDeletionTargets([plugin], cleanCtx)
-    const fallbackPlan = await fallbackModule.collectDeletionTargets([plugin], cleanCtx)
-
-    const sortPaths = (value: {filesToDelete: string[], dirsToDelete: string[], excludedScanGlobs: string[]}) => ({
-      ...value,
-      filesToDelete: [...value.filesToDelete].sort(),
-      dirsToDelete: [...value.dirsToDelete].sort(),
-      excludedScanGlobs: [...value.excludedScanGlobs].sort()
-    })
-
-    if (JSON.stringify(sortPaths(nativePlan)) !== JSON.stringify(sortPaths(fallbackPlan))) {
-      throw new Error(`Native cleanup plan mismatch.\nNative: ${JSON.stringify(nativePlan, null, 2)}\nFallback: ${JSON.stringify(fallbackPlan, null, 2)}`)
+    expectSetEqual(nativePlan.filesToDelete, [rootOutput, childOutput], 'native cleanup plan files')
+    expectSetEqual(nativePlan.dirsToDelete, [
+      legacySkillDir,
+      path.join(workspaceDir, 'project-a', 'commands'),
+      path.join(workspaceDir, 'project-a')
+    ], 'native cleanup plan directories')
+    if (nativePlan.violations.length > 0 || nativePlan.conflicts.length > 0) {
+      throw new Error(`Unexpected native cleanup plan: ${JSON.stringify(nativePlan, null, 2)}`)
     }
 
     const result = await cleanupModule.performCleanup([plugin], cleanCtx, createMockLogger())
-    if (result.deletedFiles !== 2 || result.deletedDirs !== 1 || result.errors.length > 0) {
+    if (result.deletedFiles !== 2 || result.deletedDirs !== 3 || result.errors.length > 0) {
       throw new Error(`Unexpected native cleanup result: ${JSON.stringify(result, null, 2)}`)
     }
 
@@ -138,4 +134,12 @@ async function main(): Promise<void> {
   }
 }
 
+function expectSetEqual(actual: readonly string[], expected: readonly string[], label: string): void {
+  const actualSorted = [...actual].sort()
+  const expectedSorted = [...expected].sort()
+  if (JSON.stringify(actualSorted) !== JSON.stringify(expectedSorted)) {
+    throw new Error(`Unexpected ${label}: ${JSON.stringify(actualSorted)} !== ${JSON.stringify(expectedSorted)}`)
+  }
+}
+
 await main()

cli/src/cleanup/empty-directories.ts

@@ -0,0 +1,97 @@
+import type * as fs from 'node:fs'
+import {resolveAbsolutePath} from '../ProtectedDeletionGuard'
+
+const EMPTY_DIRECTORY_SCAN_EXCLUDED_BASENAMES = new Set([
+  '.git',
+  'node_modules',
+  'dist',
+  'target',
+  '.next',
+  '.turbo',
+  'coverage',
+  '.nyc_output',
+  '.cache',
+  '.vite',
+  '.vite-temp',
+  '.pnpm-store',
+  '.yarn',
+  '.idea',
+  '.vscode'
+])
+
+export interface WorkspaceEmptyDirectoryPlan {
+  readonly emptyDirsToDelete: string[]
+}
+
+export interface WorkspaceEmptyDirectoryPlannerOptions {
+  readonly fs: typeof import('node:fs')
+  readonly path: typeof import('node:path')
+  readonly workspaceDir: string
+  readonly filesToDelete: readonly string[]
+  readonly dirsToDelete: readonly string[]
+}
+
+function shouldSkipEmptyDirectoryTree(
+  nodePath: typeof import('node:path'),
+  workspaceDir: string,
+  currentDir: string
+): boolean {
+  if (currentDir === workspaceDir) return false
+  return EMPTY_DIRECTORY_SCAN_EXCLUDED_BASENAMES.has(nodePath.basename(currentDir))
+}
+
+export function planWorkspaceEmptyDirectoryCleanup(
+  options: WorkspaceEmptyDirectoryPlannerOptions
+): WorkspaceEmptyDirectoryPlan {
+  const workspaceDir = resolveAbsolutePath(options.workspaceDir)
+  const filesToDelete = new Set(options.filesToDelete.map(resolveAbsolutePath))
+  const dirsToDelete = new Set(options.dirsToDelete.map(resolveAbsolutePath))
+  const emptyDirsToDelete = new Set<string>()
+
+  const collectEmptyDirectories = (currentDir: string): boolean => {
+    if (dirsToDelete.has(currentDir)) return true
+    if (shouldSkipEmptyDirectoryTree(options.path, workspaceDir, currentDir)) return false
+
+    let entries: fs.Dirent[]
+    try {
+      entries = options.fs.readdirSync(currentDir, {withFileTypes: true})
+    }
+    catch {
+      return false
+    }
+
+    let hasRetainedEntries = false
+
+    for (const entry of entries) {
+      const entryPath = resolveAbsolutePath(options.path.join(currentDir, entry.name))
+
+      if (dirsToDelete.has(entryPath)) continue
+
+      if (entry.isDirectory()) {
+        if (shouldSkipEmptyDirectoryTree(options.path, workspaceDir, entryPath)) {
+          hasRetainedEntries = true
+          continue
+        }
+
+        if (collectEmptyDirectories(entryPath)) {
+          emptyDirsToDelete.add(entryPath)
+          continue
+        }
+
+        hasRetainedEntries = true
+        continue
+      }
+
+      if (filesToDelete.has(entryPath)) continue
+      hasRetainedEntries = true
+    }
+
+    return !hasRetainedEntries
+  }
+
+  collectEmptyDirectories(workspaceDir)
+
+  return {
+    emptyDirsToDelete: [...emptyDirsToDelete].sort((a, b) => a.localeCompare(b))
+  }
+}

cli/src/commands/CleanupUtils.adapter.test.ts

@@ -12,6 +12,7 @@ const nativeBindingMocks = vi.hoisted(() => ({
 
 vi.mock('../core/native-binding', () => ({
   getNativeBinding: () => ({
+    ...globalThis.__TNMSC_TEST_NATIVE_BINDING__,
     planCleanup: nativeBindingMocks.planCleanup,
     performCleanup: nativeBindingMocks.performCleanup
   })
@@ -88,18 +89,20 @@ describe('cleanupUtils native adapter', () => {
     nativeBindingMocks.planCleanup.mockReturnValue(JSON.stringify({
       filesToDelete: ['/tmp/project-a/AGENTS.md'],
       dirsToDelete: ['/tmp/.codex/skills/legacy'],
+      emptyDirsToDelete: ['/tmp/.codex/skills'],
       violations: [],
       conflicts: [],
       excludedScanGlobs: ['**/.git/**']
     }))
     nativeBindingMocks.performCleanup.mockReturnValue(JSON.stringify({
       deletedFiles: 1,
-      deletedDirs: 1,
+      deletedDirs: 2,
       errors: [],
       violations: [],
       conflicts: [],
       filesToDelete: ['/tmp/project-a/AGENTS.md'],
       dirsToDelete: ['/tmp/.codex/skills/legacy'],
+      emptyDirsToDelete: ['/tmp/.codex/skills'],
       excludedScanGlobs: ['**/.git/**']
     }))
 
@@ -113,7 +116,7 @@ describe('cleanupUtils native adapter', () => {
     const plan = await collectDeletionTargets([plugin], cleanCtx)
     expect(plan).toEqual({
       filesToDelete: ['/tmp/project-a/AGENTS.md'],
-      dirsToDelete: ['/tmp/.codex/skills/legacy'],
+      dirsToDelete: ['/tmp/.codex/skills', '/tmp/.codex/skills/legacy'],
       violations: [],
       conflicts: [],
       excludedScanGlobs: ['**/.git/**']
@@ -136,7 +139,7 @@ describe('cleanupUtils native adapter', () => {
     const result = await performCleanup([plugin], cleanCtx, createMockLogger())
     expect(result).toEqual({
       deletedFiles: 1,
-      deletedDirs: 1,
+      deletedDirs: 2,
       errors: [],
       violations: [],
       conflicts: []