diff --git a/apps/cli/tests/desktop-host.e2e.ts b/apps/cli/tests/desktop-host.e2e.ts
index a7326e5860..dce2ecbce0 100644
--- a/apps/cli/tests/desktop-host.e2e.ts
+++ b/apps/cli/tests/desktop-host.e2e.ts
@@ -47,7 +47,7 @@ it.each([false, true])('settles startup after parent IPC disconnect (boot failur
   copyFileSync(join(hostDirectory, 'lib', 'index.js'), entry)
   const pnpm = join(root, 'bundled-pnpm.mjs')
   const nodeBin = join(root, 'bin')
-  const child = fork(entry, [root, root, root, 'runtime', pnpm, nodeBin], { execArgv: [], stdio: ['ignore', 'ignore', 'pipe', 'ipc'] })
+  const child = fork(entry, [root, root, root, pnpm, nodeBin], { execArgv: [], stdio: ['ignore', 'ignore', 'pipe', 'ipc'] })
   let stderr = ''
   child.stderr!.setEncoding('utf8').on('data', (chunk: string) => { stderr += chunk })
   const exited = new Promise<number | null>(resolve => child.once('exit', resolve))
diff --git a/packages/boot/app-boot/src/profile-resolution/legacy-links.ts b/packages/boot/app-boot/src/profile-resolution/legacy-links.ts
index 82d63c4a4f..b7d01a5639 100644
--- a/packages/boot/app-boot/src/profile-resolution/legacy-links.ts
+++ b/packages/boot/app-boot/src/profile-resolution/legacy-links.ts
@@ -1,6 +1,10 @@
-/** Package directory canonicalization for Node and packaged executables. */
+/** Package directory canonicalization and stale profile-projection recognition. */
 
-import { realpathSync } from 'node:fs'
+import { lstatSync, readlinkSync, realpathSync } from 'node:fs'
+import { basename, dirname, join, resolve } from 'node:path'
+
+/** Profile-private package links projected into its pnpm-managed node_modules. */
+export const PROFILE_MODULE_FALLBACK_DIR = '.dsh-module-fallback'
 
 /**
  * Return whether the process reads application modules from pkg's virtual filesystem.
@@ -18,3 +22,52 @@ export function isPackagedExecutable(): boolean {
 export function realModuleDirectory(path: string): string {
   return isPackagedExecutable() ? realpathSync(path) : realpathSync.native(path)
 }
+
+/**
+ * Resolve a link target without following the final path component.
+ * @param path - candidate path whose parent is canonicalized.
+ * @returns the canonical candidate, or undefined when its parent is absent.
+ */
+export function canonicalLinkPath(path: string): string | undefined {
+  try {
+    return join(realModuleDirectory(dirname(path)), basename(path))
+  } catch (error) {
+    // A missing parent means the candidate cannot identify an existing owned link.
+    /* v8 ignore next 2 -- a non-ENOENT realpath failure requires a host filesystem fault */
+    if ((error as NodeJS.ErrnoException).code === 'ENOENT') return undefined
+    /* v8 ignore next -- see the host-filesystem exception above */
+    throw error
+  }
+}
+
+/**
+ * Return whether a symlink or junction points at the same path as `target`.
+ * @param link - symlink or junction to inspect.
+ * @param target - expected target path.
+ * @returns whether both paths identify the same entry.
+ */
+export function symlinkPointsTo(link: string, target: string): boolean {
+  const actual = resolve(dirname(link), readlinkSync(link))
+  const canonicalActual = canonicalLinkPath(actual)
+  const canonicalTarget = canonicalLinkPath(resolve(target))
+  return canonicalActual !== undefined && canonicalActual === canonicalTarget
+}
+
+/**
+ * Return whether an observed profile package must not claim local precedence.
+ * @param profileDir - profile directory containing the package projection.
+ * @param packageName - bare package name to inspect.
+ * @returns whether the entry is a managed fallback link or disappeared during inspection.
+ */
+export function isProfileModuleFallbackLink(profileDir: string, packageName: string): boolean {
+  const link = join(profileDir, 'node_modules', packageName)
+  const target = join(profileDir, PROFILE_MODULE_FALLBACK_DIR, 'node_modules', packageName)
+  try {
+    return lstatSync(link).isSymbolicLink() && symlinkPointsTo(link, target)
+  } catch (error) {
+    /* v8 ignore next 2 -- a vanished candidate cannot claim local precedence */
+    if ((error as NodeJS.ErrnoException).code === 'ENOENT') return true
+    /* v8 ignore next -- non-ENOENT lstat/readlink failures require a host filesystem fault */
+    throw error
+  }
+}
diff --git a/packages/boot/app-boot/src/profile-resolution/resolver.ts b/packages/boot/app-boot/src/profile-resolution/resolver.ts
index 788bf44764..e9774e917d 100644
--- a/packages/boot/app-boot/src/profile-resolution/resolver.ts
+++ b/packages/boot/app-boot/src/profile-resolution/resolver.ts
@@ -7,6 +7,7 @@ import { fileURLToPath, pathToFileURL } from 'node:url'
 import { getEnvironmentData, setEnvironmentData } from 'node:worker_threads'
 import type { ModuleLoaderV1, ModuleLoaderV2, ResolveResult } from '@deepseek-ai/cordis-plugin-loader'
 import { imports as resolvePackageImports, type Package as ResolvePackageManifest } from 'resolve.exports'
+import { isProfileModuleFallbackLink } from './legacy-links.ts'
 import type { ProfileResolutionEntry, ProfileResolutionGeneration } from '../profile.ts'
 
 const WORKER_RESOLUTION_KEY = '@deepseek-ai/dsh-app-boot/profile-resolution'
@@ -167,14 +168,14 @@ function nativePackageDir(parent: string, name: string): string | undefined {
 
 function localPackageCandidate(
   searchPath: string, name: string, flavor: 'esm' | 'cjs',
-): { packageDir: string } | undefined {
+): { packageDir: string; canBeManagedLink: boolean } | undefined {
   const candidate = join(searchPath, name)
   const stat = statSync(candidate, { throwIfNoEntry: false })
   const found = flavor === 'esm'
     ? stat?.isDirectory() === true
     : stat !== undefined
       || ['.js', '.json', '.node'].some(extension => existsSync(candidate + extension))
-  return found ? { packageDir: candidate } : undefined
+  return found ? { packageDir: candidate, canBeManagedLink: stat !== undefined } : undefined
 }
 
 function selfReferenceName(parent: string): string | false | null {
@@ -339,13 +340,19 @@ class ResolutionRouter {
     }
 
     const target = generation.entries.get(name)
-    const candidates: Array<{ packageDir: string }> = []
+    const candidates: Array<{ packageDir: string; canBeManagedLink: boolean }> = []
     const localSearchPaths: string[] = []
     for (const searchPath of createRequire(parent).resolve.paths(name) as string[]) {
       if (generation.shared.has(resolve(searchPath))) break
       localSearchPaths.push(searchPath)
       const candidate = localPackageCandidate(searchPath, name, flavor)
-      if (candidate !== undefined) candidates.push(candidate)
+      if (candidate !== undefined) {
+        const legacy = candidate.canBeManagedLink && generation.profile.some(prefix => (
+          candidate.packageDir === join(prefix, 'node_modules', name)
+          && isProfileModuleFallbackLink(prefix.slice(0, -1), name)
+        ))
+        if (!legacy) candidates.push(candidate)
+      }
     }
     if (candidates.length > 0) {
       if (flavor === 'cjs' && nativeResolve !== undefined) {
@@ -379,7 +386,7 @@ class ResolutionRouter {
 
     const eligible = target?.scope === 'installation'
       || (target?.scope === 'profile' && parentRoutes.activeProfile)
-    const after = join(profilesDir, 'package.json')
+    const after = join(dirname(profilesDir), 'package.json')
     const route: ResolutionRoute = eligible
       ? { kind: 'fallback', entry: target, after }
       : { kind: 'after-fallback', parent: after }
diff --git a/packages/boot/app-boot/src/profile.ts b/packages/boot/app-boot/src/profile.ts
index b343acec34..0528ce189c 100644
--- a/packages/boot/app-boot/src/profile.ts
+++ b/packages/boot/app-boot/src/profile.ts
@@ -21,14 +21,16 @@
  */
 
 import { createRequire } from 'node:module'
-import { existsSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs'
+import { existsSync, lstatSync, mkdirSync, readFileSync, writeFileSync } from 'node:fs'
 import { basename, dirname, join } from 'node:path'
 import type { EntryOptions } from '@deepseek-ai/cordis-plugin-loader'
 import { applyEntryPatches, type PatchOptions } from '@deepseek-ai/cordis-plugin-include'
 import { resolveDshHome } from '@deepseek-ai/dsh-home-paths'
 import type { DshPackageManifest } from '@deepseek-ai/dsh-package-manifest'
 import { loadOverlayPatches } from './index.ts'
-import { realModuleDirectory } from './profile-resolution/legacy-links.ts'
+import {
+  canonicalLinkPath, isProfileModuleFallbackLink, PROFILE_MODULE_FALLBACK_DIR, realModuleDirectory, symlinkPointsTo,
+} from './profile-resolution/legacy-links.ts'
 
 /** Directory under the Harness home holding every profile. */
 export const PROFILES_DIR = 'profiles'
@@ -213,7 +215,7 @@ function resolveModuleFallbackEntries(
   declarers: ReadonlyMap<string, string>
   versions: ReadonlyMap<string, string | undefined>
 } {
-  // tsx skips workspace path mappings for importers under node_modules.
+  // Real declaring paths keep workspace symlinks under node_modules from disabling tsx path mappings.
   const canonicalAnchor = join(realModuleDirectory(dirname(installAnchor)), basename(installAnchor))
   const appManifest = readModuleFallbackManifest(canonicalAnchor)
   const links = new Map<string, string>()
@@ -326,13 +328,15 @@ function installedProfilePackageNames(profile: Profile, manifest: ProfileManifes
   if (manifest === undefined) return []
   return profileDependencyNames(manifest).filter((name) => {
     const candidate = join(profile.dir, 'node_modules', name)
-    return existsSync(join(candidate, 'package.json'))
+    if (!existsSync(join(candidate, 'package.json'))) return false
+    return !isProfileModuleFallbackLink(profile.dir, name)
   })
 }
 
 /** Collect the first resolvable package directory for each dependency name. */
 function dependencyClosure(
   anchors: readonly string[], reserved: ReadonlySet<string>,
+  exclude: (candidate: string, packageName: string) => boolean,
   declarers?: Map<string, string>,
   versions?: Map<string, string | undefined>,
 ): Map<string, string> {
@@ -355,7 +359,7 @@ function dependencyClosure(
       /* v8 ignore next -- an installable package manifest always declares dependencies or peers */
       for (const dep of profileDependencyNames(next.manifest)) {
         if (visited.has(dep)) continue
-        const dir = packageDirFromAnchor(next.anchor, dep)
+        const dir = packageDirFromAnchor(next.anchor, dep, exclude)
         // A declared-but-uninstalled dependency cannot be loader-visible.
         if (dir === undefined) continue
         visited.add(dep)
@@ -377,10 +381,25 @@ function resolveProfileModuleFallback(
   declarers?: Map<string, string>,
   versions?: Map<string, string | undefined>,
 ): Map<string, string> {
+  const profileModulesDir = join(profile.dir, 'node_modules')
+  const ownedModulesDir = join(profile.dir, PROFILE_MODULE_FALLBACK_DIR, 'node_modules')
   const bundleAnchors = profile.layers
     .filter(layer => !installationPackageNames.has(layer.packageName))
     .map(layer => join(layer.packageDir, 'package.json'))
-  const bundleLinks = dependencyClosure(bundleAnchors, installationPackageNames, declarers, versions)
+  const bundleLinks = dependencyClosure(bundleAnchors, installationPackageNames, (candidate, packageName) => {
+    const profileLink = join(profileModulesDir, packageName)
+    if (canonicalLinkPath(candidate) !== canonicalLinkPath(profileLink)) return false
+    try {
+      return lstatSync(profileLink).isSymbolicLink()
+        && symlinkPointsTo(profileLink, join(ownedModulesDir, packageName))
+    } catch (error) {
+      // A concurrent cleanup may remove the projection after package discovery.
+      /* v8 ignore next 2 -- a non-ENOENT lstat failure requires a host filesystem fault */
+      if ((error as NodeJS.ErrnoException).code === 'ENOENT') return true
+      /* v8 ignore next -- see the host-filesystem exception above */
+      throw error
+    }
+  }, declarers, versions)
   for (const layer of profile.layers) bundleLinks.delete(layer.packageName)
   return bundleLinks
 }
@@ -456,12 +475,13 @@ function normalizeShippedProfile(name: string, dir: string, manifest: ProfileMan
  */
 function packageDirFromAnchor(
   anchor: string, packageName: string,
+  exclude: (candidate: string, packageName: string) => boolean = () => false,
 ): string | undefined {
   // resolve.paths returns null only for builtins, which no bundle name is.
   /* v8 ignore next */
   for (const searchPath of createRequire(anchor).resolve.paths(packageName) ?? []) {
     const candidate = join(searchPath, packageName)
-    if (existsSync(join(candidate, 'package.json'))) return candidate
+    if (existsSync(join(candidate, 'package.json')) && !exclude(candidate, packageName)) return candidate
   }
   return undefined
 }
diff --git a/packages/boot/app-boot/tests/profile-resolution.spec.ts b/packages/boot/app-boot/tests/profile-resolution.spec.ts
index bf1f586a45..60dba4a1b1 100644
--- a/packages/boot/app-boot/tests/profile-resolution.spec.ts
+++ b/packages/boot/app-boot/tests/profile-resolution.spec.ts
@@ -621,7 +621,7 @@ describe('profile resolution generation', { concurrent: false }, () => {
       imports: { '#local': 'local-import', '#ancestor': 'ancestor-import' },
     }))
     const local = join(f.profile.dir, 'node_modules', 'local-import')
-    const ancestor = join(f.root, 'profiles', 'node_modules', 'ancestor-import')
+    const ancestor = join(f.root, 'node_modules', 'ancestor-import')
     pkg(local, 'local-import', 4)
     pkg(ancestor, 'ancestor-import', 5)
     const require = createRequire(join(f.profile.dir, 'entry.cjs'))
@@ -983,6 +983,84 @@ describe('profile resolution generation', { concurrent: false }, () => {
     })).toBe(alternativeSubpath)
   })
 
+  it('skips stale shared and profile-owned fallback entries when the generation misses', async () => {
+    const f = fixture()
+    pkg(join(f.root, 'profiles', 'node_modules', 'stale-shared'), 'stale-shared', 9)
+    pkg(join(f.root, 'node_modules', 'stale-shared'), 'stale-shared', 3)
+    const target = join(f.root, 'stale-private-target')
+    const owned = join(f.profile.dir, '.dsh-module-fallback', 'node_modules', 'stale-private')
+    const projected = join(f.profile.dir, 'node_modules', 'stale-private')
+    pkg(target, 'stale-private', 9)
+    mkdirSync(dirname(owned), { recursive: true })
+    symlinkSync(target, owned, process.platform === 'win32' ? 'junction' : 'dir')
+    mkdirSync(dirname(projected), { recursive: true })
+    symlinkSync(owned, projected, process.platform === 'win32' ? 'junction' : 'dir')
+    pkg(join(f.root, 'node_modules', 'stale-private'), 'stale-private', 3)
+    const registration = installProfileResolution(await generationOf(f))
+    registrations.push(registration)
+    const require = createRequire(join(f.profile.dir, 'entry.cjs'))
+    for (const name of ['stale-shared', 'stale-private']) {
+      expect(require(name)).toEqual({ marker: 3 })
+      expect(require.resolve(name, { paths: [f.profile.dir] })).toBe(join(f.root, 'node_modules', name, 'index.cjs'))
+      expect(await importFrom(name, pathToFileURL(join(f.profile.dir, `${name}.mjs`)).href))
+        .toMatchObject({ marker: 3 })
+    }
+  })
+
+  it('skips stale shared and declared profile projections when the generation supplies the package', async () => {
+    const f = fixture()
+    file(join(f.profile.dir, 'package.json'), JSON.stringify({
+      name: 'test-profile', private: true, dependencies: { 'resolution-lib': '*' },
+      imports: { '#library': 'resolution-lib' },
+    }))
+    const target = join(f.root, 'stale-target')
+    pkg(target, 'resolution-lib', 9)
+    const owned = join(f.profile.dir, '.dsh-module-fallback', 'node_modules', 'resolution-lib')
+    const projected = join(f.profile.dir, 'node_modules', 'resolution-lib')
+    const shared = join(f.root, 'profiles', 'node_modules', 'resolution-lib')
+    mkdirSync(dirname(owned), { recursive: true })
+    mkdirSync(dirname(projected), { recursive: true })
+    mkdirSync(dirname(shared), { recursive: true })
+    symlinkSync(target, owned, process.platform === 'win32' ? 'junction' : 'dir')
+    symlinkSync(owned, projected, process.platform === 'win32' ? 'junction' : 'dir')
+    symlinkSync(target, shared, process.platform === 'win32' ? 'junction' : 'dir')
+    const generation = await generationOf(f)
+    expect(generation.localPackageNames).toEqual([])
+    const registration = installProfileResolution(generation)
+    registrations.push(registration)
+    const require = createRequire(join(f.profile.dir, 'entry.cjs'))
+    for (const name of ['resolution-lib', '#library']) {
+      expect(require(name)).toEqual({ marker: 1 })
+      expect(await importFrom(name, pathToFileURL(join(f.profile.dir, 'entry.mjs')).href))
+        .toMatchObject({ marker: 1 })
+    }
+    expect(realpathSync(projected)).toBe(target)
+    expect(realpathSync(shared)).toBe(target)
+  })
+
+  it('excludes profile-owned projections from selected bundle dependency traversal', async () => {
+    const f = fixture()
+    const bundle = join(f.profile.dir, 'node_modules', 'selected-bundle')
+    pkg(bundle, 'selected-bundle', 1, { 'bundle-leaf': '*' })
+    f.profile.layers.push({
+      packageName: 'selected-bundle', packageDir: bundle,
+      patchPath: join(bundle, 'cordis.patch.yml'), patches: [],
+    })
+    const target = join(f.root, 'stale-leaf')
+    const owned = join(f.profile.dir, '.dsh-module-fallback', 'node_modules', 'bundle-leaf')
+    const projected = join(f.profile.dir, 'node_modules', 'bundle-leaf')
+    pkg(target, 'bundle-leaf', 9)
+    mkdirSync(dirname(owned), { recursive: true })
+    symlinkSync(target, owned, process.platform === 'win32' ? 'junction' : 'dir')
+    symlinkSync(owned, projected, process.platform === 'win32' ? 'junction' : 'dir')
+    const ancestor = join(f.root, 'node_modules', 'bundle-leaf')
+    pkg(ancestor, 'bundle-leaf', 3)
+    const generation = await generationOf(f)
+    expect(generation.entries.find(entry => entry.name === 'bundle-leaf'))
+      .toMatchObject({ packageDir: ancestor, version: '3.0.0', scope: 'profile' })
+    expect(realpathSync(projected)).toBe(target)
+  })
+
   it('continues after a canonicalized profiles directory from the matching parent tree', async () => {
     const root = realpathSync(mkdtempSync(join(tmpdir(), 'dsh-profile-generation-symlink-')))
     roots.push(root)
@@ -993,10 +1071,10 @@ describe('profile resolution generation', { concurrent: false }, () => {
     mkdirSync(realProfileDir, { recursive: true })
     mkdirSync(dirname(profilesDir), { recursive: true })
     symlinkSync(realProfilesDir, profilesDir, process.platform === 'win32' ? 'junction' : 'dir')
-    const parentPackage = join(realProfilesDir, 'node_modules', 'parent-lib')
-    pkg(parentPackage, 'parent-lib', 9)
-    pkg(join(carrier, 'node_modules', 'ancestor-lib'), 'ancestor-lib', 3)
-    pkg(join(root, 'home', 'node_modules', 'ancestor-lib'), 'ancestor-lib', 4)
+    pkg(join(realProfilesDir, 'node_modules', 'stale-only'), 'stale-only', 9)
+    const ancestor = join(carrier, 'node_modules', 'stale-only')
+    pkg(ancestor, 'stale-only', 3)
+    pkg(join(root, 'home', 'node_modules', 'stale-only'), 'stale-only', 4)
     const registration = installProfileResolution({
       profilesDir,
       profileDir: join(profilesDir, 'test'),
@@ -1005,11 +1083,10 @@ describe('profile resolution generation', { concurrent: false }, () => {
     })
     registrations.push(registration)
     const require = createRequire(join(realProfileDir, 'entry.cjs'))
-    expect(require('parent-lib')).toEqual({ marker: 9 })
-    expect(require('ancestor-lib')).toEqual({ marker: 3 })
+    expect(require('stale-only')).toEqual({ marker: 3 })
     const parent = pathToFileURL(join(realProfileDir, 'entry.mjs')).href
-    expect(await importFrom('parent-lib', parent)).toMatchObject({ marker: 9 })
-    expect(registration.packageDir('parent-lib', parent)).toBe(parentPackage)
+    expect(await importFrom('stale-only', parent)).toMatchObject({ marker: 3 })
+    expect(registration.packageDir('stale-only', parent)).toBe(ancestor)
   })
 
   it('leaves conditional exports to Node', async () => {
diff --git a/packages/boot/app-boot/tests/profile.spec.ts b/packages/boot/app-boot/tests/profile.spec.ts
index a694334769..d512e9565d 100644
--- a/packages/boot/app-boot/tests/profile.spec.ts
+++ b/packages/boot/app-boot/tests/profile.spec.ts
@@ -36,7 +36,7 @@ afterAll(() => {
 })
 
 const tmp = (): string => {
-  const dir = mkdtempSync(join(tmpdir(), 'dsh-profile-'))
+  const dir = realpathSync(mkdtempSync(join(tmpdir(), 'dsh-profile-')))
   tempRoots.push(dir)
   return dir
 }