diff --git a/.changeset/stable-skill-paths.md b/.changeset/stable-skill-paths.md
new file mode 100644
index 0000000..34048fe
--- /dev/null
+++ b/.changeset/stable-skill-paths.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/intent': patch
+---
+
+Use stable `node_modules/<name>/...` paths for skill references instead of absolute filesystem paths containing package-manager-internal directories with version numbers. Paths no longer break when packages are updated.
diff --git a/packages/intent/src/commands/install.ts b/packages/intent/src/commands/install.ts
index 91fa79a..f7c1708 100644
--- a/packages/intent/src/commands/install.ts
+++ b/packages/intent/src/commands/install.ts
@@ -50,6 +50,13 @@ skills:
    Rules:
    - Use the user's own words for task descriptions
    - Include the exact path from \`npx @tanstack/intent@latest list\` output so agents can load it directly
+   - Paths should use the stable \`node_modules/<package-name>/skills/...\` format (no version numbers)
+   - If a skill path from \`list\` contains package-manager-internal directories (e.g. \`.pnpm/\`, \`.bun/\`)
+     with version numbers, it is a transitive dependency without a stable top-level symlink.
+     For these skills, do NOT embed the versioned path. Instead, add a comment telling the agent
+     how to locate the skill at runtime:
+       - task: "describe the task"
+         # To load this skill, run: npx @tanstack/intent@latest list | grep <skill-name>
    - Keep entries concise - this block is read on every agent task
    - Preserve all content outside the block tags unchanged
    - If the user is on Deno, note that this setup is best-effort today and relies on npm interop`
diff --git a/packages/intent/src/library-scanner.ts b/packages/intent/src/library-scanner.ts
index 44e3e81..b50989f 100644
--- a/packages/intent/src/library-scanner.ts
+++ b/packages/intent/src/library-scanner.ts
@@ -1,6 +1,11 @@
 import { existsSync, readFileSync, readdirSync } from 'node:fs'
-import { dirname, join, relative, sep } from 'node:path'
-import { getDeps, parseFrontmatter, resolveDepDir } from './utils.js'
+import { dirname, join, relative } from 'node:path'
+import {
+  getDeps,
+  parseFrontmatter,
+  resolveDepDir,
+  toPosixPath,
+} from './utils.js'
 import type { SkillEntry } from './types.js'
 import type { Dirent } from 'node:fs'
 
@@ -76,7 +81,7 @@ function discoverSkills(skillsDir: string): Array<SkillEntry> {
       const skillFile = join(childDir, 'SKILL.md')
       if (existsSync(skillFile)) {
         const fm = parseFrontmatter(skillFile)
-        const relName = relative(skillsDir, childDir).split(sep).join('/')
+        const relName = toPosixPath(relative(skillsDir, childDir))
         skills.push({
           name: typeof fm?.name === 'string' ? fm.name : relName,
           path: skillFile,
@@ -135,11 +140,21 @@ export function scanLibrary(
     }
 
     const skillsDir = join(dir, 'skills')
+    const skills = existsSync(skillsDir) ? discoverSkills(skillsDir) : []
+
+    // Convert absolute skill paths to stable node_modules/<name>/... paths
+    if (name) {
+      for (const skill of skills) {
+        const relFromPkg = toPosixPath(relative(dir, skill.path))
+        skill.path = `node_modules/${name}/${relFromPkg}`
+      }
+    }
+
     packages.push({
       name,
       version: typeof pkg.version === 'string' ? pkg.version : '0.0.0',
       description: typeof pkg.description === 'string' ? pkg.description : '',
-      skills: existsSync(skillsDir) ? discoverSkills(skillsDir) : [],
+      skills,
     })
 
     for (const depName of getDeps(pkg)) {
diff --git a/packages/intent/src/scanner.ts b/packages/intent/src/scanner.ts
index ca15745..100da63 100644
--- a/packages/intent/src/scanner.ts
+++ b/packages/intent/src/scanner.ts
@@ -6,6 +6,7 @@ import {
   listNodeModulesPackageDirs,
   parseFrontmatter,
   resolveDepDir,
+  toPosixPath,
 } from './utils.js'
 import {
   findWorkspaceRoot,
@@ -156,7 +157,7 @@ function discoverSkills(
       const skillFile = join(childDir, 'SKILL.md')
       if (existsSync(skillFile)) {
         const fm = parseFrontmatter(skillFile)
-        const relName = relative(skillsDir, childDir).split(sep).join('/')
+        const relName = toPosixPath(relative(skillsDir, childDir))
         const desc =
           typeof fm?.description === 'string'
             ? fm.description.replace(/\s+/g, ' ').trim()
@@ -432,11 +433,32 @@ export function scanForIntents(root?: string): ScanResult {
       return false
     }
 
+    const skills = discoverSkills(skillsDir, name)
+
+    // Convert absolute skill paths to stable relative paths, preferring
+    // node_modules/<name>/... when a top-level symlink exists, otherwise
+    // falling back to a path relative to the project root.
+    const isLocal =
+      dirPath.startsWith(projectRoot + sep) ||
+      dirPath.startsWith(projectRoot + '/')
+    if (isLocal) {
+      const hasStableSymlink =
+        name !== '' && existsSync(join(projectRoot, 'node_modules', name))
+      for (const skill of skills) {
+        if (hasStableSymlink) {
+          const relFromPkg = toPosixPath(relative(dirPath, skill.path))
+          skill.path = `node_modules/${name}/${relFromPkg}`
+        } else {
+          skill.path = toPosixPath(relative(projectRoot, skill.path))
+        }
+      }
+    }
+
     const candidate: IntentPackage = {
       name,
       version,
       intent,
-      skills: discoverSkills(skillsDir, name),
+      skills,
       packageRoot: dirPath,
     }
     const existingIndex = packageIndexes.get(name)
diff --git a/packages/intent/src/utils.ts b/packages/intent/src/utils.ts
index 4e68b5b..e70b98e 100644
--- a/packages/intent/src/utils.ts
+++ b/packages/intent/src/utils.ts
@@ -1,9 +1,16 @@
 import { execFileSync } from 'node:child_process'
 import { existsSync, readFileSync, readdirSync, type Dirent } from 'node:fs'
 import { createRequire } from 'node:module'
-import { dirname, join } from 'node:path'
+import { dirname, join, sep } from 'node:path'
 import { parse as parseYaml } from 'yaml'
 
+/**
+ * Convert a path to use forward slashes (for cross-platform consistency).
+ */
+export function toPosixPath(p: string): string {
+  return p.split(sep).join('/')
+}
+
 /**
  * Recursively find all SKILL.md files under a directory.
  */
diff --git a/packages/intent/tests/library-scanner.test.ts b/packages/intent/tests/library-scanner.test.ts
index e7eaf26..a243dc8 100644
--- a/packages/intent/tests/library-scanner.test.ts
+++ b/packages/intent/tests/library-scanner.test.ts
@@ -94,7 +94,9 @@ describe('scanLibrary', () => {
     const result = scanLibrary(scriptPath(pkgDir), root)
 
     const skill = result.packages[0]!.skills[0]!
-    expect(skill.path).toBe(join(pkgDir, 'skills', 'routing', 'SKILL.md'))
+    expect(skill.path).toBe(
+      'node_modules/@tanstack/router/skills/routing/SKILL.md',
+    )
   })
 
   it('recursively discovers deps with tanstack-intent keyword', () => {
@@ -308,6 +310,22 @@ describe('scanLibrary', () => {
     expect(names).toContain('routing/nested-routes')
   })
 
+  it('handles missing package name without producing double slashes in paths', () => {
+    const pkgDir = createDir(root, 'node_modules', 'no-name-pkg')
+    writeJson(join(pkgDir, 'package.json'), {
+      version: '1.0.0',
+      keywords: ['tanstack-intent'],
+    })
+    const skillDir = createDir(pkgDir, 'skills', 'core')
+    writeSkillMd(skillDir, { name: 'core', description: 'Core skill' })
+
+    const result = scanLibrary(scriptPath(pkgDir), root)
+
+    expect(result.packages).toHaveLength(1)
+    const skill = result.packages[0]!.skills[0]!
+    expect(skill.path).not.toContain('//')
+  })
+
   it('returns a warning when home package.json cannot be found', () => {
     const fakeScript = join(root, 'nowhere', 'bin', 'intent.js')
 
diff --git a/packages/intent/tests/scanner.test.ts b/packages/intent/tests/scanner.test.ts
index 50ceeb2..3722415 100644
--- a/packages/intent/tests/scanner.test.ts
+++ b/packages/intent/tests/scanner.test.ts
@@ -76,6 +76,21 @@ describe('scanForIntents', () => {
     expect(result.packages).toEqual([])
   })
 
+  it('handles empty package name without producing double-slash paths', () => {
+    const pkgDir = createDir(root, 'node_modules', 'no-name-pkg')
+    writeJson(join(pkgDir, 'package.json'), {
+      name: '',
+      version: '1.0.0',
+      intent: { version: 1, repo: 'test/pkg', docs: 'docs/' },
+    })
+    const skillDir = createDir(pkgDir, 'skills', 'core')
+    writeSkillMd(skillDir, { name: 'core', description: 'Core skill' })
+
+    const result = scanForIntents(root)
+    expect(result.packages).toHaveLength(1)
+    expect(result.packages[0]!.skills[0]!.path).not.toContain('//')
+  })
+
   it('discovers an intent-enabled package with skills', () => {
     const pkgDir = createDir(root, 'node_modules', '@tanstack', 'db')
     writeJson(join(pkgDir, 'package.json'), {
diff --git a/packages/intent/tests/workspace-patterns.test.ts b/packages/intent/tests/workspace-patterns.test.ts
index 9176d38..e48f646 100644
--- a/packages/intent/tests/workspace-patterns.test.ts
+++ b/packages/intent/tests/workspace-patterns.test.ts
@@ -1,4 +1,10 @@
-import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from 'node:fs'
+import {
+  mkdirSync,
+  mkdtempSync,
+  realpathSync,
+  rmSync,
+  writeFileSync,
+} from 'node:fs'
 import { join } from 'node:path'
 import { tmpdir } from 'node:os'
 import { afterEach, describe, expect, it } from 'vitest'
@@ -13,7 +19,9 @@ const roots: Array<string> = []
 const cwdStack: Array<string> = []
 
 function createRoot(): string {
-  const root = mkdtempSync(join(tmpdir(), 'workspace-patterns-test-'))
+  const root = realpathSync(
+    mkdtempSync(join(tmpdir(), 'workspace-patterns-test-')),
+  )
   roots.push(root)
   return root
 }