diff --git a/.changeset/cuddly-games-cheer.md b/.changeset/cuddly-games-cheer.md
new file mode 100644
index 0000000..eee9d94
--- /dev/null
+++ b/.changeset/cuddly-games-cheer.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/intent': patch
+---
+
+Adds package source-kind metadata to scanner results, tightens scan stats to match the runtime contract, and adds focused markdown destination rewrite coverage while preserving the current name-based allowlist behavior.
diff --git a/packages/intent/src/core.ts b/packages/intent/src/core.ts
index 1490696..bf593cd 100644
--- a/packages/intent/src/core.ts
+++ b/packages/intent/src/core.ts
@@ -147,7 +147,7 @@ export function listIntentSkills(
       warningCount: result.warnings.length,
       noticeCount: result.notices.length,
       conflictCount: result.conflicts.length,
-      scan: scan.stats ?? fsCache.getStats(),
+      scan: scan.stats,
     }
   }
 
@@ -344,7 +344,7 @@ function resolveIntentSkillInCwd(
           excludes: excludePatterns,
           resolution: 'full-scan',
           resolved,
-          scan: scanResult.stats ?? fsCache.getStats(),
+          scan: scanResult.stats,
           scope,
         })
       : undefined,
diff --git a/packages/intent/src/discovery/register.ts b/packages/intent/src/discovery/register.ts
index b734e95..b606830 100644
--- a/packages/intent/src/discovery/register.ts
+++ b/packages/intent/src/discovery/register.ts
@@ -23,6 +23,7 @@ export interface CreatePackageRegistrarOptions {
   deriveIntentConfig: (pkgJson: PackageJson) => IntentConfig | null
   discoverSkills: (skillsDir: string, packageName: string) => Array<SkillEntry>
   getPackageDepth: (packageRoot: string, projectRoot: string) => number
+  getPackageKind: (packageRoot: string) => IntentPackage['kind']
   packageIndexes: Map<string, number>
   packages: Array<IntentPackage>
   projectRoot: string
@@ -120,6 +121,7 @@ export function createPackageRegistrar(opts: CreatePackageRegistrarOptions) {
       intent,
       skills,
       packageRoot: dirPath,
+      kind: opts.getPackageKind(dirPath),
       source,
     }
     const existingIndex = opts.packageIndexes.get(name)
diff --git a/packages/intent/src/scanner.ts b/packages/intent/src/scanner.ts
index 51baf42..22ed833 100644
--- a/packages/intent/src/scanner.ts
+++ b/packages/intent/src/scanner.ts
@@ -19,7 +19,10 @@ import {
 } from './utils.js'
 import { createIntentFsCache } from './fs-cache.js'
 import { detectPackageManager } from './package-manager.js'
-import { findWorkspaceRoot } from './workspace-patterns.js'
+import {
+  findWorkspacePackages,
+  findWorkspaceRoot,
+} from './workspace-patterns.js'
 import type { IntentFsCache } from './fs-cache.js'
 import type { ReadFs } from './utils.js'
 import type {
@@ -451,6 +454,28 @@ function getScanScope(options: ScanOptions): ScanScope {
   return options.scope ?? (options.includeGlobal ? 'local-and-global' : 'local')
 }
 
+function createWorkspacePackageKeySet(
+  workspaceRoot: string | null,
+  getFsIdentity: (path: string) => string,
+): Set<string> {
+  if (!workspaceRoot) return new Set()
+
+  return new Set(
+    findWorkspacePackages(workspaceRoot).map((dir) => getFsIdentity(dir)),
+  )
+}
+
+function createPackageKindResolver(
+  workspacePackageKeys: Set<string>,
+  getFsIdentity: (path: string) => string,
+): (packageRoot: string) => IntentPackage['kind'] {
+  return (packageRoot: string): IntentPackage['kind'] => {
+    return workspacePackageKeys.has(getFsIdentity(packageRoot))
+      ? 'workspace'
+      : 'npm'
+  }
+}
+
 export function scanForIntents(
   root?: string,
   options: ScanOptions = {},
@@ -495,6 +520,11 @@ export function scanForIntents(
   >()
   let pnpApi: PnpApi | null | undefined
 
+  const getPackageKind = createPackageKindResolver(
+    createWorkspacePackageKeySet(workspaceRoot, fsCache.getFsIdentity),
+    fsCache.getFsIdentity,
+  )
+
   function getPnpApi(): PnpApi | null {
     if (scanScope === 'global') return null
     if (pnpApi === undefined) {
@@ -545,6 +575,7 @@ export function scanForIntents(
       deriveIntentConfig,
       discoverSkills: (skillsDir) => discoverSkills(skillsDir, fsCache),
       getPackageDepth,
+      getPackageKind,
       getFsIdentity: fsCache.getFsIdentity,
       exists: fsCache.exists,
       packageIndexes,
@@ -726,6 +757,13 @@ export function scanIntentPackageAtRoot(
   const warnings: Array<string> = []
   const packageIndexes = new Map<string, number>()
   const fsCache = options.fsCache ?? createIntentFsCache()
+  const getPackageKind = createPackageKindResolver(
+    createWorkspacePackageKeySet(
+      findWorkspaceRoot(projectRoot),
+      fsCache.getFsIdentity,
+    ),
+    fsCache.getFsIdentity,
+  )
 
   function readPkgJson(dirPath: string): Record<string, unknown> | null {
     return fsCache.readPackageJson(dirPath)
@@ -744,6 +782,7 @@ export function scanIntentPackageAtRoot(
           )
       : (skillsDir) => discoverSkills(skillsDir, fsCache),
     getPackageDepth,
+    getPackageKind,
     getFsIdentity: fsCache.getFsIdentity,
     exists: fsCache.exists,
     packageIndexes,
diff --git a/packages/intent/src/types.ts b/packages/intent/src/types.ts
index 00e5228..994ed53 100644
--- a/packages/intent/src/types.ts
+++ b/packages/intent/src/types.ts
@@ -23,7 +23,7 @@ export interface ScanResult {
     local: NodeModulesScanTarget
     global: NodeModulesScanTarget
   }
-  stats?: ScanStats
+  stats: ScanStats
 }
 
 export type PackageManager = 'npm' | 'pnpm' | 'yarn' | 'bun' | 'unknown'
@@ -54,6 +54,7 @@ export interface IntentPackage {
   intent: IntentConfig
   skills: Array<SkillEntry>
   packageRoot: string
+  kind: 'npm' | 'workspace'
   source: 'local' | 'global'
 }
 
diff --git a/packages/intent/tests/install-writer.test.ts b/packages/intent/tests/install-writer.test.ts
index 0a76adb..09539e1 100644
--- a/packages/intent/tests/install-writer.test.ts
+++ b/packages/intent/tests/install-writer.test.ts
@@ -47,6 +47,7 @@ function pkg(overrides: Partial<IntentPackage>): IntentPackage {
     intent: { version: 1, repo: 'test/pkg', docs: 'docs/' },
     skills: [],
     packageRoot: 'node_modules/pkg',
+    kind: 'npm',
     source: 'local',
     ...overrides,
   }
@@ -73,6 +74,10 @@ function scanResult(packages: Array<IntentPackage>): ScanResult {
         scanned: false,
       },
     },
+    stats: {
+      packageJsonCacheHits: 0,
+      packageJsonReadCount: 0,
+    },
   }
 }
 
diff --git a/packages/intent/tests/markdown.test.ts b/packages/intent/tests/markdown.test.ts
new file mode 100644
index 0000000..419d8f8
--- /dev/null
+++ b/packages/intent/tests/markdown.test.ts
@@ -0,0 +1,40 @@
+import { join } from 'node:path'
+import { describe, expect, it } from 'vitest'
+import { rewriteLoadedSkillMarkdownDestinations } from '../src/core/markdown.js'
+
+const cwd = '/repo'
+const packageRoot = join(cwd, 'node_modules', 'pkg')
+const skillFilePath = join(packageRoot, 'skills', 'core', 'SKILL.md')
+
+function rewrite(content: string): string {
+  return rewriteLoadedSkillMarkdownDestinations({
+    content,
+    cwd,
+    packageRoot,
+    skillFilePath,
+  })
+}
+
+describe('rewriteLoadedSkillMarkdownDestinations', () => {
+  it('rewrites nested-label links while preserving query and hash suffixes', () => {
+    expect(rewrite('[API [v1]](docs/api.md?raw=1#setup)')).toBe(
+      '[API [v1]](node_modules/pkg/skills/core/docs/api.md?raw=1#setup)',
+    )
+  })
+
+  it('rewrites image destinations with escaped closing parens', () => {
+    expect(rewrite('![Diagram](assets/flow\\).png)')).toBe(
+      '![Diagram](node_modules/pkg/skills/core/assets/flow\\).png)',
+    )
+  })
+
+  it('preserves malformed inline links', () => {
+    expect(rewrite('[Broken](docs/api.md')).toBe('[Broken](docs/api.md')
+  })
+
+  it('does not rewrite links in fenced code blocks', () => {
+    expect(rewrite('~~~md\n[Keep](docs/api.md)\n~~~')).toBe(
+      '~~~md\n[Keep](docs/api.md)\n~~~',
+    )
+  })
+})
diff --git a/packages/intent/tests/resolver.test.ts b/packages/intent/tests/resolver.test.ts
index 6a6e502..78df895 100644
--- a/packages/intent/tests/resolver.test.ts
+++ b/packages/intent/tests/resolver.test.ts
@@ -29,6 +29,7 @@ function intentPackage(
     },
     packageRoot: `node_modules/${overrides.name}`,
     skills: [skill('core')],
+    kind: 'npm',
     source: 'local',
     version: '1.0.0',
     ...overrides,
@@ -64,6 +65,10 @@ function scanResult(
     },
     packageManager: 'npm',
     packages,
+    stats: {
+      packageJsonCacheHits: 0,
+      packageJsonReadCount: 0,
+    },
     warnings,
   }
 }
diff --git a/packages/intent/tests/scanner.test.ts b/packages/intent/tests/scanner.test.ts
index 735d950..289e86d 100644
--- a/packages/intent/tests/scanner.test.ts
+++ b/packages/intent/tests/scanner.test.ts
@@ -115,6 +115,7 @@ describe('scanForIntents', () => {
     const result = scanForIntents(root)
     expect(result.packages).toHaveLength(1)
     expect(result.packages[0]!.name).toBe('@tanstack/db')
+    expect(result.packages[0]!.kind).toBe('npm')
     expect(result.packages[0]!.version).toBe('0.5.2')
     expect(result.packages[0]!.packageRoot).toBe(pkgDir)
     expect(result.packages[0]!.skills).toHaveLength(1)
@@ -128,7 +129,7 @@ describe('scanForIntents', () => {
         packageJsonCacheHits: expect.any(Number),
       }),
     )
-    expect(result.stats!.packageJsonReadCount).toBeGreaterThan(0)
+    expect(result.stats.packageJsonReadCount).toBeGreaterThan(0)
   })
 
   it('does not throw when skills exists but is not a directory', () => {
@@ -1556,7 +1557,7 @@ describe('scanForIntents', () => {
       '@tanstack/query',
       '@tanstack/store',
     ])
-    expect(result.stats!.packageJsonReadCount).toBeLessThan(10)
+    expect(result.stats.packageJsonReadCount).toBeLessThan(10)
   })
 
   it('does not crawl package source trees during nested node_modules discovery', () => {
@@ -1591,7 +1592,7 @@ describe('scanForIntents', () => {
     const result = scanForIntents(root)
 
     expect(result.packages).toEqual([])
-    expect(result.stats!.packageJsonReadCount).toBeLessThan(4)
+    expect(result.stats.packageJsonReadCount).toBeLessThan(4)
   })
 
   it('dedupes recursive workspace symlink paths by real package identity', () => {
@@ -1639,7 +1640,8 @@ describe('scanForIntents', () => {
 
     expect(result.packages).toHaveLength(1)
     expect(result.packages[0]!.name).toBe('b')
-    expect(result.stats!.packageJsonReadCount).toBeLessThan(10)
+    expect(result.packages[0]!.kind).toBe('workspace')
+    expect(result.stats.packageJsonReadCount).toBeLessThan(10)
   })
 
   it('prefers valid semver versions over invalid ones at the same depth', () => {
diff --git a/packages/intent/tests/source-policy.test.ts b/packages/intent/tests/source-policy.test.ts
index 4948e7c..0c565a4 100644
--- a/packages/intent/tests/source-policy.test.ts
+++ b/packages/intent/tests/source-policy.test.ts
@@ -32,6 +32,7 @@ function pkg(name: string, skillNames: Array<string>): IntentPackage {
     intent: { version: 1, repo: 'owner/repo', docs: '' },
     skills: skillNames.map(skill),
     packageRoot: `/root/node_modules/${name}`,
+    kind: 'npm',
     source: 'local',
   }
 }