diff --git a/cli/README.md b/cli/README.md
index 277cc70e..98d93fda 100644
--- a/cli/README.md
+++ b/cli/README.md
@@ -75,6 +75,7 @@ set SKILLHUB_REGISTRY=https://skillhub.yourcompany.com
 
 - `skillhub version` - Display CLI version
 - `skillhub help` - Show help information
+- `skillhub doctor [--json]` - Scan the current project for installed skills and merge findings into the local inventory. Existing entries outside the scan are preserved; conflicts are reported but unrelated records are not deleted.
 
 ## 💡 Examples
 
diff --git a/cli/src/clients/skillhub-client.ts b/cli/src/clients/skillhub-client.ts
index 47bf5fca..fa876ad8 100644
--- a/cli/src/clients/skillhub-client.ts
+++ b/cli/src/clients/skillhub-client.ts
@@ -87,7 +87,7 @@ export class SkillHubClient {
       throw new CliError('skill or version not found', EXIT.generic, { registry: this.registry })
     }
     if (!response.ok) {
-      throw new CliError(`download failed with status ${response.status}`, EXIT.network, { registry: this.registry })
+      throw new CliError(`download failed with status ${response.status}`, EXIT.generic, { registry: this.registry })
     }
     return response
   }
@@ -134,7 +134,7 @@ export class SkillHubClient {
     }
     if (!response.ok) {
       const text = await response.text().catch(() => '')
-      throw new CliError(`registry returned ${response.status}`, EXIT.network, { registry: this.registry, detail: text })
+      throw new CliError(`registry returned ${response.status}`, EXIT.generic, { registry: this.registry, detail: text })
     }
     const body = await response.json()
     return body.data as T
diff --git a/cli/src/commands/doctor.ts b/cli/src/commands/doctor.ts
index 5d8ef28e..965ec8ab 100644
--- a/cli/src/commands/doctor.ts
+++ b/cli/src/commands/doctor.ts
@@ -11,8 +11,10 @@ export async function doctorCommand(options: DoctorCommandOptions): Promise<stri
       ok: true,
       inventoryPath: result.inventoryPath,
       backupPath: result.backupPath,
-      itemsRestored: result.itemsRestored,
-      targetsRestored: result.targetsRestored,
+      itemsScanned: result.itemsScanned,
+      targetsScanned: result.targetsScanned,
+      itemsPreserved: result.itemsPreserved,
+      targetsPreserved: result.targetsPreserved,
       skipped: result.skipped,
       conflicts: result.conflicts
     })
@@ -20,7 +22,10 @@ export async function doctorCommand(options: DoctorCommandOptions): Promise<stri
   const lines = [
     `Inventory: ${result.inventoryPath}`,
     result.backupPath ? `Backup: ${result.backupPath}` : null,
-    `Restored: ${result.itemsRestored} items, ${result.targetsRestored} targets`,
+    `Scanned: ${result.itemsScanned} items, ${result.targetsScanned} targets`,
+    result.itemsPreserved > 0
+      ? `Preserved (outside scan): ${result.itemsPreserved} items, ${result.targetsPreserved} targets`
+      : null,
     result.skipped.length > 0 ? `Skipped: ${result.skipped.length} directories` : null,
     result.conflicts.length > 0 ? `Conflicts: ${result.conflicts.length} groups` : null
   ].filter(Boolean)
diff --git a/cli/src/commands/help.ts b/cli/src/commands/help.ts
index ee482942..e463a39e 100644
--- a/cli/src/commands/help.ts
+++ b/cli/src/commands/help.ts
@@ -47,7 +47,7 @@ export const commands = {
     examples: ['skillhub remove pdf-parser', 'skillhub remove pdf-parser --remote --hard']
   },
   doctor: {
-    summary: 'Rebuild local inventory',
+    summary: 'Scan project and merge into local inventory (preserves entries outside scan scope)',
     usage: 'skillhub doctor [--json]',
     examples: ['skillhub doctor', 'skillhub doctor --json']
   },
diff --git a/cli/src/index.ts b/cli/src/index.ts
index ba9d8974..97f3f34f 100644
--- a/cli/src/index.ts
+++ b/cli/src/index.ts
@@ -268,7 +268,7 @@ cli
   })
 
 cli
-  .command('doctor', 'Rebuild local inventory')
+  .command('doctor', 'Scan project and merge into local inventory')
   .option('--json', 'Output JSON')
   .action((options: { json?: boolean }) => {
     return runCommand(() => doctorCommand(options), Boolean(options.json))
diff --git a/cli/src/services/doctor-service.ts b/cli/src/services/doctor-service.ts
index 0ebd5add..cea2e201 100644
--- a/cli/src/services/doctor-service.ts
+++ b/cli/src/services/doctor-service.ts
@@ -16,8 +16,10 @@ interface MetadataJson {
 interface DoctorResult {
   inventoryPath: string
   backupPath: string | null
-  itemsRestored: number
-  targetsRestored: number
+  itemsScanned: number
+  targetsScanned: number
+  itemsPreserved: number
+  targetsPreserved: number
   skipped: Array<{ path: string; reason: string }>
   conflicts: Array<{ key: string; versions: string[] }>
 }
@@ -38,8 +40,8 @@ export async function runDoctor(cwd: string, home?: string): Promise<DoctorResul
     groups.get(key)!.push(entry)
   }
 
-  // Build new inventory
-  const items: InventoryItem[] = []
+  // Build scanned items
+  const scannedItems: InventoryItem[] = []
   for (const [key, group] of groups) {
     const versions = new Set(group.map(e => e.metadata.version))
     if (versions.size > 1) {
@@ -53,7 +55,7 @@ export async function runDoctor(cwd: string, home?: string): Promise<DoctorResul
       installDir: e.installDir,
       installedAt: e.metadata.installedAt
     }))
-    items.push({
+    scannedItems.push({
       registry: first.metadata.registry,
       namespace: first.metadata.namespace,
       slug: first.metadata.slug,
@@ -62,6 +64,38 @@ export async function runDoctor(cwd: string, home?: string): Promise<DoctorResul
     })
   }
 
+  // Read old inventory
+  let oldInventory: Inventory
+  try {
+    oldInventory = await store.read()
+  } catch {
+    oldInventory = { items: [] }
+  }
+
+  // Collect scanned installDirs
+  const scannedInstallDirs = new Set<string>()
+  for (const item of scannedItems) {
+    for (const target of item.targets) {
+      scannedInstallDirs.add(target.installDir)
+    }
+  }
+
+  // Preserve old items where installDir is not in scanned set
+  // This allows the same slug to coexist in different installDirs (e.g., different projects)
+  const preservedItems: InventoryItem[] = []
+  for (const oldItem of oldInventory.items) {
+    const preservedTargets = oldItem.targets.filter(t => !scannedInstallDirs.has(t.installDir))
+    if (preservedTargets.length > 0) {
+      preservedItems.push({
+        ...oldItem,
+        targets: preservedTargets
+      })
+    }
+  }
+
+  // Merge scanned and preserved items
+  const items = [...scannedItems, ...preservedItems]
+
   // Backup old inventory
   let backupPath: string | null = null
   try {
@@ -79,8 +113,10 @@ export async function runDoctor(cwd: string, home?: string): Promise<DoctorResul
   return {
     inventoryPath: store.path,
     backupPath,
-    itemsRestored: items.length,
-    targetsRestored: items.reduce((sum, item) => sum + item.targets.length, 0),
+    itemsScanned: scannedItems.length,
+    targetsScanned: scannedItems.reduce((sum, item) => sum + item.targets.length, 0),
+    itemsPreserved: preservedItems.length,
+    targetsPreserved: preservedItems.reduce((sum, item) => sum + item.targets.length, 0),
     skipped,
     conflicts
   }
diff --git a/cli/test/integration/doctor-command.test.ts b/cli/test/integration/doctor-command.test.ts
index 6896dabb..f2afecb1 100644
--- a/cli/test/integration/doctor-command.test.ts
+++ b/cli/test/integration/doctor-command.test.ts
@@ -44,8 +44,10 @@ describe('doctor command', () => {
     expect(json.inventoryPath).toContain('.skillhub')
     expect(json.inventoryPath).toContain('inventory.json')
     expect(json.backupPath).toBeNull()
-    expect(json.itemsRestored).toBe(0)
-    expect(json.targetsRestored).toBe(0)
+    expect(json.itemsScanned).toBe(0)
+    expect(json.targetsScanned).toBe(0)
+    expect(json.itemsPreserved).toBe(0)
+    expect(json.targetsPreserved).toBe(0)
     expect(Array.isArray(json.skipped)).toBe(true)
     expect(Array.isArray(json.conflicts)).toBe(true)
   })
@@ -62,7 +64,7 @@ describe('doctor command', () => {
     expect(result.stdout).toContain('Inventory:')
     expect(result.stdout).toContain('.skillhub')
     expect(result.stdout).toContain('inventory.json')
-    expect(result.stdout).toContain('Restored: 0 items, 0 targets')
+    expect(result.stdout).toContain('Scanned: 0 items, 0 targets')
     expect(result.stdout).not.toContain('Backup:')
   })
 
@@ -132,8 +134,8 @@ describe('doctor command', () => {
 
     const json = JSON.parse(result.stdout)
     expect(json.ok).toBe(true)
-    expect(json.itemsRestored).toBe(1)
-    expect(json.targetsRestored).toBe(1)
+    expect(json.itemsScanned).toBe(1)
+    expect(json.targetsScanned).toBe(1)
     expect(json.backupPath).toBeNull()
     expect(Array.isArray(json.skipped)).toBe(true)
     expect(json.conflicts).toHaveLength(0)
@@ -164,4 +166,65 @@ describe('doctor command', () => {
     expect(result.stdout).toContain('Backup:')
     expect(result.stdout).toContain('inventory.json.bak')
   })
+
+  test('doctor merges with existing inventory and preserves out-of-cwd entries', async () => {
+    const { home, cwd } = await createTempHome()
+
+    const skillhubDir = join(home, '.skillhub')
+    await mkdir(skillhubDir, { recursive: true })
+    const inventoryPath = join(skillhubDir, 'inventory.json')
+
+    await writeFile(inventoryPath, JSON.stringify({
+      items: [
+        {
+          registry: 'https://skill.xfyun.cn',
+          namespace: 'global',
+          slug: 'external-skill',
+          version: '1.0.0',
+          targets: [
+            {
+              agent: 'claude-code',
+              rootDir: '/external/project/.claude',
+              installDir: '/external/project/.claude/skills/external-skill',
+              installedAt: '2026-04-01T00:00:00Z'
+            }
+          ]
+        }
+      ]
+    }))
+
+    await seedSkill(cwd, {
+      agentDir: '.claude',
+      slug: 'local-skill',
+      metadata: {
+        registry: 'https://skill.xfyun.cn',
+        namespace: 'global',
+        slug: 'local-skill',
+        version: '2.0.0',
+        agent: 'claude-code',
+        installedAt: '2026-04-21T09:00:00Z'
+      }
+    })
+
+    const result = await runCli(['doctor', '--json'], {
+      HOME: home,
+      USERPROFILE: home
+    }, { cwd })
+
+    expect(result.exitCode).toBe(0)
+
+    const json = JSON.parse(result.stdout)
+    expect(json.itemsScanned).toBe(1)
+    expect(json.itemsPreserved).toBe(1)
+    expect(json.targetsPreserved).toBe(1)
+
+    const raw = await readFile(inventoryPath, 'utf-8')
+    const inventory = JSON.parse(raw) as {
+      items: Array<{ slug: string }>
+    }
+
+    expect(inventory.items.map(item => item.slug)).toEqual(
+      expect.arrayContaining(['external-skill', 'local-skill'])
+    )
+  })
 })
diff --git a/cli/test/integration/publish-command.test.ts b/cli/test/integration/publish-command.test.ts
index 4fde1012..5f382fdf 100644
--- a/cli/test/integration/publish-command.test.ts
+++ b/cli/test/integration/publish-command.test.ts
@@ -221,9 +221,9 @@ describe('publish command — P1', () => {
     expect(json.detailUrl).toContain(encodeURIComponent(json.slug))
   })
 
-  test('server error during publish returns EXIT.network', async () => {
+  test('server error during publish returns EXIT.generic', async () => {
     const env = await createTempHome()
-    // 'server_error' returns HTTP 500, which the client maps to EXIT.network.
+    // 'server_error' returns HTTP 500; request reached registry but failed, so EXIT.generic.
     registry = await startFakeRegistry({ token: 'sk_ok', failures: { publish: 'server_error' } })
     await login(env, registry.url)
 
@@ -233,7 +233,7 @@ describe('publish command — P1', () => {
       USERPROFILE: env.home
     })
 
-    expect(result.exitCode).toBe(3)
+    expect(result.exitCode).toBe(1)
     expect(result.stderr).toContain('registry')
   })
 })
diff --git a/cli/test/unit/clients/skillhub-client.test.ts b/cli/test/unit/clients/skillhub-client.test.ts
index a4d9fac8..3ed6f19e 100644
--- a/cli/test/unit/clients/skillhub-client.test.ts
+++ b/cli/test/unit/clients/skillhub-client.test.ts
@@ -54,6 +54,24 @@ describe('SkillHubClient', () => {
     await err.toHaveProperty('exitCode', EXIT.generic)
   })
 
+  test('download() throws generic error on 400', async () => {
+    const fetchImpl = (async () => new Response(null, { status: 400 })) as unknown as typeof fetch
+    const client = new SkillHubClient('http://registry.test', 'token', fetchImpl)
+    const err = expect(client.download('ns', 'slug')).rejects
+    await err.toBeInstanceOf(CliError)
+    await err.toHaveProperty('message', 'download failed with status 400')
+    await err.toHaveProperty('exitCode', EXIT.generic)
+  })
+
+  test('download() throws generic error on 500', async () => {
+    const fetchImpl = (async () => new Response(null, { status: 500 })) as unknown as typeof fetch
+    const client = new SkillHubClient('http://registry.test', 'token', fetchImpl)
+    const err = expect(client.download('ns', 'slug')).rejects
+    await err.toBeInstanceOf(CliError)
+    await err.toHaveProperty('message', 'download failed with status 500')
+    await err.toHaveProperty('exitCode', EXIT.generic)
+  })
+
   test('download() throws network error on fetch failure', async () => {
     const fetchImpl = (async () => { throw new TypeError('fetch failed') }) as unknown as typeof fetch
     const client = new SkillHubClient('http://registry.test', 'token', fetchImpl)
@@ -139,6 +157,24 @@ describe('SkillHubClient', () => {
     expect(capturedUrl).toContain('?version=2.0.0')
   })
 
+  // --- handleJsonResponse() non-2xx classification ---
+
+  test('whoami() throws generic error on 500', async () => {
+    const fetchImpl = (async () => new Response(null, { status: 500 })) as unknown as typeof fetch
+    const client = new SkillHubClient('http://registry.test', 'token', fetchImpl)
+    const err = expect(client.whoami()).rejects
+    await err.toBeInstanceOf(CliError)
+    await err.toHaveProperty('exitCode', EXIT.generic)
+  })
+
+  test('search() throws generic error on 502', async () => {
+    const fetchImpl = (async () => new Response(null, { status: 502 })) as unknown as typeof fetch
+    const client = new SkillHubClient('http://registry.test', 'token', fetchImpl)
+    const err = expect(client.search('test', 20)).rejects
+    await err.toBeInstanceOf(CliError)
+    await err.toHaveProperty('exitCode', EXIT.generic)
+  })
+
   // --- deleteRemote() (P1) ---
 
   test('deleteRemote() returns result on success', async () => {
diff --git a/cli/test/unit/services/doctor-service.test.ts b/cli/test/unit/services/doctor-service.test.ts
index 7272d6d0..8f24fc89 100644
--- a/cli/test/unit/services/doctor-service.test.ts
+++ b/cli/test/unit/services/doctor-service.test.ts
@@ -1,9 +1,17 @@
 import { describe, expect, test } from 'bun:test'
-import { mkdtemp, mkdir, writeFile, symlink } from 'node:fs/promises'
+import { mkdtemp, mkdir, writeFile, symlink, readFile } from 'node:fs/promises'
 import { tmpdir } from 'node:os'
 import { join } from 'node:path'
 import { runDoctor } from '../../../src/services/doctor-service'
 
+type InventoryFile = {
+  items: Array<{
+    slug: string
+    version: string
+    targets: unknown[]
+  }>
+}
+
 async function setupSkillDir(cwd: string, agentDir: string, slug: string, metadata: Record<string, string>) {
   const skillDir = join(cwd, agentDir, 'skills', slug)
   const metaDir = join(skillDir, '.skillhub')
@@ -27,8 +35,8 @@ describe('doctor-service', () => {
     })
 
     const result = await runDoctor(cwd, home)
-    expect(result.itemsRestored).toBe(1)
-    expect(result.targetsRestored).toBe(1)
+    expect(result.itemsScanned).toBe(1)
+    expect(result.targetsScanned).toBe(1)
     expect(result.skipped).toHaveLength(0)
     expect(result.conflicts).toHaveLength(0)
   })
@@ -40,7 +48,7 @@ describe('doctor-service', () => {
     await mkdir(join(cwd, '.codex', 'skills', 'no-meta'), { recursive: true })
 
     const result = await runDoctor(cwd, home)
-    expect(result.itemsRestored).toBe(0)
+    expect(result.itemsScanned).toBe(0)
     expect(result.skipped).toHaveLength(1)
     expect(result.skipped[0]!.reason).toBe('no .skillhub directory')
   })
@@ -59,7 +67,7 @@ describe('doctor-service', () => {
     })
 
     const result = await runDoctor(cwd, home)
-    expect(result.itemsRestored).toBe(0)
+    expect(result.itemsScanned).toBe(0)
     expect(result.conflicts).toHaveLength(1)
     expect(result.conflicts[0]!.versions).toContain('1.0.0')
     expect(result.conflicts[0]!.versions).toContain('2.0.0')
@@ -79,7 +87,7 @@ describe('doctor-service', () => {
     await symlink(realDir, join(skillsDir, 'symlink-skill'))
 
     const result = await runDoctor(cwd, home)
-    expect(result.itemsRestored).toBe(1)
+    expect(result.itemsScanned).toBe(1)
     expect(result.skipped.some(s => s.reason === 'not a regular directory')).toBe(true)
   })
 
@@ -95,8 +103,8 @@ describe('doctor-service', () => {
     await symlink(join(cwd, '.codex'), join(cwd, '.fake-agent'))
 
     const result = await runDoctor(cwd, home)
-    expect(result.itemsRestored).toBe(1)
-    expect(result.targetsRestored).toBe(1)
+    expect(result.itemsScanned).toBe(1)
+    expect(result.targetsScanned).toBe(1)
   })
 
   test('skips symlinked .skillhub directories', async () => {
@@ -118,7 +126,177 @@ describe('doctor-service', () => {
     await symlink(realMetaDir, join(skillDir, '.skillhub'))
 
     const result = await runDoctor(cwd, home)
-    expect(result.itemsRestored).toBe(0)
+    expect(result.itemsScanned).toBe(0)
     expect(result.skipped.some(s => s.reason === '.skillhub is not a regular directory')).toBe(true)
   })
+
+  test('merges scan results with existing inventory', async () => {
+    const cwd = await mkdtemp(join(tmpdir(), 'doctor-test-'))
+    const home = await mkdtemp(join(tmpdir(), 'doctor-home-'))
+
+    // Pre-seed old inventory with one item NOT in current cwd
+    const inventoryPath = join(home, '.skillhub', 'inventory.json')
+    await mkdir(join(home, '.skillhub'), { recursive: true })
+    await writeFile(inventoryPath, JSON.stringify({
+      items: [
+        {
+          registry: 'https://skill.xfyun.cn',
+          namespace: 'global',
+          slug: 'external-skill',
+          version: '1.0.0',
+          targets: [
+            {
+              agent: 'codex',
+              rootDir: '/external/project/.codex',
+              installDir: '/external/project/.codex/skills/external-skill',
+              installedAt: '2026-04-01T10:00:00Z'
+            }
+          ]
+        }
+      ]
+    }))
+
+    // Scan cwd finds one new item
+    await setupSkillDir(cwd, '.claude', 'local-skill', {
+      registry: 'https://skill.xfyun.cn',
+      namespace: 'global',
+      slug: 'local-skill',
+      version: '2.0.0',
+      agent: 'claude-code',
+      installedAt: '2026-04-20T12:00:00Z'
+    })
+
+    const result = await runDoctor(cwd, home)
+
+    // Final inventory should contain BOTH items
+    expect(result.itemsScanned).toBe(1)
+    expect(result.targetsScanned).toBe(1)
+    expect(result.itemsPreserved).toBe(1)
+    expect(result.targetsPreserved).toBe(1)
+    expect(result.conflicts).toHaveLength(0)
+
+    const finalInventory = JSON.parse(await readFile(inventoryPath, 'utf-8')) as InventoryFile
+    expect(finalInventory.items).toHaveLength(2)
+
+    const externalSkillItem = finalInventory.items.find(item => item.slug === 'external-skill')!
+    expect(externalSkillItem).toBeDefined()
+    expect(externalSkillItem.version).toBe('1.0.0')
+    expect(externalSkillItem.targets).toHaveLength(1)
+
+    const localSkillItem = finalInventory.items.find(item => item.slug === 'local-skill')!
+    expect(localSkillItem).toBeDefined()
+    expect(localSkillItem.version).toBe('2.0.0')
+    expect(localSkillItem.targets).toHaveLength(1)
+  })
+
+  test('refreshes old record when scan hits same installDir', async () => {
+    const cwd = await mkdtemp(join(tmpdir(), 'doctor-test-'))
+    const home = await mkdtemp(join(tmpdir(), 'doctor-home-'))
+
+    const installDir = join(cwd, '.codex', 'skills', 'pdf-parser')
+
+    // Pre-seed old inventory with pdf-parser v1.0.0 at specific installDir
+    const inventoryPath = join(home, '.skillhub', 'inventory.json')
+    await mkdir(join(home, '.skillhub'), { recursive: true })
+    await writeFile(inventoryPath, JSON.stringify({
+      items: [
+        {
+          registry: 'https://skill.xfyun.cn',
+          namespace: 'global',
+          slug: 'pdf-parser',
+          version: '1.0.0',
+          targets: [
+            {
+              agent: 'codex',
+              rootDir: join(cwd, '.codex'),
+              installDir,
+              installedAt: '2026-04-01T10:00:00Z'
+            }
+          ]
+        }
+      ]
+    }))
+
+    // Place metadata for pdf-parser v2.0.0 at the SAME installDir
+    await setupSkillDir(cwd, '.codex', 'pdf-parser', {
+      registry: 'https://skill.xfyun.cn',
+      namespace: 'global',
+      slug: 'pdf-parser',
+      version: '2.0.0',
+      agent: 'codex',
+      installedAt: '2026-04-20T12:00:00Z'
+    })
+
+    const result = await runDoctor(cwd, home)
+
+    // Final inventory should have 1 item with version 2.0.0 and 1 target
+    expect(result.itemsScanned).toBe(1)
+    expect(result.targetsScanned).toBe(1)
+    expect(result.conflicts).toHaveLength(0)
+
+    // Verify the inventory file has the updated version
+    const finalInventory = JSON.parse(await readFile(inventoryPath, 'utf-8'))
+    expect(finalInventory.items).toHaveLength(1)
+    expect(finalInventory.items[0].version).toBe('2.0.0')
+    expect(finalInventory.items[0].targets).toHaveLength(1)
+  })
+
+  test('conflict groups do not delete unrelated old items', async () => {
+    const cwd = await mkdtemp(join(tmpdir(), 'doctor-test-'))
+    const home = await mkdtemp(join(tmpdir(), 'doctor-home-'))
+
+    // Pre-seed old inventory with image-resizer at /external/proj (NOT in cwd)
+    const inventoryPath = join(home, '.skillhub', 'inventory.json')
+    await mkdir(join(home, '.skillhub'), { recursive: true })
+    await writeFile(inventoryPath, JSON.stringify({
+      items: [
+        {
+          registry: 'https://skill.xfyun.cn',
+          namespace: 'global',
+          slug: 'image-resizer',
+          version: '3.0.0',
+          targets: [
+            {
+              agent: 'codex',
+              rootDir: '/external/proj/.codex',
+              installDir: '/external/proj/.codex/skills/image-resizer',
+              installedAt: '2026-03-15T08:00:00Z'
+            }
+          ]
+        }
+      ]
+    }))
+
+    // In cwd, create conflict: pdf-parser v1.0.0 in .codex, pdf-parser v2.0.0 in .claude
+    await setupSkillDir(cwd, '.codex', 'pdf-parser', {
+      registry: 'https://skill.xfyun.cn',
+      namespace: 'global',
+      slug: 'pdf-parser',
+      version: '1.0.0',
+      agent: 'codex',
+      installedAt: '2026-04-20T12:00:00Z'
+    })
+    await setupSkillDir(cwd, '.claude', 'pdf-parser', {
+      registry: 'https://skill.xfyun.cn',
+      namespace: 'global',
+      slug: 'pdf-parser',
+      version: '2.0.0',
+      agent: 'claude-code',
+      installedAt: '2026-04-20T12:00:00Z'
+    })
+
+    const result = await runDoctor(cwd, home)
+
+    // Should detect conflict
+    expect(result.conflicts).toHaveLength(1)
+    expect(result.conflicts[0]!.versions).toContain('1.0.0')
+    expect(result.conflicts[0]!.versions).toContain('2.0.0')
+
+    // Final inventory should still contain image-resizer
+    const finalInventory = JSON.parse(await readFile(inventoryPath, 'utf-8')) as InventoryFile
+    const imageResizerItem = finalInventory.items.find(item => item.slug === 'image-resizer')!
+    expect(imageResizerItem).toBeDefined()
+    expect(imageResizerItem.version).toBe('3.0.0')
+    expect(imageResizerItem.targets).toHaveLength(1)
+  })
 })