test(plugins): cover portable read failures and refresh the module graph

docs/module-graph.i18n.yaml

@@ -2,5 +2,5 @@
 # side as of the last confirmed-consistent state. Both languages carry equal authority;
 # after editing either side, bring the other along and re-record with:
 #   pnpm run verify-translation-pairing --write docs/module-graph.md
-module-graph.md: a3898f8eb6ce58c9753b3515aeb2a5ec1f227ad3
-module-graph.zh.md: 2e818319f19f3b8eefb8e1a31d238c24273e1b5f
+module-graph.md: 74319fd35422752e2803c7605bfff0fdf6e30e38
+module-graph.zh.md: a0adbe2e119487f6b1cf44ab7440fee7a3216397

docs/module-graph.md

@@ -1471,10 +1471,8 @@ flowchart TD
 | [`tool-ask-user`](../packages/interaction/tool-ask-user) | `interaction` | [`agent`](../packages/core/agent), [`tools`](../packages/core/tools), [`user-questions`](../packages/interaction/user-questions) |
 | [`tool-jobs`](../packages/jobs/tool-jobs) | `jobs` | [`agent`](../packages/core/agent), [`jobs`](../packages/jobs/jobs), [`llm`](../packages/llm/llm), [`output-retention`](../packages/util/output-retention), [`system-prompt`](../packages/core/system-prompt), [`tools`](../packages/core/tools) |
 | [`tool-lsp`](../packages/lsp/tool-lsp) | `lsp` | [`llm`](../packages/llm/llm), [`lsp`](../packages/lsp/lsp), [`system-prompt`](../packages/core/system-prompt), [`timeout`](../packages/util/timeout), [`tools`](../packages/core/tools) |
-| [`mcp-client`](../packages/mcp/mcp-client) | `mcp` | [`attachment`](../packages/attachment/attachment), [`llm`](../packages/llm/llm), [`scope`](../packages/core/scope), [`subprocess`](../packages/subprocess/subprocess), [`timeout`](../packages/util/timeout), [`tools`](../packages/core/tools) |
-| [`agent-presets`](../packages/preset/agent-presets) | `preset` | [`agent`](../packages/core/agent), [`app-boot`](../packages/boot/app-boot), [`atomic-write`](../packages/util/atomic-write), [`home-paths`](../packages/util/home-paths), [`invariants`](../packages/runtime-diagnostics/invariants), [`scope`](../packages/core/scope), [`session`](../packages/core/session), [`session-projection`](../packages/session/session-projection), [`settings`](../packages/settings/settings), [`system-prompt`](../packages/core/system-prompt), [`tools`](../packages/core/tools), [`typert-protocol`](../packages/typert/protocol) |
 | [`mcp-resources`](../packages/mcp/mcp-resources) | `mcp` | [`llm`](../packages/llm/llm), [`scope`](../packages/core/scope), [`system-prompt`](../packages/core/system-prompt), [`tools`](../packages/core/tools) |
-| [`agent-presets`](../packages/preset/agent-presets) | `preset` | [`agent`](../packages/core/agent), [`atomic-write`](../packages/util/atomic-write), [`home-paths`](../packages/util/home-paths), [`invariants`](../packages/runtime-diagnostics/invariants), [`scope`](../packages/core/scope), [`session`](../packages/core/session), [`session-projection`](../packages/session/session-projection), [`settings`](../packages/settings/settings), [`system-prompt`](../packages/core/system-prompt), [`tools`](../packages/core/tools), [`typert-protocol`](../packages/typert/protocol) |
+| [`agent-presets`](../packages/preset/agent-presets) | `preset` | [`agent`](../packages/core/agent), [`app-boot`](../packages/boot/app-boot), [`atomic-write`](../packages/util/atomic-write), [`home-paths`](../packages/util/home-paths), [`invariants`](../packages/runtime-diagnostics/invariants), [`scope`](../packages/core/scope), [`session`](../packages/core/session), [`session-projection`](../packages/session/session-projection), [`settings`](../packages/settings/settings), [`system-prompt`](../packages/core/system-prompt), [`tools`](../packages/core/tools), [`typert-protocol`](../packages/typert/protocol) |
 | [`schedule`](../packages/schedule/schedule) | `schedule` | [`agent`](../packages/core/agent), [`brand`](../packages/util/brand), [`invariants`](../packages/runtime-diagnostics/invariants), [`llm`](../packages/llm/llm), [`session`](../packages/core/session), [`session-persistence`](../packages/session/session-persistence), [`session-projection`](../packages/session/session-projection), [`tools`](../packages/core/tools) |
 | [`session-checkpoint-policy`](../packages/session/session-checkpoint-policy) | `session` | [`agent`](../packages/core/agent), [`llm`](../packages/llm/llm), [`session`](../packages/core/session), [`session-persistence`](../packages/session/session-persistence), [`tools`](../packages/core/tools) |
 | [`session-title-all-prompts-llm`](../packages/session/session-title-all-prompts-llm) | `session` | [`llm`](../packages/llm/llm), [`session`](../packages/core/session), [`session-title`](../packages/session/session-title), [`session-title-llm`](../packages/session/session-title-llm) |

docs/module-graph.zh.md

@@ -1473,10 +1473,8 @@ flowchart TD
 | [`tool-ask-user`](../packages/interaction/tool-ask-user) | `interaction` | [`agent`](../packages/core/agent), [`tools`](../packages/core/tools), [`user-questions`](../packages/interaction/user-questions) |
 | [`tool-jobs`](../packages/jobs/tool-jobs) | `jobs` | [`agent`](../packages/core/agent), [`jobs`](../packages/jobs/jobs), [`llm`](../packages/llm/llm), [`output-retention`](../packages/util/output-retention), [`system-prompt`](../packages/core/system-prompt), [`tools`](../packages/core/tools) |
 | [`tool-lsp`](../packages/lsp/tool-lsp) | `lsp` | [`llm`](../packages/llm/llm), [`lsp`](../packages/lsp/lsp), [`system-prompt`](../packages/core/system-prompt), [`timeout`](../packages/util/timeout), [`tools`](../packages/core/tools) |
-| [`mcp-client`](../packages/mcp/mcp-client) | `mcp` | [`attachment`](../packages/attachment/attachment), [`llm`](../packages/llm/llm), [`scope`](../packages/core/scope), [`subprocess`](../packages/subprocess/subprocess), [`timeout`](../packages/util/timeout), [`tools`](../packages/core/tools) |
-| [`agent-presets`](../packages/preset/agent-presets) | `preset` | [`agent`](../packages/core/agent), [`app-boot`](../packages/boot/app-boot), [`atomic-write`](../packages/util/atomic-write), [`home-paths`](../packages/util/home-paths), [`invariants`](../packages/runtime-diagnostics/invariants), [`scope`](../packages/core/scope), [`session`](../packages/core/session), [`session-projection`](../packages/session/session-projection), [`settings`](../packages/settings/settings), [`system-prompt`](../packages/core/system-prompt), [`tools`](../packages/core/tools), [`typert-protocol`](../packages/typert/protocol) |
 | [`mcp-resources`](../packages/mcp/mcp-resources) | `mcp` | [`llm`](../packages/llm/llm), [`scope`](../packages/core/scope), [`system-prompt`](../packages/core/system-prompt), [`tools`](../packages/core/tools) |
-| [`agent-presets`](../packages/preset/agent-presets) | `preset` | [`agent`](../packages/core/agent), [`atomic-write`](../packages/util/atomic-write), [`home-paths`](../packages/util/home-paths), [`invariants`](../packages/runtime-diagnostics/invariants), [`scope`](../packages/core/scope), [`session`](../packages/core/session), [`session-projection`](../packages/session/session-projection), [`settings`](../packages/settings/settings), [`system-prompt`](../packages/core/system-prompt), [`tools`](../packages/core/tools), [`typert-protocol`](../packages/typert/protocol) |
+| [`agent-presets`](../packages/preset/agent-presets) | `preset` | [`agent`](../packages/core/agent), [`app-boot`](../packages/boot/app-boot), [`atomic-write`](../packages/util/atomic-write), [`home-paths`](../packages/util/home-paths), [`invariants`](../packages/runtime-diagnostics/invariants), [`scope`](../packages/core/scope), [`session`](../packages/core/session), [`session-projection`](../packages/session/session-projection), [`settings`](../packages/settings/settings), [`system-prompt`](../packages/core/system-prompt), [`tools`](../packages/core/tools), [`typert-protocol`](../packages/typert/protocol) |
 | [`schedule`](../packages/schedule/schedule) | `schedule` | [`agent`](../packages/core/agent), [`brand`](../packages/util/brand), [`invariants`](../packages/runtime-diagnostics/invariants), [`llm`](../packages/llm/llm), [`session`](../packages/core/session), [`session-persistence`](../packages/session/session-persistence), [`session-projection`](../packages/session/session-projection), [`tools`](../packages/core/tools) |
 | [`session-checkpoint-policy`](../packages/session/session-checkpoint-policy) | `session` | [`agent`](../packages/core/agent), [`llm`](../packages/llm/llm), [`session`](../packages/core/session), [`session-persistence`](../packages/session/session-persistence), [`tools`](../packages/core/tools) |
 | [`session-title-all-prompts-llm`](../packages/session/session-title-all-prompts-llm) | `session` | [`llm`](../packages/llm/llm), [`session`](../packages/core/session), [`session-title`](../packages/session/session-title), [`session-title-llm`](../packages/session/session-title-llm) |

packages/boot/app-boot/tests/patch-file.spec.ts

@@ -1,9 +1,9 @@
-import { mkdtemp, readFile, stat, writeFile } from 'node:fs/promises'
+import { mkdir, mkdtemp, readFile, stat, writeFile } from 'node:fs/promises'
 import { existsSync } from 'node:fs'
 import { tmpdir } from 'node:os'
 import { join, resolve } from 'node:path'
 import { pathToFileURL } from 'node:url'
-import { describe, expect, it } from 'vitest'
+import { describe, expect, it, vi } from 'vitest'
 import { isJsExpr } from '@deepseek-ai/cordis-plugin-loader'
 import {
   anchorInsertedPluginNames,
@@ -230,6 +230,18 @@ describe('mutatePatchFile', () => {
     expect(existsSync(file)).toBe(false)
   })
 
+  it('rejects a directory as the patch file before editing and releases its lock', async () => {
+    const dir = await tempDir()
+    const file = join(dir, 'cordis.patch.yml')
+    await mkdir(file)
+    const mutate = vi.fn()
+    await expect(mutatePatchFile(file, mutate, { binName: 'spec', mode: 0o600 }))
+      .rejects.toThrow(`spec: failed to read patches ${file}`)
+    expect(mutate).not.toHaveBeenCalled()
+    expect((await stat(file)).isDirectory()).toBe(true)
+    expect(existsSync(`${file}.lock`)).toBe(false)
+  })
+
   it.skipIf(process.platform === 'win32' || process.getuid?.() === 0)('reports a file that exists but cannot be read', async () => {
     const dir = await tempDir()
     const file = join(dir, 'cordis.patch.yml')