`apply_patch` fails to replace the whole contet of files

[tamuratak]

Version: 1.107.0-insider (Universal)
Commit: 6b29ec0
Date: 2025-12-05T22:20:51.110Z
Electron: 39.2.3
ElectronBuildId: 12895514
Chromium: 142.0.7444.175
Node.js: 22.21.1
V8: 14.2.231.21-electron.0
OS: Darwin arm64 24.6.0

Name: GitHub Copilot Chat
Id: GitHub.copilot-chat
Description: AI chat features powered by Copilot
Version: 0.35.2025120504
Publisher: GitHub
VS Marketplace Link: https://marketplace.visualstudio.com/items?itemName=GitHub.copilot-chat

Using gpt-5-mini.

apply_patch fails to replace the entire content of files. At the beginning of its argument, the string '```markdown' appears, which may be causing the issue. When that string is removed, apply_patch works correctly.

1. Create a file t.md

    "type": "git",
    "url": "https://github.com/tamuratak/vscode-able.git"
  },
  "engines": {
    "vscode": "^1.106.1"
  },
  "files": [
    "pyodide/pyodide/*.json",
    "pyodide/pyodide/*.ts",
    "pyodide/pyodide/*.js",
    "pyodide/pyodide/*.mjs",
    "pyodide/pyodide/*.wasm",
    "pyodide/pyodide/micropip*",
    "node_modules",
    "out",
    "LICENSE"
  ],
  "capabilities": {
    "virtualWorkspaces": true,
    "untrustedWorkspaces": {
      "supported": true
    }
  },
  "enabledApiProposals": [
    "embeddings",
    "chatParticipantAdditions",
    "chatProvider",
    "languageModelSystem",
    "languageModelThinkingPart"
  ],
  "contributes": {
    "authentication": [
      {
        "id": "gemini_api",
        "label": "Gemini (with Able)"
      },
      {
        "id": "openai_api",

2. Tell Agent

- When using apply_patch, please note that Delete File is not supported. 
- Replace the whole content of #file:t.md  with the following. 

```
a

b

c

```

3. After edited, t.md becomes

    "type": "git",
    "url": "https://github.com/tamuratak/vscode-able.git"
  },
  "engines": {
    "vscode": "^1.106.1"
  },
  "files": [
    "pyodide/pyodide/*.json",
    "pyodide/pyodide/*.ts",
    "pyodide/pyodide/*.js",
    "pyodide/pyodide/*.mjs",
    "pyodide/pyodide/*.wasm",
    "pyodide/pyodide/micropip*",
    "node_modules",
    "out",
    a

    b

    c

The argument of apply_patch begins with '```markdown', which might causes the issue.

id   : call_WKUiqipxAAZWKqUMhJjwARKL__vscode-1764995950953
tool : apply_patch
args : {
  "input": "*** Begin Patch
*** Update File: /Users/tamura/src/github/vscode-able/t.md
@@
-```markdown
-
-    \"type\": \"git\",
-    \"url\": \"https://github.com/tamuratak/vscode-able.git\"
-  },
-  \"engines\": {
-    \"vscode\": \"^1.106.1\"
-  },
-  \"files\": [
-    \"pyodide/pyodide/*.json\",
-    \"pyodide/pyodide/*.ts\",
-    \"pyodide/pyodide/*.js\",
-    \"pyodide/pyodide/*.mjs\",
-    \"pyodide/pyodide/*.wasm\",
-    \"pyodide/pyodide/micropip*\",
-    \"node_modules\",
-    \"out\",
-    \"LICENSE\"
-  ],
-  \"capabilities\": {
-    \"virtualWorkspaces\": true,
-    \"untrustedWorkspaces\": {
-      \"supported\": true
-    }
-  },
-  \"enabledApiProposals\": [
-    \"embeddings\",
-    \"chatParticipantAdditions\",
-    \"chatProvider\",
-    \"languageModelSystem\",
-    \"languageModelThinkingPart\"
-  ],
-  \"contributes\": {
-    \"authentication\": [
-      {
-        \"id\": \"gemini_api\",
-        \"label\": \"Gemini (with Able)\"
-      },
-      {
-        \"id\": \"openai_api\",
+a
+
+b
+
+c
+
*** End Patch",
  "explanation": "Replace entire file content with the three requested lines"
}

__When_using_apply_patch__please_note_that_Delete__logs.chatreplay.json

panel_editAgent_9de6a602.copilotmd

[tamuratak]

I confirmed that when read_file returns its result using <Tag name='file'> instead of code blocks, apply_patch works correctly.

• https://github.com/microsoft/vscode-copilot-chat/blob/52126b6cf26316c7bf12bcbd5498ef6f211c901b/src/extension/tools/node/readFileTool.tsx#L284