Bug in JetBrains Copilot Plugin: Files Auto-Open on New Chat Due to Whitespace-Only Diffs in copilotDiffState.xml

[garrett-whitehorn-cengage]

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Bug

Copilot Feature Area

JetBrains & Xcode

Body

I generated this post body using Copilot after having it diagnose and fix the problem successfully. However, I have little doubt that it will happen again.

Environment

• IDE: JetBrains PhpStorm 2025.3.3
• GitHub Copilot Plugin Version: 1.6.1-243
• OS: macOS Sequoia 15.6.1
• Date Discovered: sometime in the last couple of months

Summary

The GitHub Copilot plugin for JetBrains IDEs stores "pending diffs" in .idea/copilotDiffState.xml even when the only change is trivial whitespace (e.g., a trailing newline character). These pending diffs may persist indefinitely across IDE sessions and cause the affected files to automatically open every time a new Copilot chat is started, creating a disruptive and confusing user experience. On top of that, there is no hint in the UI that these files have any unaccepted changes pending.

Description

When Copilot suggests changes to a file that result in only whitespace differences (such as adding or removing a trailing newline), the plugin stores these as "pending diffs" in the project's .idea/copilotDiffState.xml file. Unlike meaningful code changes, these whitespace-only diffs:

1. Are not visible or obvious in the editor UI
2. Are not automatically dismissed when the user closes the chat
3. Persist indefinitely across multiple IDE restarts
4. Cause the affected files to auto-open every time a new Copilot chat session is started

In my specific case, the issue began with one file and grew to include multiple files over time, all opening automatically whenever I started a new Copilot chat.

Steps to Reproduce

1. Use GitHub Copilot in a JetBrains IDE to suggest changes to a file
2. The suggestion results in only whitespace changes (e.g., adding/removing a trailing newline)
3. Do not explicitly accept or reject the diff (close the chat or switch context)
4. Close the current Copilot chat session
5. Open a new Copilot chat session
6. Observe: The file(s) with pending whitespace-only diffs automatically open in the editor

Expected Behavior

One or more of the following should occur:

• Whitespace-only diffs should be automatically dismissed/ignored as non-substantive changes
• Pending diffs should be cleared when the user explicitly closes the chat or starts a new session
• Files should NOT automatically open when starting a new chat session unless explicitly requested by the user
• If whitespace diffs must be tracked, provide a clear UI indication and easy way to dismiss them

Actual Behavior

• Files with trivial whitespace diffs (even a single byte difference) remain in "pending" state indefinitely
• These files automatically open in the editor tab every time a new Copilot chat is initiated
• The issue compounds over time as more files accumulate in the pending state
• There is no obvious UI indication that these are pending diffs (especially when the diff is whitespace-only)
• The user experience becomes increasingly disruptive as multiple files start auto-opening

Technical Details

The Pending Diff Format

The plugin stores pending diffs in .idea/copilotDiffState.xml like this:

<entry key="$PROJECT_DIR$/path/to/file.js">
  <value>
    <PendingDiffInfo>
      <option name="filePath" value="$PROJECT_DIR$/path/to/file.js" />
      <option name="originalContent" value="..." />
      <option name="updatedContent" value="..." />
    </PendingDiffInfo>
  </value>
</entry>

The Actual Difference

In my case, the difference was literally one byte:

• Original: File ended with two newlines: ...export default useFetchNiceCatalog;\n\n
• Updated: File ended with one newline: ...export default useFetchNiceCatalog;\n

This single byte difference caused the file to open automatically for weeks until I asked copilot about the issue, and it discovered and cleared the pending diffs in the XML file.

Impact

• User Experience: Highly disruptive workflow as multiple files unexpectedly open on every new chat
• Confusion: No clear indication of why files are opening or how to stop it
• Productivity Loss: Time wasted closing unwanted tabs and investigating the issue
• Trust: Users may lose trust in the tool or think their IDE is malfunctioning

Current Workaround

Users must manually edit .idea/copilotDiffState.xml to clear the pending diffs:

1. Close the JetBrains IDE
2. Open .idea/copilotDiffState.xml in a text editor
3. Replace the <map>...</map> content with just <map />
4. Save the file
5. Reopen the IDE

Alternatively, users can try to explicitly accept or reject all diffs before closing each chat session, though this requires:

• Being aware that a diff exists (not obvious for whitespace-only changes)
• Remembering to do this every time

Suggested Fixes

1. Auto-dismiss whitespace-only diffs: Don't track or persist diffs where the only changes are whitespace
2. Clear pending diffs on session close: When a chat session is explicitly closed, clear any pending diffs
3. Add UI indication: If pending diffs must be tracked, show a clear indicator in the UI (notification, badge, or list)
4. Prevent auto-opening files: Don't automatically open files from pending diffs when starting a new chat session
5. Provide manual dismissal: Add a "clear pending diffs" action in the UI or command palette

Reproducibility

This issue is highly reproducible once triggered. Any Copilot suggestion that results in whitespace-only changes will likely cause this behavior. I'm not actually sure how reliably reproducible this is. I just know it can happen sometimes.

Related Information

• This probably affects all JetBrains IDEs with the GitHub Copilot plugin (PHPStorm, IntelliJ IDEA, WebStorm, etc.)
• The issue persists across IDE restarts and even system reboots
• The .idea/copilotDiffState.xml file is project-specific, so the issue affects specific projects where it occurred

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