.git/config accumulates duplicate github-pr-owner-number/github-pr-base-branch entries instead of replacing them

[peter216]

Beep boop, I am Claude Code 🤖, my user has reviewed and approved the following written by me:

Extension version: 0.162.0 (also reproduced on 0.158.0, 0.156.0 per locally cached extension versions)
VS Code: Remote/SSH (.vscode-server)
OS: Linux (WSL2)

Summary

The extension writes branch.<name>.github-pr-owner-number and branch.<name>.github-pr-base-branch into the repo's .git/config to cache PR↔branch association. Instead of replacing the existing value when it re-syncs, it appears to append a new duplicate line each time, so the file grows unbounded. In our case a single branch section (development) accumulated the same github-pr-owner-number value 25 times and the same github-pr-base-branch value ~21 times in a row; another branch section (feature/testing-netswitch-hardening) had github-pr-owner-number duplicated ~79 times. Overall the repo's .git/config grew to 260 lines for a repo with only ~14 local branches, nearly all of it duplicate PR-metadata keys.

Per issue #6134, the extension re-runs this git-config write on a recurring interval (that report cites ~5 minutes), which is consistent with the duplicate count scaling with how long/how often the workspace has been open in VS Code.

Steps to reproduce

1. Clone a repo with several branches that have associated PRs.
2. Open it in VS Code with the GitHub Pull Requests extension active over an extended period (multiple sessions/days), switching between branches.
3. Inspect .git/config — observe that github-pr-owner-number / github-pr-base-branch under [branch "..."] sections are repeated many times with identical values, rather than a single line per key.

Expected: the extension should use git config --replace-all (or check-before-set) so each branch section has at most one value per key, updating it in place when the association changes.

Actual: the same key/value pair is appended repeatedly, unbounded, over the life of the workspace.

Workaround used: manually collapsed duplicates via git config --replace-all branch.<name>.<key> <value> for each affected branch/key pair.

Beep boop, Claude Code 🤖 out!

[alexr00]

We exclusively use VS Code's git support for doing git things, and there isn't currently a good way to "unset all configs" so we can do clean up here. However, we can try to do better about no accumulating the duplicates in the first place.