Buildkite checkout fails, and deletes most of the repo, if any user-owned files in the checkout path are non-writable

Agent User: `buildkite-agent`
Example Checkout path: `/var/lib/buildkite-agent/software`
Read-only File: `/var/lib/buildkite-agent/software/tmp/file`

```
ls -l /var/lib/buildkite-agent/software/tmp/file
-r-xr-xr-x 1 buildkite-agent buildkite-agent 186824 Jan 11 11:49 /var/lib/buildkite-agent/software/tmp/file
```

In our case, a previous build rsyncs to the checkout directory, and writes `tmp/file`. While the owner is `buildkite-agent`, the permissions are set as `u+rx` and `u-w`, aka the file is "read-only".

On the next build will fail to `git clean`, and then it will try to delete the whole repo (and fail), and then try to clone (and fail). However, the user actually owns those files, and buildkite-agent could simply chmod o+w any files that it tries to delete, or `rm -f `. Assuming buildkite-agent is using a filesystem interface in golang, it's likely some argument would have to change for it to delete write-only files.

Start by tracing the checkout cleanup path that runs git clean before the repository deletion and clone fallback, using the reported checkout path and non-writable tmp/file example as the reproduction case. Done means a user-owned read-only file can be removed during cleanup and the checkout proceeds without deleting or recloning the repository.

Written by the indexing model from the issue text.