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Without Ensure clean checkout directory you will only get warnings about modified and deleted files.

Use Paths to ignore setting to specify files that should be ignored be swabra. A path can be checkout directory relative path or a mask with ant-style wild cards.
Ignoring a directory leads to ignoring the whole it's content.

Use Locking processes setting to inspect the checkout directory for processes locking files in this directory.
Choose Report or Kill options to get report about such processes in the build log or kill them.
Note that for locking processes detection handle.exe is required on agents. Click the Download handle.exe link for downloading.

Check Verbose output option to enable detailed logging to build log.

Paths to ignore

If the build is set up to checkout on agent swabra by default ignores all .svn, .git, .hg, CVS folders and their content.
To turn off this behaviour specify empty swabra.ignored.paths

Note that after removing some ignore rules it's advisable to run clean checkout.

Downloading Handle

Specify URL for downloading, press Download button and TeamCity will automatically download Handle, extract and send to Windows agents.
handle.exe will be present on agents only after the upgrade process.
Note that you need to have enough permissions to start the download.