If you try to use git gui on a folder that has more than 5000 files, you might notice that the git gui client only displays the first 5000 files and you will also receive the following message
Display limit (gui.maxfilesdisplayed = 5000) reached, not showing all xxxxx files
The limit is coming from the following line in the git gui source
5000 is just the default limit if gui.maxfilesdisplayed setting is not set. Therefore, you can increase the limit by updating the git configuration. For example to increase it to 10000, add the following to the git configuration.
[gui] maxfilesdisplayed = 10000
You can add the configuration in any of the git config files like ~/.gitconfig. On windows, you can also set it in $PROGRAMDATA/Git/config, this is a (Windows-only) System-wide configuration file shared with other Git implementations. Typically $PROGRAMDATA points to C:\ProgramData.