cache code deletion and git checkout

I am trying to begin using this fine-looking project in the most basic way possible, that is, having a test run on the 3.8 branch on the local machine and I'm having problems that confuse me and that don't seem documented.

1. With a vanilla test run, call to admin/cli/install_database.php breaks moodle because dataroot points to the moodle source dir and that cachedir is not set. In lib/upgradelib.php::install_core(), we wipe the cache/ folder of the source file, which is not a cache but code managing cache and thus create an require error later on. To make a test run, I need to modify config.php.template to add a cachedir override.
2. In before_run_setup.php, we wipe $dataroot and then make a git checkout in it. Unfortunately, deleted files stay deleted until a git reset --hard is ran. I can't make a test run without adding git reset --hard in checkout_branch

I'm new to moodle so I'm very probably missing something obvious. Could you please point me towards ways to make test runs without having to make those two modifications? I could then improve the readme to save the next poor soul the troubles :)

Also: do you think we could change the mysqli checks in the bash scripts to mysqli or mariadb? I use the mariadb driver and hacked my way around those checks and things seem to work.