Move `runtests` to Resources directory

`runtests` is an internal module that is not used by the plug-in, so it got moved to the Resources directory.
Also, cleanup.
Make 'overwrite_mode' the last parameter

It looks cleaner that way, since it's only used in non-interactive mode, unlike all the other main settings.
Minor cleanup
Remove `tee_plugin`

Instead, define log file paths in `constants` and directly use the `tee` module in `export_layers`.
Update CHANGELOG.md