The `apply_modifiers` property of the `RunTest` class overrides
all of the test level `apply_modifier` properties. This prevents
modifiers from manually specifying when a modifier is applied and forces
the modifier to be applied immediately after it is added.
The vast majority of tests do not override the `apply_modifier`
property, the primary usecase for this property is to work in
combination with the `do_compare` property to allow examining the
corresponding .blend file to debug test failures.
This commit simplifies the settings by removing this parameter. It now
only disables applying the modifier if `do_compare` is set to False.
Pull Request: https://projects.blender.org/blender/blender/pulls/140893
f99b35463a