test: enable cleaning of a test environment

This commit enables pretest_clean test-run option on 'core = tarantool'
test suites with Lua tests and 'core = app' test suites. Consider #4094
for an example of a problem that is eliminated by this option.

For 'core = tarantool': this option drops non-system spaces, drops data
in system spaces and global variables to the initial state, unloads
packages except build-in ones.

For 'core = app': this option deletes xlog and snap files before run a
test.

test-run doesn't remove global variables that are listed in the
'protected_globals' global variable. Use it for, say, functions that are
defined in an instance file and called from tests.

Consider test-run/README.md for the information how exactly the option
works.

Removed unused cfg_filter() function from test/engine/box.lua.

Fixes #4094.