test: update test-run (--replication-sync-timeout)

See commits in the PR [1] for detailed description of the changes. User
visible changes are the following.

1. Now test-run.py can be invoked from any directory without changing a
   current working directory to `test/`.
2. The `test/.tarantoolctl` configuration file is not mandatory and can
   be removed. It is shipped now within the test-run repository.
3. test-run sets the `replication_sync_timeout` box.cfg() option when
   the `test/.tarantoolctl` is not present in a parent repository. The
   value is controlled by the --replication-sync-timeout argument and
   defaults to 100 seconds (unlike tarantool's default, which is 300
   seconds).

The reason of the changes is to set default `replication_sync_timeout`
for all tests to a value lower than `--no-output-timeout` (120 seconds)
to allow instances to step into the orphan mode before this deadline and
see more descriptive picture when it leads to failure of a test. What is
also important, when a test fails before the `--no-output-timeout`, we
able to restart it based on the `fragile` suite.ini option and / or
collect artifacts to store them in CI.

The `--no-output-timeout` deadline remains the show-stopper. We'll
introduce a test execution timeout later to step into the general
`--no-output-timeout` only in quite rare and unusual cases.

The next commit will actually remove `test/.tarantoolctl`, so the new
`replication_sync_timeout` will be in effect.

[1]: https://github.com/tarantool/test-run/pull/242

Part of #5504