libtracker-miner: Call check_directory() on root dir to crawl

Unit tests were failing, pre-release because the count of directories we
notify about finding was 1 less than we expected.
libtracker-miner: Pass flags explicitly when creating crawling root data

Those might differ from the flags reported by the TrackerIndexingTree,
specially during ::directory-removed.
libtracker-miner: Pass parent flags when reindexing a previously ignored folder

If a folder with the "ignored" flag is removed from the configuration, and its
parent folder indexing is recursive, the folder contents must be indexed
recursively obeying the parent folder configuration flags, so pass those when
queueing the directory for crawling.