Major compactions can be requested via the HBase shell or HBaseAdmin.majorCompact.
Note: major compactions do NOT do region merges. See Section 18.104.22.168, “Compaction” for more information about compactions.
Merge is a utility that can merge adjoining regions in the same table (see org.apache.hadoop.hbase.util.Merge).
$ bin/hbase org.apache.hadoop.hbase.util.Merge <tablename> <region1> <region2>
If you feel you have too many regions and want to consolidate them, Merge is the utility you need. Merge must run be done when the cluster is down. See the O'Reilly HBase Book for an example of usage.
Additionally, there is a Ruby script attached to HBASE-1621 for region merging.