Digger comments such as digger plan and digger apply accept the following flags: 
-d value
    	directory (short form)
  -directory value
    	directory (long form)
  -p value
    	project (short form)
  -project value
    	project (long form)
  -layer value (only for layering)
    	layer to plan or apply (default -1)
The -p and -d flags can be specified multiple times. In the case of projects they will select the projects from the flags. Same goes for directories. Some example comments with flags: 
digger plan -p dev_vpc

digger plan --project dev_vpc

digger plan -d dev/vpc

digger plan --directory dev/vpc

digger plan -p dev_vpc -p staging_vpc

digger plan -p dev_vpc -d staging/vpc